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Alfonso I. Supramolecular chemical biology: designed receptors and dynamic chemical systems. Chem Commun (Camb) 2024; 60:9692-9703. [PMID: 39129537 DOI: 10.1039/d4cc03163f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Supramolecular chemistry focuses on the study of species joined by non-covalent interactions, and therefore on dynamic and relatively ill-defined structures. Despite being a well-developed field, it has to face important challenges when dealing with the selective recognition of biomolecules in highly competitive biomimetic media. However, supramolecular interactions reside at the core of chemical biology systems, since many processes in nature are governed by weak, non-covalent, strongly dynamic contacts. Therefore, there is a natural connection between these two research fields, which are not frequently related or share interests. In this feature article, I will highlight our most recent results in the molecular recognition of biologically relevant species, following different conceptual approaches from the most conventional design of elaborated receptors to the less popular dynamic combinatorial chemistry methodology. Selected illustrative examples from other groups will be also included. The discussion has been focused mainly on systems with potential biomedical applications.
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Affiliation(s)
- Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC), The Spanish National Research Council (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
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2
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Gupta MN, Uversky VN. Reexamining the diverse functions of arginine in biochemistry. Biochem Biophys Res Commun 2024; 705:149731. [PMID: 38432110 DOI: 10.1016/j.bbrc.2024.149731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya Str., 7, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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3
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Porfetye AT, Stege P, Rebollido-Rios R, Hoffmann D, Schrader T, Vetter IR. How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography. Molecules 2024; 29:1764. [PMID: 38675584 PMCID: PMC11051928 DOI: 10.3390/molecules29081764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
To understand the biological relevance and mode of action of artificial protein ligands, crystal structures with their protein targets are essential. Here, we describe and investigate all known crystal structures that contain a so-called "molecular tweezer" or one of its derivatives with an attached natural ligand on the respective target protein. The aromatic ring system of these compounds is able to include lysine and arginine side chains, supported by one or two phosphate groups that are attached to the half-moon-shaped molecule. Due to their marked preference for basic amino acids and the fully reversible binding mode, molecular tweezers are able to counteract pathologic protein aggregation and are currently being developed as disease-modifying therapies against neurodegenerative diseases such as Alzheimer's and Parkinson's disease. We analyzed the corresponding crystal structures with 14-3-3 proteins in complex with mono- and diphosphate tweezers. Furthermore, we solved crystal structures of two different tweezer variants in complex with the enzyme Δ1-Pyrroline-5-carboxyl-dehydrogenase (P5CDH) and found that the tweezers are bound to a lysine and methionine side chain, respectively. The different binding modes and their implications for affinity and specificity are discussed, as well as the general problems in crystallizing protein complexes with artificial ligands.
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Affiliation(s)
- Arthur T. Porfetye
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Patricia Stege
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Rocio Rebollido-Rios
- Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Daniel Hoffmann
- Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Ingrid R. Vetter
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
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4
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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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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Rodger AT, ALNasser M, Carter WG. Are Therapies That Target α-Synuclein Effective at Halting Parkinson's Disease Progression? A Systematic Review. Int J Mol Sci 2023; 24:11022. [PMID: 37446200 DOI: 10.3390/ijms241311022] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
There are currently no pharmacological treatments available that completely halt or reverse the progression of Parkinson's Disease (PD). Hence, there is an unmet need for neuroprotective therapies. Lewy bodies are a neuropathological hallmark of PD and contain aggregated α-synuclein (α-syn) which is thought to be neurotoxic and therefore a suitable target for therapeutic interventions. To investigate this further, a systematic review was undertaken to evaluate whether anti-α-syn therapies are effective at preventing PD progression in preclinical in vivo models of PD and via current human clinical trials. An electronic literature search was performed using MEDLINE and EMBASE (Ovid), PubMed, the Web of Science Core Collection, and Cochrane databases to collate clinical evidence that investigated the targeting of α-syn. Novel preclinical anti-α-syn therapeutics provided a significant reduction of α-syn aggregations. Biochemical and immunohistochemical analysis of rodent brain tissue demonstrated that treatments reduced α-syn-associated pathology and rescued dopaminergic neuronal loss. Some of the clinical studies did not provide endpoints since they had not yet been completed or were terminated before completion. Completed clinical trials displayed significant tolerability and efficacy at reducing α-syn in patients with PD with minimal adverse effects. Collectively, this review highlights the capacity of anti-α-syn therapies to reduce the accumulation of α-syn in both preclinical and clinical trials. Hence, there is potential and optimism to target α-syn with further clinical trials to restrict dopaminergic neuronal loss and PD progression and/or provide prophylactic protection to avoid the onset of α-syn-induced PD.
