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Mishra R, Gerlach GJ, Sahoo B, Camacho CJ, Wetzel R. A Targetable Self-association Surface of the Huntingtin exon1 Helical Tetramer Required for Assembly of Amyloid Pre-nucleation Oligomers. J Mol Biol 2024; 436:168607. [PMID: 38734203 DOI: 10.1016/j.jmb.2024.168607] [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: 12/13/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Polyglutamine (polyQ) sequences undergo repeat-length dependent formation of disease-associated, amyloid-like cross-β core structures with kinetics and aggregate morphologies often influenced by the flanking sequences. In Huntington's disease (HD), the httNT segment on the polyQ's N-terminal flank enhances aggregation rates by changing amyloid nucleation from a classical homogeneous mechanism to a two-step process requiring an ɑ-helix-rich oligomeric intermediate. A folded, helix-rich httNT tetrameric structure suggested to be this critical intermediate was recently reported. Here we employ single alanine replacements along the httNT sequence to assess this proposed structure and refine the mechanistic model. We find that Ala replacement of hydrophobic residues within simple httNT peptides greatly suppresses helicity, supporting the tetramer model. These same helix-disruptive replacements in the httNT segment of an exon-1 analog greatly reduce aggregation kinetics, suggesting that an ɑ-helix rich multimer - either the tetramer or a larger multimer - plays an on-pathway role in nucleation. Surprisingly, several other Ala replacements actually enhance helicity and/or amyloid aggregation. The spatial localization of these residues on the tetramer surface suggests a self-association interface responsible for formation of the octomers and higher-order multimers most likely required for polyQ amyloid nucleation. Multimer docking of the tetramer, using the protein-protein docking algorithm ClusPro, predicts this symmetric surface to be a viable tetramer dimerization interface. Intriguingly, octomer formation brings the emerging polyQ chains into closer proximity at this tetramer-tetramer interface. Further supporting the potential importance of tetramer super-assembly, computational docking with a known exon-1 aggregation inhibitor predicts ligand contacts with residues at this interface.
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Affiliation(s)
- Rakesh Mishra
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Gabriella J Gerlach
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA
| | - Bankanidhi Sahoo
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Ronald Wetzel
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
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2
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Lantz C, Lopez J, Goring AK, Zenaidee MA, Biggs K, Whitelegge JP, Ogorzalek Loo RR, Klärner FG, Schrader T, Bitan G, Loo JA. Characterization of Molecular Tweezer Binding on α-Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation Inhibition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2739-2747. [PMID: 37936057 PMCID: PMC10959575 DOI: 10.1021/jasms.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Parkinson's disease, a neurodegenerative disease that affects 15 million people worldwide, is characterized by deposition of α-synuclein into Lewy Bodies in brain neurons. Although this disease is prevalent worldwide, a therapy or cure has yet to be found. Several small compounds have been reported to disrupt fibril formation. Among these compounds is a molecular tweezer known as CLR01 that targets lysine and arginine residues. This study aims to characterize how CLR01 interacts with various proteoforms of α-synuclein and how the structure of α-synuclein is subsequently altered. Native mass spectrometry (nMS) measurements of α-synuclein/CLR01 complexes reveal that multiple CLR01 molecules can bind to α-synuclein proteoforms such as α-synuclein phosphorylated at Ser-129 and α-synuclein bound with copper and manganese ions. The binding of one CLR01 molecule shifts the ability for α-synuclein to bind other ligands. Electron capture dissociation (ECD) with Fourier transform-ion cyclotron resonance (FT-ICR) top-down (TD) mass spectrometry of α-synuclein/CLR01 complexes pinpoints the locations of the modifications on each proteoform and reveals that CLR01 binds to the N-terminal region of α-synuclein. CLR01 binding compacts the gas-phase structure of α-synuclein, as shown by ion mobility-mass spectrometry (IM-MS). These data suggest that when multiple CLR01 molecules bind, the N-terminus of α-synuclein shifts toward a more compact state. This compaction suggests a mechanism for CLR01 halting the formation of oligomers and fibrils involved in many neurodegenerative diseases.
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Affiliation(s)
- Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jaybree Lopez
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Muhammad A. Zenaidee
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
| | - Karl Biggs
- Department of Neurology and Brain Research Institute, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | | | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
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3
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Taha HB, Chawla E, Bitan G. IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2066-2086. [PMID: 37607351 DOI: 10.1021/jasms.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodegenerative proteinopathies are characterized by formation and deposition of misfolded, aggregated proteins in the nervous system leading to neuronal dysfunction and death. It is widely believed that metastable oligomers of the offending proteins, preceding the fibrillar aggregates found in the tissue, are the proximal neurotoxins. There are currently almost no disease-modifying therapies for these diseases despite an active pipeline of preclinical development and clinical trials for over two decades, largely because studying the metastable oligomers and their interaction with potential therapeutics is notoriously difficult. Mass spectrometry (MS) is a powerful analytical tool for structural investigation of proteins, including protein-protein and protein-ligand interactions. Specific MS tools have been useful in determining the composition and conformation of abnormal protein oligomers involved in proteinopathies and the way they interact with drug candidates. Here, we analyze critically the utilization of ion-mobility spectroscopy-MS (IM-MS) and electron-capture dissociation (ECD) MS/MS for analyzing the oligomerization and conformation of multiple amyloidogenic proteins. We also discuss IM-MS investigation of their interaction with two classes of compounds developed by our group over the last two decades: C-terminal fragments derived from the 42-residue form of amyloid β-protein (Aβ42) and molecular tweezers. Finally, we review the utilization of ECD-MS/MS for elucidating the binding sites of the ligands on multiple proteins. These approaches are readily applicable to future studies addressing similar questions and hold promise for facilitating the development of successful disease-modifying drugs against neurodegenerative proteinopathies.
