1
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Melse O, Antes I, Kaila VRI, Zacharias M. Benchmarking biomolecular force field-based Zn 2+ for mono- and bimetallic ligand binding sites. J Comput Chem 2023; 44:912-926. [PMID: 36495007 DOI: 10.1002/jcc.27052] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Zn2+ is one of the most versatile biologically available metal ions, but accurate modeling of Zn2+ -containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn2+ models are parameterized in bulk solvent, in-depth knowledge about their performance in a protein environment is limited. Thus, we systematically investigate here the behavior of non-polarizable Zn2+ models for their ability to reproduce experimentally determined metal coordination and ligand binding in metalloproteins. The benchmarking is performed in challenging environments, including mono- (carbonic anhydrase II) and bimetallic (metallo-β-lactamase VIM-2) ligand binding sites. We identify key differences in the performance between the Zn2+ models with regard to the preferred ligating atoms (charged/non-charged), attraction of water molecules, and the preferred coordination geometry. Based on these results, we suggest suitable simulation conditions for varying Zn2+ site geometries that could guide the further development of biomolecular Zn2+ models.
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Affiliation(s)
- Okke Melse
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Iris Antes
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany
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2
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Andújar SA, Gutiérrez LJ, Enriz RD, Baldoni HA. Structure, interface stability and hot-spots identification for RBD(SARS-CoV-2):hACE2 complex formation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1979229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sebastián A. Andújar
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Lucas J. Gutiérrez
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Ricardo D. Enriz
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, Institute of Applied Mathematics of San Luis (IMASL. CONICET), National University of San Luis, San Luis, Argentina
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3
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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4
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Selberg S, Blokhina D, Aatonen M, Koivisto P, Siltanen A, Mervaala E, Kankuri E, Karelson M. Discovery of Small Molecules that Activate RNA Methylation through Cooperative Binding to the METTL3-14-WTAP Complex Active Site. Cell Rep 2020; 26:3762-3771.e5. [PMID: 30917327 DOI: 10.1016/j.celrep.2019.02.100] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 10/19/2018] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
Chemical modifications of RNA provide an additional, epitranscriptomic, level of control over cellular functions. N-6-methylated adenosines (m6As) are found in several types of RNA, and their amounts are regulated by methyltransferases and demethylases. One of the most important enzymes catalyzing generation of m6A on mRNA is the trimer N-6-methyltransferase METTL3-14-WTAP complex. Its activity has been linked to such critical biological processes as cell differentiation, proliferation, and death. We used in silico-based discovery to identify small-molecule ligands that bind to METTL3-14-WTAP and determined experimentally their binding affinity and kinetics, as well as their effect on enzymatic function. We show that these ligands serve as activators of the METTL3-14-WTAP complex.
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Affiliation(s)
- Simona Selberg
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Daria Blokhina
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Maria Aatonen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pertti Koivisto
- Organic Residues Section, Laboratory and Research Division, Chemistry Unit, Finnish Food Authority, Helsinki, Finland
| | - Antti Siltanen
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Eero Mervaala
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Tartu, Estonia.
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5
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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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6
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Carvalho HF, Branco RJF, Leite FAS, Matzapetakis M, Roque ACA, Iranzo O. Hydrolytic zinc metallopeptides using a computational multi-state design approach. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01364d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combination of multi-state design and long-timescale conformational dynamics as a powerful strategy to obtain metalloenzymes.
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Affiliation(s)
- Henrique F. Carvalho
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Ricardo J. F. Branco
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Fábio A. S. Leite
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- 2780-157 Oeiras
- Portugal
| | - A. Cecília A. Roque
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
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7
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Ivanova L, Tammiku-Taul J, García-Sosa AT, Sidorova Y, Saarma M, Karelson M. Molecular Dynamics Simulations of the Interactions between Glial Cell Line-Derived Neurotrophic Factor Family Receptor GFRα1 and Small-Molecule Ligands. ACS OMEGA 2018; 3:11407-11414. [PMID: 30320260 PMCID: PMC6173496 DOI: 10.1021/acsomega.8b01524] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/06/2018] [Indexed: 06/01/2023]
Abstract
The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) support the survival and functioning of various neuronal populations. Thus, they could be attractive therapeutic agents against a multitude of neurodegenerative diseases caused by progressive death of GFLs responsive neurons. Small-molecule ligands BT13 and BT18 show an effect on GDNF family receptor GFRα1 and RET receptor tyrosine kinase RetA function. Thus, their potential binding sites and interactions were explored in the GDNF-GFRα1-RetA complex using molecular docking calculations as well as molecular dynamics (MD) simulations. Three possible regions were examined: the interface between GDNF and GFRα1 (region A), the RetA interface with GFRα1 (region B), and a possible allosteric site in GFRα1 (region C). The results obtained by the docking calculations and the MD simulations indicate that the preferable binding occurs at the allosteric site. A less preferable binding site was detected on the RetA surface interfacing GFRα1. In the membrane-bound state of RetA this can enable compounds BT13 and BT18 to act as direct RetA agonists. The analysis of the MD simulations shows hydrogen bonds for BT13 and significant hydrophobic interactions with GFRα1 for BT13 and BT18 at the allosteric site.