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Affiliation(s)
- Abbie T Rodger
- School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby DE22 3DT, UK
| | - Maryam ALNasser
- School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby DE22 3DT, UK
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Wayne G Carter
- School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby DE22 3DT, UK
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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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8
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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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9
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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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10
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Khan S, Hassan MI, Shahid M, Islam A. Nature's Toolbox Against Tau Aggregation: An Updated Review of Current Research. Ageing Res Rev 2023; 87:101924. [PMID: 37004844 DOI: 10.1016/j.arr.2023.101924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
Tau aggregation is a hallmark of several neurodegenerative disorders, such as Alzheimer's disease (AD), frontotemporal dementia, and progressive supranuclear palsy. Hyperphosphorylated tau is believed to contribute to the degeneration of neurons and the development of these complex diseases. Therefore, one potential treatment for these illnesses is to prevent or counteract tau aggregation. In recent years, interest has been increasing in developing nature-derived tau aggregation inhibitors as a potential treatment for neurodegenerative disorders. Researchers have become increasingly interested in natural compounds with multifunctional features, such as flavonoids, alkaloids, resveratrol, and curcumin, since these molecules can interact simultaneously with the various targets of AD. Recent studies have demonstrated that several natural compounds can inhibit tau aggregation and promote the disassembly of pre-formed tau aggregates. Nature-derived tau aggregation inhibitors hold promise as a potential treatment for neurodegenerative disorders. However, it is important to note that more research is needed to fully understand the mechanisms by which these compounds exert their effects and their safety and efficacy in preclinical and clinical studies. Nature-derived inhibitors of tau aggregation are a promising new direction in the research of neurodegenerative complexities. This review focuses on the natural products that have proven to be a rich supply for inhibitors in tau aggregation and their uses in neurodegenerative complexities, including AD.
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11
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Park S, Cho NJ. Lipid Membrane Interface Viewpoint: From Viral Entry to Antiviral and Vaccine Development. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1-11. [PMID: 36576966 DOI: 10.1021/acs.langmuir.2c02501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Membrane-enveloped viruses are responsible for most viral pandemics in history, and more effort is needed to advance broadly applicable countermeasures to mitigate the impact of future outbreaks. In this Perspective, we discuss how biosensing techniques associated with lipid model membrane platforms are contributing to improving our mechanistic knowledge of membrane fusion and destabilization that is closely linked to viral entry as well as vaccine and antiviral drug development. A key benefit of these platforms is the simplicity of interpreting the results which can be complemented by other techniques to decipher more complicated biological observations and evaluate the biophysical functionalities that can be correlated to biological activities. Then, we introduce exciting application examples of membrane-targeting antivirals that have been refined over time and will continue to improve based on biophysical insights. Two ways to abrogate the function of viral membranes are introduced here: (1) selective disruption of the viral membrane structure and (2) alteration of the membrane component. While both methods are suitable for broadly useful antivirals, the latter also has the potential to produce an inactivated vaccine. Collectively, we emphasize how biosensing tools based on membrane interfacial science can provide valuable information that could be translated into biomedicines and improve their selectivity and performance.