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Affiliation(s)
- Hash Brown Taha
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Integrative Biology & Physiology, University of California Los Angeles, California 90095, United States
| | - Esha Chawla
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Brain Research Institute, University of California Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California Los Angeles, California 90095, United States
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4
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Maity D. Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches. Biophys Chem 2023; 297:107022. [PMID: 37058879 DOI: 10.1016/j.bpc.2023.107022] [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: 01/22/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.
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Affiliation(s)
- Debabrata Maity
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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5
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Shahpasand-Kroner H, Siddique I, Malik R, Linares GR, Ivanova MI, Ichida J, Weil T, Münch J, Sanchez-Garcia E, Klärner FG, Schrader T, Bitan G. Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications. Pharmacol Rev 2023; 75:263-308. [PMID: 36549866 PMCID: PMC9976797 DOI: 10.1124/pharmrev.122.000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.
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Affiliation(s)
- Hedieh Shahpasand-Kroner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gabriel R Linares
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Magdalena I Ivanova
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Justin Ichida
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Tatjana Weil
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Jan Münch
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Frank-Gerrit Klärner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Thomas Schrader
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [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: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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7
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Khaled M, Strodel B, Sayyed-Ahmad A. Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers. Front Mol Biosci 2023; 10:1143353. [PMID: 37101557 PMCID: PMC10123271 DOI: 10.3389/fmolb.2023.1143353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures and aggregation mechanism are still poorly understood. We performed microsecond-long all-atom molecular dynamics simulations to study the folding and dimerization of Htt-ex1 (about 100 residues) with non-pathogenic and pathogenic polyQ lengths, and uncovered substantial differences. The non-pathogenic monomer adopts a long α-helix that includes most of the polyQ residues, which forms the interaction interface for dimerization, and a PPII-turn-PPII motif in the proline-rich region. In the pathogenic monomer, the polyQ region is disordered, leading to compact structures with many intra-protein interactions and the formation of short β-sheets. Dimerization can proceed via different modes, where those involving the N-terminal headpiece bury more hydrophobic residues and are thus more stable. Moreover, in the pathogenic Htt-ex1 dimers the proline-rich region interacts with the polyQ region, which slows the formation of β-sheets.
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Affiliation(s)
- Mohammed Khaled
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Birgit Strodel, ; Abdallah Sayyed-Ahmad,
| | - Abdallah Sayyed-Ahmad
- Department of Physics, Birzeit University, Birzeit, Palestine
- *Correspondence: Birgit Strodel, ; Abdallah Sayyed-Ahmad,
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8
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Samanta N, Ruiz‐Blanco YB, Fetahaj Z, Gnutt D, Lantz C, Loo JA, Sanchez‐Garcia E, Ebbinghaus S. Superoxide Dismutase 1 Folding Stability as a Target for Molecular Tweezers in SOD1-Related Amyotrophic Lateral Sclerosis. Chembiochem 2022; 23:e202200396. [PMID: 36083789 PMCID: PMC9828543 DOI: 10.1002/cbic.202200396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Indexed: 01/12/2023]
Abstract
Protein misfolding and aggregation are hallmarks of many severe neurodegenerative diseases including Alzheimer's, Parkinson's and Huntington's disease. As a supramolecular ligand that binds to lysine and arginine residues, the molecular tweezer CLR01 was found to modify the aggregation pathway of disease-relevant proteins in vitro and in vivo with beneficial effects on toxicity. However, the molecular mechanisms of how tweezers exert these effects remain mainly unknown, hampering further drug development. Here, we investigate the modulation mechanism of unfolding and aggregation pathways of SOD1, which are involved in amyotrophic lateral sclerosis (ALS), by CLR01. Using a truncated version of the wildtype SOD1 protein, SOD1bar , we show that CLR01 acts on the first step of the aggregation pathway, the unfolding of the SOD1 monomer. CLR01 increases, by ∼10 °C, the melting temperatures of the A4V and G41D SOD1 mutants, which are commonly observed mutations in familial ALS. Molecular dynamics simulations and binding free energy calculations as well as native mass spectrometry and mutational studies allowed us to identify K61 and K92 as binding sites for the tweezers to mediate the stability increase. The data suggest that the modulation of SOD1 conformational stability is a promising target for future developments of supramolecular ligands against neurodegenerative diseases.
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Affiliation(s)
- Nirnay Samanta
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany
| | - Yasser B. Ruiz‐Blanco
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen45141EssenGermany
| | - Zamira Fetahaj
- Department of Physical Chemistry IIRuhr University44780BochumGermany
| | - David Gnutt
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany,Department of Physical Chemistry IIRuhr University44780BochumGermany
| | - Carter Lantz
- Department of Chemistry and BiochemistryUniversity of California-Los Angeles90095Los Angeles, CAUSA
| | - Joseph A. Loo
- Department of Chemistry and BiochemistryUniversity of California-Los Angeles90095Los Angeles, CAUSA
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen45141EssenGermany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany,Department of Physical Chemistry IIRuhr University44780BochumGermany
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9
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Zhou X, Shi M, Wang X, Xu D. Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics. Front Chem 2022; 10:921695. [PMID: 35646830 PMCID: PMC9133541 DOI: 10.3389/fchem.2022.921695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Using supramolecules for protein function regulation is an effective strategy in chemical biology and drug discovery. However, due to the presence of multiple binding sites on protein surfaces, protein function regulation via selective binding of supramolecules is challenging. Recently, the functions of 14-3-3 proteins, which play an important role in regulating intracellular signaling pathways via protein–protein interactions, have been modulated using a supramolecular tweezer, CLR01. However, the binding mechanisms of the tweezer molecule to 14-3-3 proteins are still unclear, which has hindered the development of novel supramolecules targeting the 14-3-3 proteins. Herein, the binding mechanisms of the tweezer to the lysine residues on 14-3-3σ (an isoform in 14-3-3 protein family) were explored by well-tempered metadynamics. The results indicated that the inclusion complex formed between the protein and supramolecule is affected by both kinetic and thermodynamic factors. In particular, simulations confirmed that K214 could form a strong binding complex with the tweezer; the binding free energy was calculated to be −10.5 kcal·mol−1 with an association barrier height of 3.7 kcal·mol−1. In addition, several other lysine residues on 14-3-3σ were identified as being well-recognized by the tweezer, which agrees with experimental results, although only K214/tweezer was co-crystallized. Additionally, the binding mechanisms of the tweezer to all lysine residues were analyzed by exploring the representative conformations during the formation of the inclusion complex. This could be helpful for the development of new inhibitors based on tweezers with more functions against 14-3-3 proteins via modifications of CLR01. We also believe that the proposed computational strategies can be extended to understand the binding mechanism of multi-binding sites proteins with supramolecules and will, thus, be useful toward drug design.