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Affiliation(s)
- Larisa Ivanova
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
| | - Jaana Tammiku-Taul
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
| | | | - Yulia Sidorova
- Laboratory of Molecular
Neuroscience, Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5D, 00014 Helsinki, Finland
| | - Mart Saarma
- Laboratory of Molecular
Neuroscience, Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5D, 00014 Helsinki, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
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8
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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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9
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Minnow YV, Goldberg R, Tummalapalli SR, Rotella DP, Goodey NM. Mechanism of inhibition of botulinum neurotoxin type A light chain by two quinolinol compounds. Arch Biochem Biophys 2017; 618:15-22. [DOI: 10.1016/j.abb.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/06/2017] [Accepted: 01/12/2017] [Indexed: 11/26/2022]
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10
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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11
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Pang YP. Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation. Biochem Biophys Rep 2015; 4:126-133. [PMID: 29124195 PMCID: PMC5668912 DOI: 10.1016/j.bbrep.2015.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022] Open
Abstract
It has been reported recently that classical, isothermal-isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00 fs of the standard-mass time (Δt=1.00 fssmt) and a temperature of ≤340 K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic masses can also be increased to improve configurational sampling because higher atomic masses permit the use of a longer time step. It is worth investigating whether standard-mass NTP MD simulations at Δt=2.00 or 3.16 fssmt can offer better or comparable configurational sampling than low-mass NTP MD simulations at Δt=1.00 fssmt. This article reports folding simulations of two β-hairpins showing that the configurational sampling efficiency of NTP MD simulations using atomic masses uniformly reduced by tenfold at Δt=1.00 fssmt is statistically equivalent to and better than those using standard masses at Δt=3.16 and 2.00 fssmt, respectively. The results confirm that, relative to those using standard masses at routine Δt=2.00 fssmt, the low-mass NTP MD simulations at Δt=1.00 fssmt are a simple and generic technique to enhance configurational sampling at temperatures of ≤340 K.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Stabile 12-26, 200 First Street SW, Rochester, MN 55905, USA
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12
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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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13
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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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14
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Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling. Biochem Biophys Res Commun 2014; 452:588-92. [PMID: 25181342 DOI: 10.1016/j.bbrc.2014.08.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 11/24/2022]
Abstract
CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277K and 1atm with the first folding event occurring as early as 66.1ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers-an important step forward in quantitative biology.
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15
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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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16
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Wang C, Sperry J. Total syntheses of the dipyrrolobenzoquinone (+)-terreusinone enabled by an evaluation of 4-methylpent-1-yn-3-ols in the Larock indole synthesis. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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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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18
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O'Malley S, Sareth S, Jiao GS, Kim S, Thai A, Cregar-Hernandez L, McKasson L, Margosiak SA, Johnson AT. Virtual medicinal chemistry: in silico pre-docking functional group transformation for discovery of novel inhibitors of botulinum toxin serotype A light chain. Bioorg Med Chem Lett 2013; 23:2505-11. [PMID: 23545109 DOI: 10.1016/j.bmcl.2013.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/01/2013] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
Abstract
A novel method for applying high-throughput docking to challenging metalloenzyme targets is described. The method utilizes information-based virtual transformation of library carboxylates to hydroxamic acids prior to docking, followed by compound acquisition, one-pot (two steps) chemical synthesis and in vitro screening. In two experiments targeting the botulinum neurotoxin serotype A metalloprotease light chain, hit rates of 32% and 18% were observed.