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Affiliation(s)
- Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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12
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Devi M, Paul S. The chaotropic effect of ions on the self-aggregating propensity of Whitlock's molecular tweezers. Phys Chem Chem Phys 2022; 24:14452-14471. [PMID: 35661176 DOI: 10.1039/d2cp00033d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular tweezers feature the first class of artificial receptors to pique the interest of researchers and emerge as an effective therapeutic candidate. The exceptional structure and exquisite binding specificity of tweezers establish this overall class of receptors as a promising tool, with abundant applications. However, their inclination to self-aggregate by mutual π-π stacking interactions of their aromatic arms diminishes their efficacy as a therapeutic candidate. Therefore, following up on sporadic studies, since the discovery of the Hofmeister series, on the ability of ions to either solvate (salting-in) or induce aggregation (salting-out) of hydrophobic solutes, the notions of ion-specificity effects are utilized on tweezer moieties. The impacts of three different aluminum salts bearing anions Cl-, ClO4- and SCN- on the self-association propensity of Whitlock's caffeine-pincered molecular tweezers are investigated, with a specific emphasis placed on elucidating the varied behavior of the ions on the hydration ability of tweezers. The comparative investigation is conducted employing a series of all-atom molecular dynamics simulations of five tweezer molecules in pure water and three salt solutions, at two different concentrations each, maintaining a temperature of 300 K and a pressure of 1 atm, respectively. Radial distribution functions, coordination numbers, and SASA calculations display a steady reduction in the aggregation proclivity of the receptor molecules with an increase in salt concentration, as progressed along the Hofmeister series. Orientational preferences between the tweezer arms reveal a disruptive effect in the regular π-π stacking interactions, in the presence of high concentrations of ClO4- and SCN- ions, while preferential interactions and tetrahedral order parameters unveil the underlying mechanism, by which the anions alter the solubility of the hydrophobic molecules. Overall, it is observed that SCN- exhibits the highest salting-in effect, followed by ClO4-, with both anions inhibiting tweezer aggregation through different mechanisms. ClO4- ions impart an effect by moderately interacting with the solute molecules as well as modifying the water structure of the bulk solution promoting solvation, whereas, SCN- ions engage entirely in interaction with specific tweezer sites. Cl- being the most charge-dense of the three anionic species experiences stronger hydration and therefore, imparts a very negligible salting-in effect.
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Affiliation(s)
- Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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13
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Yao L, Zhou Z, Wang S, Zou Q, Wang HX, Ma LX, Wang S, Zhang X. Phosphorylation of covalent organic framework nanospheres for inhibition of amyloid-β peptide fibrillation. Chem Sci 2022; 13:5902-5912. [PMID: 35685783 PMCID: PMC9132083 DOI: 10.1039/d2sc00253a] [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: 01/14/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022] Open
Abstract
The development and exploration of new nanostructural inhibitors against Alzheimer's disease (AD)-associated amyloid-β (Aβ) fibrillation have attracted extensive attention and become a new frontier in nanomedicine. However, focusing on finding an effective nanostructure is one of the most challenging parts of the therapeutics task. Herein, nanoscale spherical covalent organic frameworks (COFs) via post-synthetic functionalization with sodium phosphate (SP) groups on the channel networks were found to efficiently inhibit Aβ fibrillation. The as-prepared uniform SP-COF nanospheres with high surface area, good crystallinity, and chemical stability were characterized by multifarious microscopic and spectroscopic techniques. Moreover, molecular dynamics simulation together with fibrillation kinetics and cytotoxicity assay experiments shows that there were restricted-access adsorption channels in the SP-COFs which were formed by the cavities with size and functional groups accommodated to the Aβ peptide sequence and significantly affected the fibrillation and cytotoxicity of Aβ. Transmission electron microscopy (TEM), dynamic light scattering (DLS) monitoring, isothermal titration calorimetry (ITC), Fourier transform infrared (FT-IR) and circular dichroism (CD) spectra measurements, and confocal imaging observation were performed to understand the inhibition mechanism and influencing factors of the SP-COFs. To our knowledge, our strategy is the first exploration of COF-based anti-amyloidogenic nanomaterials with high affinity and specific targeting, which are crucial for the inhibition of Aβ fibrillation for AD prevention and treatment. Nanoscale spherical COFs via phosphorylation functionalization were found to efficiently inhibit fibrillation of the Alzheimer's disease-associated Aβ peptide.![]()