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Affiliation(s)
- Xin Zhou
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
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10
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Jozeliu Naitė A, Javorskis T, Vaitkevičius V, Klimavičius V, Orentas E. Fully Supramolecular Chiral Hydrogen-Bonded Molecular Tweezer. J Am Chem Soc 2022; 144:8231-8241. [PMID: 35500199 DOI: 10.1021/jacs.2c01455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular tweezers are open-ended, cavity-possessing U-shaped molecular architectures with high potential for various applications in supramolecular chemistry. Their covalent synthesis, however, is often tedious and the structures obtained lack structural responsiveness beyond the limited conformational flexibility of the scaffold. Herein we present a proof-of-concept study on the design, synthesis, assembly, and transformations of a novel supramolecular construct─a fully noncovalent molecular tweezer. The supramolecular tweezer was assembled from a set of four building blocks, composed of two identical molecular angle bars and two flat aromatic extension wings, using hydrogen bonding only. The chirality-assisted aggregation process was utilized to ensure scaffold bending directionality using enantiomerically pure bicyclic angle bars. To address the challenges associated with shifting of the equilibrium from strong cooperative narcissistic self-sorting of self-complementary angle bars in cyclic aggregates toward integrative self-sorting in molecular tweezers, a rational desymmetrization strategy was applied. The dynamic supramolecular tweezer has been shown to display rich supramolecular chemistry, allowing for stimuli-responsive change in aggregate topology and solvent-responsive supramolecular polymerization.
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Affiliation(s)
- Augustina Jozeliu Naitė
- Department of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania
| | - Tomas Javorskis
- Department of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania
| | - Vytenis Vaitkevičius
- Department of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania
| | | | - Edvinas Orentas
- Department of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania
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11
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Brylski O, Shrestha P, House PJ, Gnutt P, Mueller JW, Ebbinghaus S. Disease-Related Protein Variants of the Highly Conserved Enzyme PAPSS2 Show Marginal Stability and Aggregation in Cells. Front Mol Biosci 2022; 9:860387. [PMID: 35463959 PMCID: PMC9024126 DOI: 10.3389/fmolb.2022.860387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular sulfation pathways rely on the activated sulfate 3′-phosphoadenosine-5′-phosphosulfate (PAPS). In humans, PAPS is exclusively provided by the two PAPS synthases PAPSS1 and PAPSS2. Mutations found in the PAPSS2 gene result in severe disease states such as bone dysplasia, androgen excess and polycystic ovary syndrome. The APS kinase domain of PAPSS2 catalyzes the rate-limiting step in PAPS biosynthesis. In this study, we show that clinically described disease mutations located in the naturally fragile APS kinase domain are associated either with its destabilization and aggregation or its deactivation. Our findings provide novel insights into possible molecular mechanisms that could give rise to disease phenotypes associated with sulfation pathway genes.
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Affiliation(s)
- Oliver Brylski
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
| | - Puja Shrestha
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Philip J. House
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
| | - Patricia Gnutt
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, United Kingdom
- *Correspondence: Jonathan Wolf Mueller, ; Simon Ebbinghaus,
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
- *Correspondence: Jonathan Wolf Mueller, ; Simon Ebbinghaus,
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12
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Li Y, Xia Y, Yin S, Wan F, Hu J, Kou L, Sun Y, Wu J, Zhou Q, Huang J, Xiong N, Wang T. Targeting Microglial α-Synuclein/TLRs/NF-kappaB/NLRP3 Inflammasome Axis in Parkinson's Disease. Front Immunol 2021; 12:719807. [PMID: 34691027 PMCID: PMC8531525 DOI: 10.3389/fimmu.2021.719807] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/22/2021] [Indexed: 01/04/2023] Open
Abstract
According to emerging studies, the excessive activation of microglia and the subsequent release of pro-inflammatory cytokines play important roles in the pathogenesis and progression of Parkinson's disease (PD). However, the exact mechanisms governing chronic neuroinflammation remain elusive. Findings demonstrate an elevated level of NLRP3 inflammasome in activated microglia in the substantia nigra of PD patients. Activated NLRP3 inflammasome aggravates the pathology and accelerates the progression of neurodegenerative diseases. Abnormal protein aggregation of α-synuclein (α-syn), a pathologically relevant protein of PD, were reported to activate the NLRP3 inflammasome of microglia through interaction with toll-like receptors (TLRs). This eventually releases pro-inflammatory cytokines through the translocation of nuclear factor kappa-B (NF-κB) and causes an impairment of mitochondria, thus damaging the dopaminergic neurons. Currently, therapeutic drugs for PD are primarily aimed at providing relief from its clinical symptoms, and there are no well-established strategies to halt or reverse this disease. In this review, we aimed to update existing knowledge on the role of the α-syn/TLRs/NF-κB/NLRP3 inflammasome axis and microglial activation in PD. In addition, this review summarizes recent progress on the α-syn/TLRs/NF-κB/NLRP3 inflammasome axis of microglia as a potential target for PD treatment by inhibiting microglial activation.