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Hamasaki A, Ishida T, Tokunaga M. Novel Feature and Catalysis of Metal Oxide Supported Gold Nanoparticles. J SYN ORG CHEM JPN 2013. [DOI: 10.5059/yukigoseikyokaishi.71.443] [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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20
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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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21
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Li L, Li D, Chen H, Han JG. Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations. J Biomol Struct Dyn 2012; 31:299-315. [PMID: 22871039 DOI: 10.1080/07391102.2012.703061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Lassa virus can cause dreadful human hemorrhagic disease, for which there is no effective therapy. A recent study points out that the amino (N)-terminal domain of Lassa virus nucleoprotein (NP) plays an important role in viral RNA synthesis and firstly solved the X-ray crystal structures of NP complexed with the capped Deoxythymidine triphosphate (dTTP) analog, but the binding mode of m7GpppG to the N domain of NP, which is required for viral RNA transcription, has not been studied. In this study, molecular dynamics (MD) simulations have been carried out to investigate the characters of dTTP binding to two forms of NP, i.e. the NP without the C domain and the full-length NP model, using two different force fields, ff03 and ff99SB, respectively. Our calculated results show that the truncated model is reasonable and can replace the full protein model in the following MD simulations, and that ff99SB combined with the general AMBER force field is more suitable for sampling the structure of small molecule NP complex. From the comparisons of stability of hydrogen bonds between small molecule and protein in the dTTP and Uridine 5'-Triphosphate complexes, one finds that the stable hydrogen bonds between the second phosphate group of small molecules and two residues, Thr178 and Arg323, are critical for cap analogs binding to the N domain of NP. Additionally, docking method combined with MD simulations have been applied to predict the binding mode of m7GpppG to NP; and the hydrogen bond analysis and the binding free energy decomposition method (MM/GBSA) are conducted to study the interactions in the putative binding mode. The calculated results are expected to provide guidance for drug development.
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Affiliation(s)
- Liang Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China , 230029 Hefei , People's Republic of China
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22
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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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Takeda D, Yamashita M, Hirano K, Satoh T, Miura M. Palladium-catalyzed Direct Monoarylation of Thiophene-, Benzothiophene-, and Indoleacetic Acids through Regioselective C–H Bond Cleavage. CHEM LETT 2011. [DOI: 10.1246/cl.2011.1015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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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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25
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Potavathri S, Kantak A, DeBoef B. Increasing synthetic efficiency via direct C–H functionalization: formal synthesis of an inhibitor of botulinum neurotoxin. Chem Commun (Camb) 2011; 47:4679-81. [DOI: 10.1039/c1cc10755k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Murru S, Gallo AA, Srivastava RS. Gold-Catalyzed Synthesis of 3-Arylindoles via Annulation of Nitrosoarenes and Alkynes. ACS Catal 2010. [DOI: 10.1021/cs100024n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Siva Murru
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - August A. Gallo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Radhey S. Srivastava
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
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27
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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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28
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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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29
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Burnett JC, Li B, Pai R, Cardinale SC, Butler MM, Peet NP, Moir D, Bavari S, Bowlin T. Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore. OPEN ACCESS BIOINFORMATICS 2010; 2010:11-18. [PMID: 21103387 PMCID: PMC2983112 DOI: 10.2147/oab.s7251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Botulinum neurotoxins (BoNTs), and in particular serotype A, are the most poisonous of known biological substances, and are responsible for the flaccid paralysis of the disease state botulism. Because of the extreme toxicity of these enzymes, BoNTs are considered highest priority biothreat agents. To counter BoNT serotype A (BoNT/A) poisoning, the discovery and development of small molecule, drug-like inhibitors as post-intoxication therapeutic agents has been/is being pursued. Specifically, we are focusing on inhibitors of the BoNT/A light chain (LC) (ie, a metalloprotease) subunit, since such compounds can enter neurons and provide post-intoxication protection of the enzyme target substrate. To aid/facilitate this drug development effort, a pharmacophore for inhibition of the BoNT/A LC subunit was previously developed, and is continually being refined via the incorporation of novel and diverse inhibitor chemotypes. Here, we describe several analogs of a promising therapeutic chemotype in the context of the pharmacophore for BoNT/A LC inhibition. Specifically, we describe: 1) the pharmacophoric 'fits' of the analogs and how these 'fits' rationalize the in vitro inhibitory potencies of the analogs and 2) pharmacophore refinement via the inclusion of new components from the most potent of the presented analogs.