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Affiliation(s)
- Linli Yao
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
| | - Zhe Zhou
- Department of Neurology, The First Hospital of Lanzhou University Lanzhou 730000 China
| | - Suxiao Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
| | - Qichao Zou
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
| | - Hang-Xing Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
| | - Li-Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University Wuhan 430062 China
| | - Shengfu Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
| | - Xiuhua Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University Wuhan 430062 China
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14
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Vidović M, Rikalovic MG. Alpha-Synuclein Aggregation Pathway in Parkinson's Disease: Current Status and Novel Therapeutic Approaches. Cells 2022; 11:cells11111732. [PMID: 35681426 PMCID: PMC9179656 DOI: 10.3390/cells11111732] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Following Alzheimer’s, Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, sharing an unclear pathophysiology, a multifactorial profile, and massive social costs worldwide. Despite this, no disease-modifying therapy is available. PD is tightly associated with α-synuclein (α-Syn) deposits, which become organised into insoluble, amyloid fibrils. As a typical intrinsically disordered protein, α-Syn adopts a monomeric, random coil conformation in an aqueous solution, while its interaction with lipid membranes drives the transition of the molecule part into an α-helical structure. The central unstructured region of α-Syn is involved in fibril formation by converting to well-defined, β-sheet rich secondary structures. Presently, most therapeutic strategies against PD are focused on designing small molecules, peptides, and peptidomimetics that can directly target α-Syn and its aggregation pathway. Other approaches include gene silencing, cell transplantation, stimulation of intracellular clearance with autophagy promoters, and degradation pathways based on immunotherapy of amyloid fibrils. In the present review, we sum marise the current advances related to α-Syn aggregation/neurotoxicity. These findings present a valuable arsenal for the further development of efficient, nontoxic, and non-invasive therapeutic protocols for disease-modifying therapy that tackles disease onset and progression in the future.
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Affiliation(s)
- Marija Vidović
- Laboratory for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
- Correspondence: ; Tel.: +38-16-4276-3221
| | - Milena G. Rikalovic
- Environment and Sustainable Development, Singidunum Univeristy, Danijelova 32, 11010 Belgrade, Serbia;
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15
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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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16
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. ChemistryOpen 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität KaiserslauternFachbereich Chemie – Organische ChemieErwin-Schrödinger-Straße 5467663KaiserslauternGermany
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17
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Shahpasand‐Kroner H, Portillo J, Lantz C, Seidler PM, Sarafian N, Loo JA, Bitan G. Three-repeat and four-repeat tau isoforms form different oligomers. Protein Sci 2022; 31:613-627. [PMID: 34902187 PMCID: PMC8862439 DOI: 10.1002/pro.4257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/11/2022]
Abstract
Different tauopathies are characterized by the isoform-specific composition of the aggregates found in the brain and by structurally distinct tau strains. Although tau oligomers have been implicated as important neurotoxic species, little is known about how the primary structures of the six human tau isoforms affect tau oligomerization because the oligomers are metastable and difficult to analyze. To address this knowledge gap, here, we analyzed the initial oligomers formed by the six tau isoforms in the absence of posttranslational modifications or other manipulations using dot blots probed by an oligomer-specific antibody, native-PAGE/western blots, photo-induced cross-linking of unmodified proteins, mass-spectrometry, and ion-mobility spectroscopy. We found that under these conditions, three-repeat (3R) isoforms are more prone than four-repeat (4R) isoforms to form oligomers. We also tested whether known inhibitors of tau aggregation affect its oligomerization using three small molecules representing different classes of tau aggregation inhibitors, Methylene Blue (MB), the molecular tweezer CLR01, and the all-D peptide TLKIVW, for their ability to inhibit or modulate the oligomerization of the six tau isoforms. Unlike their reported inhibitory effect on tau fibrillation, the inhibitors had little or no effect on the initial oligomerization. Our study provides novel insight into the primary-quaternary structure relationship of human tau and suggests that 3R-tau oligomers may be an important target for future development of compounds targeting pathological tau assemblies.