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Affiliation(s)
- Yunna Li
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Xia
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sijia Yin
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Wan
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Hu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Kou
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yadi Sun
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiawei Wu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiulu Zhou
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinsha Huang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nian Xiong
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Cao W, Qin X, Liu T. When Supramolecular Chemistry Meets Chemical Biology: New Strategies to Target Proteins through Host-Guest Interactions. Chembiochem 2021; 22:2914-2917. [PMID: 34487417 DOI: 10.1002/cbic.202100357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/24/2021] [Indexed: 11/11/2022]
Abstract
Supramolecular chemistry for targeting proteins is of great interest for the development of novel approaches to recognize, isolate and control proteins. Taking advantage of chemical biology approaches, such as genetic-code expansion and enzyme-mediated ligation, guest recognition elements can be built into proteins of interest, allowing supramolecular control of protein function and regulation. In this viewpoint article, we will discuss the methods, applications, limitations, and future perspectives of supramolecular chemistry for targeting proteins in a site-specific manner.
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Affiliation(s)
- Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China.,College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
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14
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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15
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Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wenbing Cao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhen Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xianyin Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Weimin Xuan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yingming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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16
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Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021; 60:11196-11200. [PMID: 33580548 DOI: 10.1002/anie.202100916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Indexed: 01/24/2023]
Abstract
Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.
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Affiliation(s)
- Wenbing Cao
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhen Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xianyin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Weimin Xuan
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yingming Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
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17
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Rumancev C, Vöpel T, Stuhr S, Gundlach AR, Senkbeil T, Osterhoff M, Sprung M, Garamus VM, Ebbinghaus S, Rosenhahn A. In Cellulo Analysis of Huntingtin Inclusion Bodies by Cryogenic Nanoprobe SAXS. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christoph Rumancev
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Vöpel
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Susan Stuhr
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Andreas R. Gundlach
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Senkbeil
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Markus Osterhoff
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Vasil M. Garamus
- Helmholtz-Zentrum Geesthacht: Centre for Materials and Coast Research Institute of Materials Research Max-Planck-Str. 1 21502 Geesthacht Germany
| | - Simon Ebbinghaus
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
- Institute of Physical and Theoretical Chemistry TU Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Axel Rosenhahn
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
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18
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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19
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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20
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Issa AA, Obayes HR. Capture carcinogenic aromatic compounds by the design of new tweezer compounds: a theoretical study. J Mol Model 2020; 26:292. [PMID: 32995930 DOI: 10.1007/s00894-020-04558-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
Both [5]-circulene and [7]-circulene can be selected to design the molecular tweezers theoretically using the DFT method. Leaning on the cyclic polymerization mechanism, we obtain four new tweezer compounds. Theoretical results offer that tweezer compound (I) is additionally stable than other compounds because it has better energies than other compounds. The values were as follows: - 2606.83372937 a.u. for the total energy, - 5.39820 eV for (EHOMO), and 2.87407 eV for gap energy. The thermodynamic theoretical outcome showed that all reactions are exothermic and spontaneous, suggesting that tweezer compound (I) might correlate with several aromatic compounds, such as pyrene, benzo[ghi]perylene, ovalene, and hexabenzocoronene. The correlation energy results showed an increase as the aromatic compound becomes larger, while the correlation distance decreases. All correlation energy kinds are electrostatic. The value of the electrostatic correlation energy of tweezer compound (I)-ovalene is (- 6.4928615 kJ mol-1). The tweezer compound (I) has a spherical cavity equal to 3.73640 nm3, which adds an important application in the ability to capture chemicals, bacteria, or viruses that are close to the size of the cavity with ease.
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Affiliation(s)
- Ali Abdullah Issa
- Applied Chemistry Division, Applied Science Department, University of Technology, Baghdad, Iraq
| | - Hasan R Obayes
- Applied Chemistry Division, Applied Science Department, University of Technology, Baghdad, Iraq.