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Affiliation(s)
- James C. Burnett
- Target, Structure-Based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702 (USA)
| | - Bing Li
- Microbiotix, Inc., Worcester, MA 01605 (USA)
| | - Ramdas Pai
- Microbiotix, Inc., Worcester, MA 01605 (USA)
| | | | | | | | - Donald Moir
- Microbiotix, Inc., Worcester, MA 01605 (USA)
| | - Sina Bavari
- Division of Integrated Toxicology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702 (USA)
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A single-domain llama antibody potently inhibits the enzymatic activity of botulinum neurotoxin by binding to the non-catalytic alpha-exosite binding region. J Mol Biol 2010; 397:1106-18. [PMID: 20138889 DOI: 10.1016/j.jmb.2010.01.070] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/27/2010] [Indexed: 02/07/2023]
Abstract
Ingestion or inhalation of botulinum neurotoxin (BoNT) results in botulism, a severe and frequently fatal disease. Current treatments rely on antitoxins, which, while effective, cannot reverse symptoms once BoNT has entered the neuron. For treatments that can reverse intoxication, interest has focused on developing inhibitors of the enzymatic BoNT light chain (BoNT Lc). Such inhibitors typically mimic substrate and bind in or around the substrate cleavage pocket. To explore the full range of binding sites for serotype A light chain (BoNT/A Lc) inhibitors, we created a library of non-immune llama single-domain VHH (camelid heavy-chain variable region derived from heavy-chain-only antibody) antibodies displayed on the surface of the yeast Saccharomyces cerevisiae. Library selection on BoNT/A Lc yielded 15 yeast-displayed VHH with equilibrium dissociation constants (K(d)) from 230 to 0.03 nM measured by flow cytometry. Eight of 15 VHH inhibited the cleavage of substrate SNAP25 (synaptosome-associated protein of 25,000 Da) by BoNT/A Lc. The most potent VHH (Aa1) had a solution K(d) for BoNT/A Lc of 1.47 x 10(-)(10) M and an IC(50) (50% inhibitory concentration) of 4.7 x 10(-)(10) M and was resistant to heat denaturation and reducing conditions. To understand the mechanism by which Aa1 inhibited catalysis, we solved the X-ray crystal structure of the BoNT/A Lc-Aa1 VHH complex at 2.6 A resolution. The structure reveals that the Aa1 VHH binds in the alpha-exosite of the BoNT/A Lc, far from the active site for catalysis. The study validates the utility of non-immune llama VHH libraries as a source of enzyme inhibitors and identifies the BoNT/A Lc alpha-exosite as a target for inhibitor development.
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31
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Yamane Y, Liu X, Hamasaki A, Ishida T, Haruta M, Yokoyama T, Tokunaga M. One-pot synthesis of indoles and aniline derivatives from nitroarenes under hydrogenation condition with supported gold nanoparticles. Org Lett 2010; 11:5162-5. [PMID: 19905025 DOI: 10.1021/ol902061j] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One-pot sequences of hydrogenation/hydroamination to form indoles from (2-nitroaryl)alkynes and hydrogenation/reductive amination to form aniline derivatives from nitroarenes and aldehydes were catalyzed by Au nanoparticles supported on Fe(2)O(3). Nitro group selective hydrogenations and successive reactions were efficiently catalyzed under the conditions.
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Affiliation(s)
- Yoshihiro Yamane
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 812-8581, Japan
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32
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Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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33
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Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design. PLoS One 2009; 4:e7730. [PMID: 19901994 PMCID: PMC2771286 DOI: 10.1371/journal.pone.0007730] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 10/13/2009] [Indexed: 11/19/2022] Open
Abstract
Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and offer complementary treatment for botulism. Previously we reported a serotype-selective, small-molecule BoNTAe inhibitor with a Kiapp value of 3.8±0.8 µM. This inhibitor was developed by lead identification using virtual screening followed by computer-aided optimization of a lead with an IC50 value of 100 µM. However, it was difficult to further improve the lead from micromolar to even high nanomolar potency due to the unusually large enzyme-substrate interface of BoNTAe. The enzyme-substrate interface area of 4,840 Å2 for BoNTAe is about four times larger than the typical protein-protein interface area of 750–1,500 Å2. Inhibitors must carry several functional groups to block the unusually large interface of BoNTAe, and syntheses of such inhibitors are therefore time-consuming and expensive. Herein we report the development of a serotype-selective, small-molecule, and competitive inhibitor of BoNTAe with a Ki value of 760±170 nM using synthesis-based computer-aided molecular design (SBCAMD). This new approach accounts the practicality and efficiency of inhibitor synthesis in addition to binding affinity and selectivity. We also report a three-dimensional model of BoNTAe in complex with the new inhibitor and the dynamics of the complex predicted by multiple molecular dynamics simulations, and discuss further structural optimization to achieve better in vivo efficacy in neutralizing BoNTA than those of our early micromolar leads. This work provides new insight into structural modification of known small-molecule BoNTAe inhibitors. It also demonstrates that SBCAMD is capable of improving potency of an inhibitor lead by nearly one order of magnitude, even for BoNTAe as one of the most challenging protein targets. The results are insightful for developing effective small-molecule inhibitors of protein targets with large active sites.