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Affiliation(s)
- Hedieh Shahpasand‐Kroner
- Department of NeurologyDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA
| | - Jennifer Portillo
- Department of NeurologyDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA
| | - Carter Lantz
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Paul M. Seidler
- Department of Pharmacology and Pharmaceutical SciencesUniversity of Southern California School of PharmacyLos AngelesCaliforniaUSA
| | - Natalie Sarafian
- Department of NeurologyDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA
| | - Joseph A. Loo
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Gal Bitan
- Department of NeurologyDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Brain Research InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
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18
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Krämer J, Kang R, Grimm LM, De Cola L, Picchetti P, Biedermann F. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem Rev 2022; 122:3459-3636. [PMID: 34995461 PMCID: PMC8832467 DOI: 10.1021/acs.chemrev.1c00746] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 02/08/2023]
Abstract
Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.
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Affiliation(s)
- Joana Krämer
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rui Kang
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Laura M. Grimm
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Luisa De Cola
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Dipartimento
DISFARM, University of Milano, via Camillo Golgi 19, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
| | - Pierre Picchetti
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Frank Biedermann
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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19
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Prabodh A, Sinn S, Biedermann F. Analyte sensing with unselectively binding synthetic receptors: virtues of time-resolved supramolecular assays. Chem Commun (Camb) 2022; 58:13947-13950. [DOI: 10.1039/d2cc04831k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Time-resolved supramolecular assays probe analyte-characteristic complexation and decomplexation rates. Consequently, even unselectively binding synthetic receptors can be used for analyte identification and quantification.
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Affiliation(s)
- Amrutha Prabodh
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Stephan Sinn
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Frank Biedermann
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
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20
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Le MH, Taghuo-Kaptouom E, Schrader T. Molecular Tweezers – a new class of potent broad-spectrum antivirals against enveloped viruses. Chem Commun (Camb) 2022; 58:2954-2966. [DOI: 10.1039/d1cc06737k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new supramolecular approach to broad spectrum antivirals utilizes host guest chemistry between molecular tweezers and lysine/arginine as well as choline. Basic amino acids in amyloid-forming SEVI peptides (semen-derived enhancers...
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21
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Saliba D, Trinh T, Lachance-Brais C, Prinzen AL, Rizzuto FJ, de Rochambeau D, Sleiman HF. Asymmetric patterning drives the folding of a tripodal DNA nanotweezer. Chem Sci 2021; 13:74-80. [PMID: 35059153 PMCID: PMC8694393 DOI: 10.1039/d1sc04793k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | | | - Alexander L Prinzen
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Felix J Rizzuto
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Donatien de Rochambeau
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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22
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Twum K, Bhattacharjee A, Laryea ET, Esposto J, Omolloh G, Mortensen S, Jaradi M, Stock NL, Schileru N, Elias B, Pszenica E, McCormick TM, Martic S, Beyeh NK. Functionalized resorcinarenes effectively disrupt the aggregation of αA66-80 crystallin peptide related to cataracts. RSC Med Chem 2021; 12:2022-2030. [PMID: 35028562 PMCID: PMC8672818 DOI: 10.1039/d1md00294e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 11/21/2022] Open
Abstract
Cataracts, an eye lens clouding disease, are debilitating and while operable, remain without a cure. αA66-80 crystallin peptide abundant in cataracted eye lenses contributes to aggregation of αA-crystallin protein leading to cataracts. Inspired by the versatility of macrocycles and programmable guest selectivity through discrete functionalizations, we report on three water-soluble ionic resorcinarene receptors (A, B, and C) that disrupt the aggregation of αA66-80 crystallin peptide. A and B each possess four anionic sulfonate groups, while C includes four cationic ammonium groups with four flexible extended benzyl groups. Through multiple non-covalent attractions, these receptors successfully disrupt and reverse the aggregation of αA66-80 crystallin peptide, which was studied through spectroscopic, spectrometric, calorimetric, and imaging techniques. The αA66-80·receptor complexes were also explored using molecular dynamics simulation, and binding energies were calculated. Even though each of the three receptors can bind with the peptide, receptor C was characterized by the highest binding energy and affinity for three different domains of the peptide. In effect, the most efficient inhibitor was a cationic receptor C via extended aromatic interactions. These results highlight the potential of versatile and tunable functionalized resorcinarenes as potential therapeutics to reverse the aggregation of α-crystallin dominant in eye cataracts.