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21
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Mitra G. Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins. Proteomics 2020; 21:e2000011. [PMID: 32959512 DOI: 10.1002/pmic.202000011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/30/2020] [Indexed: 12/14/2022]
Abstract
Inherent disorder is an integral part of all proteomes, represented as fully or partially unfolded proteins. The lack of order in intrinsically disordered proteins (IDPs) results in an incredibly flexible, floppy, and heterogeneous ensemble, contrary to the well-structured and unique organization of folded proteins. Despite such unusual demeanor, IDPs are crucial for numerous cellular processes and are increasingly being associated with disease-causing pathologies. These warrant more intensive investigation of this atypical class of protein. Traditional biophysical tools, however, fall short of analyzing IDPs, thus making their structure-function characterization challenging. Mass spectrometry (MS) in recent years has evolved as a valuable tool for elucidating the unusual conformational facets of IDPs. In this review, the features of advanced MS techniques such as Hydrogen-deuterium exchange (HDX)-MS, native MS, limited proteolysis (LiP)-MS, chemical cross-linking (XL)-MS, and Fast photochemical oxidation of proteins (FPOP)-MS are briefly discussed. Recent MS studies on IDPs and the unique advantages/shortfalls associated with the above methods while evaluating structural proteomics of IDPs, are illustrated. Eventually the future scope of the MS methods in further decoding the unexplored landscapes of IDPs is presented.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St John's Medical College, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore, Karnataka, 560034, India
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22
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Ruiz-Blanco YB, Sanchez-Garcia E. CL-FEP: An End-State Free Energy Perturbation Approach. J Chem Theory Comput 2020; 16:1396-1410. [DOI: 10.1021/acs.jctc.9b00725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasser B. Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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23
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Moldovean SN, Chiş V. Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review. ACS Chem Neurosci 2020; 11:105-120. [PMID: 31841621 DOI: 10.1021/acschemneuro.9b00561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the recent years, Huntington's disease (HD) has become widely discussed in the scientific literature especially because at the mutant level there are several contradictions regarding the aggregation mechanism. The specific role of the physiological huntingtin protein remains unknown, due to the lack of characterization of its entire crystallographic structure, making the experimental and theoretical research even harder when taking into consideration its involvement in multiple biological functions and its high affinity for different interacting partners. Different types of models, containing fewer (not more than 35 Qs) polyglutamine residues for the WT structure and above 35 Qs for the mutants, were subjected to classical or advanced MD simulations to establish the proteins' structural stability by evaluating their conformational changes. Outside the polyQ tract, there are two other regions of interest (the N17 domain and the polyP rich domain) considered to be essential for the aggregation kinetics at the mutant level. The polymerization process is considered to be dependent on the polyQ length. As the polyQ tract's dimension increases, the structures present more β-sheet conformations. Contrarily, it is also considered that the aggregation stability is not necessarily dependent on the number of Qs, while the initial stage of the aggregation seed might play the decisive role. A general assumption regarding the polyP domain is that it might preserve the polyQ structures soluble by acting as an antagonist for β-sheet formation.
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Affiliation(s)
| | - Vasile Chiş
- Babeş-Bolyai University, Faculty of Physics, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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24
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Quantum mechanics/molecular mechanics multiscale modeling of biomolecules. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2020. [DOI: 10.1016/bs.apoc.2020.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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25
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Study of the self-association of molecular tweezers bearing two different arms: influence of the stereoelectronic effects of the arm substituents. J INCL PHENOM MACRO 2019. [DOI: 10.1007/s10847-019-00954-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Singh V, Patel KA, Sharma RK, Patil PR, Joshi AS, Parihar R, Athilingam T, Sinha N, Ganesh S, Sinha P, Roy I, Thakur AK. Discovery of Arginine Ethyl Ester as Polyglutamine Aggregation Inhibitor: Conformational Transitioning of Huntingtin N-Terminus Augments Aggregation Suppression. ACS Chem Neurosci 2019; 10:3969-3985. [PMID: 31460743 DOI: 10.1021/acschemneuro.9b00167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Huntington's disease (HD) is a genetic disorder caused by a CAG expansion mutation in the huntingtin gene leading to polyglutamine (polyQ) expansion in the N-terminal part of huntingtin (Httex1). Expanded polyQ, through a complex aggregation pathway, forms aggregates in neurons and presents a potential therapeutic target. Here we show Httex1 aggregation suppression by arginine and arginine ethyl ester (AEE) in vitro, as well as in yeast and mammalian cell models of HD, bearing expanded polyQ. These molecules also rescue locomotion dysfunction in HD Drosophila model. Both molecules alter the hydrogen bonding network of polyQ to enhance its aqueous solubility and delay aggregation. AEE shows direct binding with the NT17 part of Httex1 to induce structural changes to impart an enhanced inhibitory effect. This study provides a platform for the development of better arginine based therapeutic molecules against polyQ-rich Httex1 aggregation.
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Affiliation(s)
- Virender Singh
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Kinjal A. Patel
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab 160062, India
| | - Raj Kumar Sharma
- Centre of Biomedical Research, SGPGIMS Campus, Raibarelly Road, Lucknow, Uttar Pradesh 226014, India
| | - Pratik R. Patil
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Abhayraj S. Joshi
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Rashmi Parihar
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Thamarailingam Athilingam
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raibarelly Road, Lucknow, Uttar Pradesh 226014, India
| | - Subramaniam Ganesh
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Pradip Sinha
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab 160062, India
| | - Ashwani Kumar Thakur
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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27
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Mitra G. Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140260. [PMID: 31382021 DOI: 10.1016/j.bbapap.2019.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore 560034, Karnataka, India.
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28
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Owen MC, Gnutt D, Gao M, Wärmländer SKTS, Jarvet J, Gräslund A, Winter R, Ebbinghaus S, Strodel B. Effects of in vivo conditions on amyloid aggregation. Chem Soc Rev 2019; 48:3946-3996. [PMID: 31192324 DOI: 10.1039/c8cs00034d] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.