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Shi X, Garcia GE, Neill RJ, Gordon RK. TCEP treatment reduces proteolytic activity of BoNT/B in human neuronal SHSY-5Y cells. J Cell Biochem 2009; 107:1021-30. [DOI: 10.1002/jcb.22205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Identification and biochemical characterization of small-molecule inhibitors of Clostridium botulinum neurotoxin serotype A. Antimicrob Agents Chemother 2009; 53:3478-86. [PMID: 19528275 DOI: 10.1128/aac.00141-09] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An integrated strategy that combined in silico screening and tiered biochemical assays (enzymatic, in vitro, and ex vivo) was used to identify and characterize effective small-molecule inhibitors of Clostridium botulinum neurotoxin serotype A (BoNT/A). Virtual screening was initially performed by computationally docking compounds of the National Cancer Institute (NCI) database into the active site of BoNT/A light chain (LC). A total of 100 high-scoring compounds were evaluated in a high-performance liquid chromatography (HPLC)-based protease assay using recombinant full-length BoNT/A LC. Seven compounds that significantly inhibited the BoNT/A protease activity were selected. Database search queries of the best candidate hit [7-((4-nitro-anilino)(phenyl)methyl)-8-quinolinol (NSC 1010)] were performed to mine its nontoxic analogs. Fifty-five analogs of NSC 1010 were synthesized and examined by the HPLC-based assay. Of these, five quinolinol derivatives that potently inhibited both full-length BoNT/A LC and truncated BoNT/A LC (residues 1 to 425) were selected for further inhibition studies in neuroblastoma (N2a) cell-based and tissue-based mouse phrenic nerve hemidiaphragm assays. Consistent with enzymatic assays, in vitro and ex vivo studies revealed that these five quinolinol-based analogs effectively neutralized BoNT/A toxicity, with CB 7969312 exhibiting ex vivo protection at 0.5 microM. To date, this is the most potent BoNT/A small-molecule inhibitor that showed activity in an ex vivo assay. The reduced toxicity and high potency demonstrated by these five compounds at the biochemical, cellular, and tissue levels are distinctive among the BoNT/A small-molecule inhibitors reported thus far. This study demonstrates the utility of a multidisciplinary approach (in silico screening coupled with biochemical testing) for identifying promising small-molecule BoNT/A inhibitors.
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Larsen JC. U.S. Army Botulinum Neurotoxin (BoNT) Medical Therapeutics Research Program: past accomplishments and future directions. Drug Dev Res 2009. [DOI: 10.1002/ddr.20304] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pharmacophore-guided lead optimization: the rational design of a non-zinc coordinating, sub-micromolar inhibitor of the botulinum neurotoxin serotype a metalloprotease. Bioorg Med Chem Lett 2009; 19:5811-3. [PMID: 19703771 DOI: 10.1016/j.bmcl.2009.01.111] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 01/07/2009] [Indexed: 11/22/2022]
Abstract
Botulinum neurotoxins, responsible for the neuroparalytic syndrome botulism, are the deadliest of known biological toxins. The work described in this study was based on a three-zone pharmacophore model for botulinum neurotoxin serotype A light chain inhibition. Specifically, the pharmacophore defined a separation between the overlaps of several different, non-zinc(II)-coordinating small molecule chemotypes, enabling the design and synthesis of a new structural hybrid possessing a Ki=600 nM (+/-100 nM).
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Hermone AR, Burnett JC, Nuss JE, Tressler LE, Nguyen TL, Solaja BA, Vennerstrom JL, Schmidt JJ, Wipf P, Bavari S, Gussio R. Three-dimensional database mining identifies a unique chemotype that unites structurally diverse botulinum neurotoxin serotype A inhibitors in a three-zone pharmacophore. ChemMedChem 2009; 3:1905-12. [PMID: 19006141 DOI: 10.1002/cmdc.200800241] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A search query consisting of two aromatic centers and two cationic centers was defined based on previously identified small molecule inhibitors of the botulinum neurotoxin serotype A light chain (BoNT/A LC) and used to mine the National Cancer Institute Open Repository. Ten small molecule hits were identified, and upon testing, three demonstrated inhibitory activity. Of these, one was structurally unique, possessing a rigid diazachrysene scaffold. The steric limitations of the diazachrysene imposed a separation between the overlaps of previously identified inhibitors, revealing an extended binding mode. As a result, the pharmacophore for BoNT/A LC inhibition has been modified to encompass three zones. To demonstrate the utility of this model, a novel three-zone inhibitor was mined and its activity was confirmed.