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Affiliation(s)
- Michael C Owen
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany and Lead Discovery Wuppertal, Bayer AG, 42096 Wuppertal, Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany and Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 42525 Jülich, Germany. and Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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29
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Li L, Erwin N, Möbitz S, Niemeyer F, Schrader T, Winter RHA. Dissociation of the Signaling Protein K‐Ras4B from Lipid Membranes Induced by a Molecular Tweezer. Chemistry 2019; 25:9827-9833. [DOI: 10.1002/chem.201901861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/29/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Lei Li
- Faculty of Chemistry and Chemical Biology, Physical Chemistry ITechnical University of Dortmund Otto-Hahn-Str. 4a 44227 Dortmund Germany
- International Max Planck Research School (IMPRS) in Chemical, and Molecular Biology. Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Physical Chemistry ITechnical University of Dortmund Otto-Hahn-Str. 4a 44227 Dortmund Germany
- International Max Planck Research School (IMPRS) in Chemical, and Molecular Biology. Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Simone Möbitz
- Faculty of Chemistry and Chemical Biology, Physical Chemistry ITechnical University of Dortmund Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Felix Niemeyer
- Faculty of Chemistry, Organic ChemistryUniversity of Duisburg-Essen Universitätsstrasse 2-5 45144 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry, Organic ChemistryUniversity of Duisburg-Essen Universitätsstrasse 2-5 45144 Essen Germany
| | - Roland Hermann Alfons Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry ITechnical University of Dortmund Otto-Hahn-Str. 4a 44227 Dortmund Germany
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30
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Gnutt D, Sistemich L, Ebbinghaus S. Protein Folding Modulation in Cells Subject to Differentiation and Stress. Front Mol Biosci 2019; 6:38. [PMID: 31179287 PMCID: PMC6544126 DOI: 10.3389/fmolb.2019.00038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/07/2019] [Indexed: 11/25/2022] Open
Abstract
Cytomimetic media are used to mimic the physicochemical properties of the cellular milieu in an in vitro experiment. The motivation is that compared to entire cells, they can be used efficiently in combination with a broad range of experimental techniques. However, the development and use of cytomimetic media is hampered by the lack of in-cell data that could be used as a hallmark to directly evaluate and improve the performance of cytomimetic media in different applications. Such data must include the study of specific biomolecular reactions in different cell types, different compartments of a single cells and different cellular conditions. In previous studies, model systems such as cancer cell lines, bacteria or oocytes were used. Here we studied how the environment of cells that undergo neuronal differentiation or proteostasis stress modulates the protein folding equilibrium. We found that NGF induced differentiation leads to a decrease of the melting temperature and a change of the folding mechanism. Proteomic changes that occur upon differentiation could explain this effect, however, we found that the crowding effect remained unchanged. Using MG132, a common proteasome inhibitor and inducer of the unfolded protein response, we show that changes to the quality control machinery modulate the folding equilibrium, leading to protein destabilization at prolonged stress exposure. Our study explores the range of protein folding modulation within cells subject to differentiation or stress that must be encountered in the development of cytomimetic media.
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Affiliation(s)
- David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany.,Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Linda Sistemich
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany.,Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
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31
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Mbarek A, Moussa G, Chain JL. Pharmaceutical Applications of Molecular Tweezers, Clefts and Clips. Molecules 2019; 24:molecules24091803. [PMID: 31075983 PMCID: PMC6539068 DOI: 10.3390/molecules24091803] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/25/2022] Open
Abstract
Synthetic acyclic receptors, composed of two arms connected with a spacer enabling molecular recognition, have been intensively explored in host-guest chemistry in the past decades. They fall into the categories of molecular tweezers, clefts and clips, depending on the geometry allowing the recognition of various guests. The advances in synthesis and mechanistic studies have pushed them forward to pharmaceutical applications, such as neurodegenerative disorders, infectious diseases, cancer, cardiovascular disease, diabetes, etc. In this review, we provide a summary of the synthetic molecular tweezers, clefts and clips that have been reported for pharmaceutical applications. Their structures, mechanism of action as well as in vitro and in vivo results are described. Such receptors were found to selectively bind biological guests, namely, nucleic acids, sugars, amino acids and proteins enabling their use as biosensors or therapeutics. Particularly interesting are dynamic molecular tweezers which are capable of controlled motion in response to an external stimulus. They proved their utility as imaging agents or in the design of controlled release systems. Despite some issues, such as stability, cytotoxicity or biocompatibility that still need to be addressed, it is obvious that molecular tweezers, clefts and clips are promising candidates for several incurable diseases as therapeutic agents, diagnostic or delivery tools.
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Affiliation(s)
- Amira Mbarek
- Gene Delivery Laboratory, Faculty of pharmacy, Université de Montréal, H3C 3J7, Montréal, Québec, Canada.
| | - Ghina Moussa
- Gene Delivery Laboratory, Faculty of pharmacy, Université de Montréal, H3C 3J7, Montréal, Québec, Canada.
| | - Jeanne Leblond Chain
- Gene Delivery Laboratory, Faculty of pharmacy, Université de Montréal, H3C 3J7, Montréal, Québec, Canada.
- Univ. Bordeaux, ARNA Laboratory, F-33016 Bordeaux, France.
- INSERM U1212, CNRS UMR 5320, ARNA Laboratory, F-33016 Bordeaux, France.
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Brylski O, Ebbinghaus S, Mueller JW. Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment. Front Mol Biosci 2019; 6:31. [PMID: 31131283 PMCID: PMC6509946 DOI: 10.3389/fmolb.2019.00031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application.
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Affiliation(s)
- Oliver Brylski
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jonathan W Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom
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33
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Shi M, Xu D. Molecular Dynamics Investigations Suggest a Non-specific Recognition Strategy of 14-3-3σ Protein by Tweezer: Implication for the Inhibition Mechanism. Front Chem 2019; 7:237. [PMID: 31058132 PMCID: PMC6478809 DOI: 10.3389/fchem.2019.00237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 03/26/2019] [Indexed: 02/04/2023] Open
Abstract
The supramolecular complex formed between protein and designed molecule has become one of the most efficient ways to modify protein functions. As one of the more well-studied model systems, 14-3-3 family proteins play an important role in regulating intracellular signaling pathways via protein-protein interactions. In this work, we selected 14-3-3σ as the target protein. Molecular dynamics simulations and binding free energy calculations were applied to identify the possible binding sites and understand its recognition ability of the supramolecular inhibitor, the tweezer molecule (CLR01). On the basis of our simulation, major interactions between lysine residues and CLR01 come from the van der Waals interactions between the long alkyl chain of lysine and the cavity formed by the norbornadiene and benzene rings of the inhibitor. Apart from K214, which was found to be crystallized with this inhibitor, other lysine sites have also shown their abilities to form inclusion complexes with the inhibitor. Such non-specific recognition features of CLR01 against 14-3-3σ can be used in the modification of protein functions via supramolecular chemistry.
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Affiliation(s)
- Mingsong Shi
- College of Chemistry, Sichuan University, Chengdu, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu, China
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34
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Malik R, Meng H, Wongkongkathep P, Corrales CI, Sepanj N, Atlasi RS, Klärner FG, Schrader T, Spencer MJ, Loo JA, Wiedau M, Bitan G. The molecular tweezer CLR01 inhibits aberrant superoxide dismutase 1 (SOD1) self-assembly in vitro and in the G93A-SOD1 mouse model of ALS. J Biol Chem 2019; 294:3501-3513. [PMID: 30602569 DOI: 10.1074/jbc.ra118.005940] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/01/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in superoxide dismutase 1 (SOD1) cause 15-20% of familial amyotrophic lateral sclerosis (fALS) cases. The resulting amino acid substitutions destabilize SOD1's protein structure, leading to its self-assembly into neurotoxic oligomers and aggregates, a process hypothesized to cause the characteristic motor-neuron degeneration in affected individuals. Currently, effective disease-modifying therapy is not available for ALS. Molecular tweezers prevent formation of toxic protein assemblies, yet their protective action has not been tested previously on SOD1 or in the context of ALS. Here, we tested the molecular tweezer CLR01-a broad-spectrum inhibitor of the self-assembly and toxicity of amyloid proteins-as a potential therapeutic agent for ALS. Using recombinant WT and mutant SOD1, we found that CLR01 inhibited the aggregation of all tested SOD1 forms in vitro Next, we examined whether CLR01 could prevent the formation of misfolded SOD1 in the G93A-SOD1 mouse model of ALS and whether such inhibition would have a beneficial therapeutic effect. CLR01 treatment decreased misfolded SOD1 in the spinal cord significantly. However, these histological findings did not correlate with improvement of the disease phenotype. A small, dose-dependent decrease in disease duration was found in CLR01-treated mice, relative to vehicle-treated animals, yet motor function did not improve in any of the treatment groups. These results demonstrate that CLR01 can inhibit SOD1 misfolding and aggregation both in vitro and in vivo, but raise the question whether such inhibition is sufficient for achieving a therapeutic effect. Additional studies in other less aggressive ALS models may be needed to determine the therapeutic potential of this approach.
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Affiliation(s)
- Ravinder Malik
- From the Department of Neurology, David Geffen School of Medicine, and
| | - Helen Meng
- From the Department of Neurology, David Geffen School of Medicine, and
| | | | | | - Niki Sepanj
- From the Department of Neurology, David Geffen School of Medicine, and
| | - Ryan S Atlasi
- From the Department of Neurology, David Geffen School of Medicine, and
| | | | - Thomas Schrader
- the Faculty of Chemistry, University of Duisburg-Essen, 47057 Essen, Germany
| | - Melissa J Spencer
- From the Department of Neurology, David Geffen School of Medicine, and.,Brain Research Institute, and
| | - Joseph A Loo
- Departments of Chemistry and Biochemistry and.,Biological Chemistry.,Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | - Martina Wiedau
- From the Department of Neurology, David Geffen School of Medicine, and .,Brain Research Institute, and
| | - Gal Bitan
- From the Department of Neurology, David Geffen School of Medicine, and .,Brain Research Institute, and.,Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
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Nshanian M, Lantz C, Wongkongkathep P, Schrader T, Klärner FG, Blümke A, Despres C, Ehrmann M, Smet-Nocca C, Bitan G, Loo JA. Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:16-23. [PMID: 30062477 PMCID: PMC6320309 DOI: 10.1007/s13361-018-2027-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 05/19/2023]
Abstract
Native top-down mass spectrometry (MS) and ion mobility spectrometry (IMS) were applied to characterize the interaction of a molecular tweezer assembly modulator, CLR01, with tau, a protein believed to be involved in a number of neurodegenerative disorders, including Alzheimer's disease. The tweezer CLR01 has been shown to inhibit aggregation of amyloidogenic polypeptides without toxic side effects. ESI-MS spectra for different forms of tau protein (full-length, fragments, phosphorylated, etc.) in the presence of CLR01 indicate a primary binding stoichiometry of 1:1. The relatively high charging of the protein measured from non-denaturing solutions is typical of intrinsically disordered proteins, such as tau. Top-down mass spectrometry using electron capture dissociation (ECD) is a tool used to determine not only the sites of post-translational modifications but also the binding site(s) of non-covalent interacting ligands to biomolecules. The intact protein and the protein-modulator complex were subjected to ECD-MS to obtain sequence information, map phosphorylation sites, and pinpoint the sites of inhibitor binding. The ESI-MS study of intact tau proteins indicates that top-down MS is amenable to the study of various tau isoforms and their post-translational modifications (PTMs). The ECD-MS data point to a CLR01 binding site in the microtubule-binding region of tau, spanning residues K294-K331, which includes a six-residue nucleating segment PHF6 (VQIVYK) implicated in aggregation. Furthermore, ion mobility experiments on the tau fragment in the presence of CLR01 and phosphorylated tau reveal a shift towards a more compact structure. The mass spectrometry study suggests a picture for the molecular mechanism of the modulation of protein-protein interactions in tau by CLR01. Graphical Abstract ᅟ.