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Affiliation(s)
- Ann R Hermone
- Target Structure-Based Drug Discovery Group, SAIC-Frederick, Inc. National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
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Wipf P, Wang C, Widom J, Petronijevic F, C. Burnett J, E. Nuss J, Bavari S, Gussio R. Synthesis and Biological Evaluation of Inhibitors of Botulinum Neurotoxin Metalloprotease. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(d)8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Willis B, Eubanks LM, Dickerson TJ, Janda KD. The strange case of the botulinum neurotoxin: using chemistry and biology to modulate the most deadly poison. Angew Chem Int Ed Engl 2008; 47:8360-79. [PMID: 18844202 DOI: 10.1002/anie.200705531] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the classic novella "The Strange Case of Dr. Jekyll and Mr. Hyde", Robert Louis Stevenson paints a stark picture of the duality of good and evil within a single man. Botulinum neurotoxin (BoNT), the most potent known toxin, possesses an analogous dichotomous nature: It shows a pronounced morbidity and mortality, but it is used with great effect in much lower doses in a wide range of clinical scenarios. Recently, tremendous strides have been made in the basic understanding of the structure and function of BoNT, which have translated into widespread efforts towards the discovery of biomacromolecules and small molecules that specifically modulate BoNT activity. Particular emphasis has been placed on the identification of inhibitors that can counteract BoNT exposure in the event of a bioterrorist attack. This Review summarizes the current advances in the development of therapeutics, including vaccines, peptides, and small-molecule inhibitors, for the prevention and treatment of botulism.
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Affiliation(s)
- Bert Willis
- Department of Chemistry, Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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41
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Willis B, Eubanks L, Dickerson T, Janda K. Der seltsame Fall des Botulinum-Neurotoxins: chemische und biologische Modulierung des tödlichsten aller Gifte. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Silvaggi NR, Wilson D, Tzipori S, Allen KN. Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex. Biochemistry 2008; 47:5736-45. [PMID: 18457419 DOI: 10.1021/bi8001067] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Clostridium botulinum neurotoxin serotype A light chain (BoNT/A-LC) is a Zn(II)-dependent metalloprotease that blocks the release of acetylcholine at the neuromuscular junction by cleaving SNAP-25, one of the SNARE proteins required for exocytosis. Because of the potential for use of the toxin in bioterrorism and the increasingly widespread application of the toxin in the medical field, there is significant interest in the development of small-molecule inhibitors of the metalloprotease. Efforts to design such inhibitors have not benefited from knowledge of how peptides bind to the active site since the enzyme-peptide structures available previously either were not occupied in the vicinity of the catalytic Zn(II) ion or did not represent the product of SNAP-25 substrate cleavage. Herein we report the 1.4 A-resolution X-ray crystal structure of a complex between the BoNT/A-LC and the inhibitory peptide N-Ac-CRATKML, the first structure of the light chain with an inhibitory peptide bound at the catalytic Zn(II) ion. The peptide is bound with the Cys S gamma atom coordinating the metal ion. Surprisingly, the cysteine sulfur is oxidized to the sulfenic acid form. Given the unstable nature of this species in solution, is it likely that oxidation occurs on the enzyme. In addition to the peptide-bound structure, we report two structures of the unliganded light chain with and without the Zn(II) cofactor bound at 1.25 and 1.20 A resolution, respectively. The two structures are nearly identical, confirming that the Zn(II) ion plays a purely catalytic role. Additionally, the structure of the Zn(II)-bound uncomplexed enzyme allows identification of the catalytic water molecule and a second water molecule that occupies the same position as the peptidic oxygen in the tetrahedral intermediate. This observation suggests that the enzyme active site is prearranged to stabilize the tetrahedral intermediate of the protease reaction.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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43
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Choi J, Park JG, Pang YP. Convenient Synthesis of a Library of Discrete Hydroxamic Acids Using the Hydroxythiophenol (Marshall) Resin. Tetrahedron Lett 2008; 49:1103-1106. [PMID: 18443652 PMCID: PMC2352145 DOI: 10.1016/j.tetlet.2007.12.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Several resins have reportedly been used to synthesize hydroxamic acids except for the hydroxythiophenol (Marshall) resin. Herein we report the use of the Marshall resin to synthesize hydroxamic acids from carboxylic acids and its application to convert a library of fourteen discrete aliphatic and aromatic carboxylic acids including N-protected amino acids to their corresponding hydroxamic acids in good yields.