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Affiliation(s)
- Michael Nshanian
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Anika Blümke
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitaetsstrasse, Essen, Germany
| | - Clément Despres
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université Lille, CNRS, 59000, Lille, France
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitaetsstrasse, Essen, Germany
| | - Caroline Smet-Nocca
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université Lille, CNRS, 59000, Lille, France
| | - Gal Bitan
- Department of Neurology and Brain Research Institute, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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Zhao L, Xin Y, Li Y, Yang X, Luo L, Meng F. Ultraeffective Inhibition of Amyloid Fibril Assembly by Nanobody–Gold Nanoparticle Conjugates. Bioconjug Chem 2018; 30:29-33. [DOI: 10.1021/acs.bioconjchem.8b00797] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Liyuan Zhao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yanru Xin
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yanan Li
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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38
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Singh V, Deepak RNVK, Sengupta B, Joshi AS, Fan H, Sen P, Thakur AK. Calmidazolium Chloride and Its Complex with Serum Albumin Prevent Huntingtin Exon1 Aggregation. Mol Pharm 2018; 15:3356-3368. [PMID: 29979597 DOI: 10.1021/acs.molpharmaceut.8b00380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Huntington's disease (HD) is a genetic disorder caused by a CAG expansion mutation in Huntingtin gene leading to polyglutamine (polyQ) expansion in the N-terminus side of Huntingtin (Httex1) protein. Neurodegeneration in HD is linked to aggregates formed by Httex1 bearing an expanded polyQ. Initiation and elongation steps of Httex1 aggregation are potential target steps for the discovery of therapeutic molecules for HD, which is currently untreatable. Here we report Httex1 aggregation inhibition by calmidazolium chloride (CLC) by acting on the initial aggregation event. Because it is hydrophobic, CLC was adsorbed to the vial surface and could not sustain an inhibition effect for a longer duration. The use of bovine serum albumin (BSA) prevented CLC adsorption by forming a BSA-CLC complex. This complex showed improved Httex1 aggregation inhibition by interacting with the aggregation initiator, the NT17 part of Httex1. Furthermore, biocompatible CLC-loaded BSA nanoparticles were made which reduced the polyQ aggregates in HD-150Q cells.
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Affiliation(s)
- Virender Singh
- Biological Sciences and Bioengineering , Indian Institute of Technology Kanpur , Kanpur 208016 , India
| | | | - Bhaswati Sengupta
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur 208016 , India
| | - Abhayraj S Joshi
- Biological Sciences and Bioengineering , Indian Institute of Technology Kanpur , Kanpur 208016 , India
| | - Hao Fan
- Bioinformatics Institute , 30 Biopolis Street, Matrix #07-01 , Singapore 138671.,Department of Biological Sciences , National University of Singapore , Singapore 117545
| | - Pratik Sen
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur 208016 , India
| | - Ashwani Kumar Thakur
- Biological Sciences and Bioengineering , Indian Institute of Technology Kanpur , Kanpur 208016 , India
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39
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Mittal S, Bravo-Rodriguez K, Sanchez-Garcia E. Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers. J Phys Chem B 2018; 122:4196-4205. [DOI: 10.1021/acs.jpcb.7b10530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sumit Mittal
- University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
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40
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Wagner AS, Politi AZ, Ast A, Bravo-Rodriguez K, Baum K, Buntru A, Strempel NU, Brusendorf L, Hänig C, Boeddrich A, Plassmann S, Klockmeier K, Ramirez-Anguita JM, Sanchez-Garcia E, Wolf J, Wanker EE. Self-assembly of Mutant Huntingtin Exon-1 Fragments into Large Complex Fibrillar Structures Involves Nucleated Branching. J Mol Biol 2018; 430:1725-1744. [PMID: 29601786 DOI: 10.1016/j.jmb.2018.03.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
Huntingtin (HTT) fragments with extended polyglutamine tracts self-assemble into amyloid-like fibrillar aggregates. Elucidating the fibril formation mechanism is critical for understanding Huntington's disease pathology and for developing novel therapeutic strategies. Here, we performed systematic experimental and theoretical studies to examine the self-assembly of an aggregation-prone N-terminal HTT exon-1 fragment with 49 glutamines (Ex1Q49). Using high-resolution imaging techniques such as electron microscopy and atomic force microscopy, we show that Ex1Q49 fragments in cell-free assays spontaneously convert into large, highly complex bundles of amyloid fibrils with multiple ends and fibril branching points. Furthermore, we present experimental evidence that two nucleation mechanisms control spontaneous Ex1Q49 fibrillogenesis: (1) a relatively slow primary fibril-independent nucleation process, which involves the spontaneous formation of aggregation-competent fibrillary structures, and (2) a fast secondary fibril-dependent nucleation process, which involves nucleated branching and promotes the rapid assembly of highly complex fibril bundles with multiple ends. The proposed aggregation mechanism is supported by studies with the small molecule O4, which perturbs early events in the aggregation cascade and delays Ex1Q49 fibril assembly, comprehensive mathematical and computational modeling studies, and seeding experiments with small, preformed fibrillar Ex1Q49 aggregates that promote the assembly of amyloid fibrils. Together, our results suggest that nucleated branching in vitro plays a critical role in the formation of complex fibrillar HTT exon-1 aggregates with multiple ends.
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Affiliation(s)
- Anne S Wagner
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Antonio Z Politi
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Anne Ast
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kenny Bravo-Rodriguez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 2, 45470 Mülheim an der Ruhr, Germany; Computational Biochemistry, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Katharina Baum
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Nadine U Strempel
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Lydia Brusendorf
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Christian Hänig
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Annett Boeddrich
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Stephanie Plassmann
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Juan M Ramirez-Anguita
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 2, 45470 Mülheim an der Ruhr, Germany
| | - Elsa Sanchez-Garcia
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 2, 45470 Mülheim an der Ruhr, Germany; Computational Biochemistry, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
| | - Erich E Wanker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
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41
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van Dun S, Ottmann C, Milroy LG, Brunsveld L. Supramolecular Chemistry Targeting Proteins. J Am Chem Soc 2017; 139:13960-13968. [PMID: 28926241 PMCID: PMC5639466 DOI: 10.1021/jacs.7b01979] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.
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Affiliation(s)
- Sam van Dun
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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