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Affiliation(s)
- Jinil Choi
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, USA
| | - Jewn Giew Park
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, USA
| | - Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, USA
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Hines HB, Kim AD, Stafford RG, Badie SS, Brueggeman EE, Newman DJ, Schmidt JJ. Use of a recombinant fluorescent substrate with cleavage sites for all botulinum neurotoxins in high-throughput screening of natural product extracts for inhibitors of serotypes A, B, and E. Appl Environ Microbiol 2008; 74:653-9. [PMID: 18083881 PMCID: PMC2227718 DOI: 10.1128/aem.01690-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 11/26/2007] [Indexed: 11/20/2022] Open
Abstract
The seven serotypes of botulinum neurotoxin (BoNTs) are zinc metalloproteases that cleave and inactivate proteins critical for neurotransmission. The synaptosomal protein of 25 kDa (SNAP-25) is cleaved by BoNTs A, C, and E, while vesicle-associated membrane protein (VAMP) is the substrate for BoNTs B, D, F, and G. BoNTs not only are medically useful drugs but also are potential bioterrorist and biowarfare threat agents. Because BoNT protease activity is required for toxicity, inhibitors of that activity might be effective for antibotulinum therapy. To expedite inhibitor discovery, we constructed a hybrid gene encoding (from the N terminus to the C terminus, with respect to the expressed product) green fluorescent protein, then a SNAP-25 fragment encompassing residues Met-127 to Gly-206, and then VAMP residues Met-1 to Lys-94. Cysteine was added as the C terminus. The expressed product, which contained the protease cleavage sites for all seven botulinum serotypes, was purified and coupled covalently through the C-terminal sulfhydryl group to maleimide-activated 96-well plates. The substrate was readily cleaved by BoNTs A, B, D, E, and F. Using this assay and an automated 96-well pipettor, we screened 528 natural product extracts for inhibitors of BoNT A, B, and E protease activities. Serotype-specific inhibition was found in 30 extracts, while 5 others inhibited two serotypes.
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Affiliation(s)
- Harry B Hines
- Department of Cell Biology and Biochemistry, Integrated Toxicology Division, USAMRIID, Frederick, MD 21702-5011, USA
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45
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Eubanks LM, Dickerson TJ. Investigating novel therapeutic targets and molecular mechanisms to treat botulinum neurotoxin A intoxication. Future Microbiol 2008; 2:677-87. [PMID: 18041908 DOI: 10.2217/17460913.2.6.677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Botulinum neurotoxin (BoNT) has recently catapulted into the public consciousness in two seemingly disparate roles: potential use as a biological weapon and treatment of neuromuscular disorders. This bacterially produced protein is the most potent toxin known to humans, with a lethal dose estimated at approximately 1 ng/kg of body weight. BoNT intoxication occurs via a multistep process that includes recognition of peripheral neuronal cell membrane receptors, endocytosis and translocation of the light chain metalloprotease into the cytosol, and catalytic cleavage of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins critical for vesicle fusion and neurotransmitter release. Each of these distinct steps has been studied at the molecular level and is a valid target for the development of pharmacological interventions to prevent the considerable mortality associated with botulism. Alternatively, clinical uses of BoNT continue to expand at an ever-increasing rate; however, further optimization of BoNT therapy is critical to maximize efficacy.
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Affiliation(s)
- Lisa M Eubanks
- The Scripps Research Institute, Department of Chemistry, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Dolle RE, Le Bourdonnec B, Goodman AJ, Morales GA, Salvino JM, Zhang W. Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2006. ACTA ACUST UNITED AC 2007; 9:855-902. [PMID: 17877417 DOI: 10.1021/cc700111e] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roland E Dolle
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, USA.
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Tang J, Park JG, Millard CB, Schmidt JJ, Pang YP. Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A. PLoS One 2007; 2:e761. [PMID: 17712409 PMCID: PMC1942119 DOI: 10.1371/journal.pone.0000761] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/16/2007] [Indexed: 11/23/2022] Open
Abstract
Optimization of a serotype-selective, small-molecule inhibitor of botulinum neurotoxin serotype A (BoNTA) endopeptidase is a formidable challenge because the enzyme-substrate interface is unusually large and the endopeptidase itself is a large, zinc-binding protein with a complex fold that is difficult to simulate computationally. We conducted multiple molecular dynamics simulations of the endopeptidase in complex with a previously described inhibitor (Kiapp of 7±2.4 µM) using the cationic dummy atom approach. Based on our computational results, we hypothesized that introducing a hydroxyl group to the inhibitor could improve its potency. Synthesis and testing of the hydroxyl-containing analog as a BoNTA endopeptidase inhibitor showed a twofold improvement in inhibitory potency (Kiapp of 3.8±0.8 µM) with a relatively small increase in molecular weight (16 Da). The results offer an improved template for further optimization of BoNTA endopeptidase inhibitors and demonstrate the effectiveness of the cationic dummy atom approach in the design and optimization of zinc protease inhibitors.
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Affiliation(s)
- Jing Tang
- 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
| | - Charles B. Millard
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - James J. Schmidt
- Department of Cell Biology and Biochemistry, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (JS); (Y-PP)
| | - Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail: (JS); (Y-PP)
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48
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Silvaggi NR, Boldt GE, Hixon MS, Kennedy JP, Tzipori S, Janda KD, Allen KN. Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain complexed with small-molecule inhibitors highlight active-site flexibility. ACTA ACUST UNITED AC 2007; 14:533-42. [PMID: 17524984 DOI: 10.1016/j.chembiol.2007.03.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 02/07/2007] [Accepted: 03/14/2007] [Indexed: 11/19/2022]
Abstract
The potential for the use of Clostridial neurotoxins as bioweapons makes the development of small-molecule inhibitors of these deadly toxins a top priority. Recently, screening of a random hydroxamate library identified a small-molecule inhibitor of C. botulinum Neurotoxin Serotype A Light Chain (BoNT/A-LC), 4-chlorocinnamic hydroxamate, a derivative of which has been shown to have in vivo efficacy in mice and no toxicity. We describe the X-ray crystal structures of BoNT/A-LC in complexes with two potent small-molecule inhibitors. The structures of the enzyme with 4-chlorocinnamic hydroxamate or 2,4-dichlorocinnamic hydroxamate bound are compared to the structure of the enzyme complexed with L-arginine hydroxamate, an inhibitor with modest affinity. Taken together, this suite of structures provides surprising insights into the BoNT/A-LC active site, including unexpected conformational flexibility at the S1' site that changes the electrostatic environment of the binding pocket. Information gained from these structures will inform the design and optimization of more effective small-molecule inhibitors of BoNT/A-LC.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
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49
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Wang Q, Pang YP. Accurate reproduction of 161 small-molecule complex crystal structures using the EUDOC program: expanding the use of EUDOC to supramolecular chemistry. PLoS One 2007; 2:e531. [PMID: 17565384 PMCID: PMC1888730 DOI: 10.1371/journal.pone.0000531] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/21/2007] [Indexed: 11/18/2022] Open
Abstract
EUDOC is a docking program that has successfully predicted small-molecule-bound protein complexes and identified drug leads from chemical databases. To expand the application of the EUDOC program to supramolecular chemistry, we tested its ability to reproduce crystal structures of small-molecule complexes. Of 161 selected crystal structures of small-molecule guest-host complexes, EUDOC reproduced all these crystal structures with guest structure mass-weighted root mean square deviations (mwRMSDs) of <1.0 A relative to the corresponding crystal structures. In addition, the average interaction energy of these 161 guest-host complexes (-50.1 kcal/mol) was found to be nearly half of that of 153 previously tested small-molecule-bound protein complexes (-108.5 kcal/mol), according to the interaction energies calculated by EUDOC. 31 of the 161 complexes could not be reproduced with mwRMSDs of <1.0 A if neighboring hosts in the crystal structure of a guest-host complex were not included as part of the multimeric host system, whereas two of the 161 complexes could not be reproduced with mwRMSDs of <1.0 A if water molecules were excluded from the host system. These results demonstrate the significant influence of crystal packing on small molecule complexation and suggest that EUDOC is able to predict small-molecule complexes and that it is useful for the design of new materials, molecular sensors, and multimeric inhibitors of protein-protein interactions.
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Affiliation(s)
- Qi Wang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Stahl AM, Ruthel G, Torres-Melendez E, Kenny TA, Panchal RG, Bavari S. Primary cultures of embryonic chicken neurons for sensitive cell-based assay of botulinum neurotoxin: implications for therapeutic discovery. ACTA ACUST UNITED AC 2007; 12:370-7. [PMID: 17332092 DOI: 10.1177/1087057106299163] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Botulinum toxin is an exceedingly potent inhibitor of neurotransmission across the neuromuscular junction, causing flaccid paralysis and death. The potential for misuse of this deadly poison as a bioweapon has added a greater urgency to the search for effective therapeutics. The development of sensitive and efficient cell-based assays for the evaluation of toxin antagonists is crucial to the rapid and successful identification of therapeutic compounds. The authors evaluated the sensitivity of primary cultures from 4 distinct regions of the embryonic chick nervous system to botulinum neurotoxin A (BoNT/A) cleavage of synaptosomal-associated protein of 25 kD (SNAP-25). Although differences in sensitivity were apparent, SNAP-25 cleavage was detectable in neuronal cells from each of the 4 regions within 3 h at BoNT/A concentrations of 1 nM or lower. Co-incubation of chick neurons with BoNT/A and toxin-neutralizing antibodies inhibited SNAP-25 cleavage, demonstrating the utility of these cultures for the assay of BoNT/A antagonists.
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Affiliation(s)
- Andrea M Stahl
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, USA
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