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Affiliation(s)
- Kwaku Twum
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
| | - Avik Bhattacharjee
- Department of Chemistry, Portland State University 1710 SW 10th Ave Portland OR 97201 USA
| | - Erving T Laryea
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
| | - Josephine Esposto
- Department of Forensic Science and Environmental and Life Sciences Program, Trent University ON K9 L0G2 Canada
| | - George Omolloh
- Department of Chemistry, Portland State University 1710 SW 10th Ave Portland OR 97201 USA
| | - Shaelyn Mortensen
- Department of Forensic Science and Environmental and Life Sciences Program, Trent University ON K9 L0G2 Canada
| | - Maya Jaradi
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
| | - Naomi L Stock
- Water Quality Centre, Trent University ON K9L 0G2 Canada
| | - Nicholas Schileru
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
- Department of Osteopathic Medicine, Midwestern University 555 31st St. Downers Grove IL 60515 USA
| | - Bianca Elias
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
| | - Elan Pszenica
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
| | - Theresa M McCormick
- Department of Chemistry, Portland State University 1710 SW 10th Ave Portland OR 97201 USA
| | - Sanela Martic
- Department of Forensic Science and Environmental and Life Sciences Program, Trent University ON K9 L0G2 Canada
- Water Quality Centre, Trent University ON K9L 0G2 Canada
| | - Ngong Kodiah Beyeh
- Department of Chemistry, Oakland University 146 Library Drive Rochester MI 48309-4479 USA
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23
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A novel multi-target strategy to attenuate the progression of Parkinson's disease by diamine hybrid AGE/ALE inhibitor. Future Med Chem 2021; 13:2185-2200. [PMID: 34634921 DOI: 10.4155/fmc-2021-0217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Instead of a conventional 'one-drug-one-target approach', this article presents a novel multi-target approach with a concept of trapping simultaneously as many detrimental factors as possible involved in the progression of Parkinson's disease. These factors include reactive carbonyl species, reactive oxygen species, Fe3+/Cu2+ and ortho-quinones (o-quinone), in particular. Different from the known multi-target strategies for Parkinson's disease, it is a sort of 'vacuum cleaning' strategy. The new agent consists of reactive carbonyl species scavenging moiety and reactive oxygen species scavenging and metal chelating moiety linked by a spacer. Provided that the capacity of scavenging o-quinones is demonstrated, this type of agent can further broaden its potential therapeutic profile. In order to support this new hypothetical approach, a number of simple in vitro experiments are proposed.
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24
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Thiele M, Octa-Smolin F, Thölke S, Wölper C, Linders J, Mayer C, Haberhauer G, Niemeyer J. A supramolecular double-helix based on complementary phosphate-guanidinium pairing. Chem Commun (Camb) 2021; 57:9842-9845. [PMID: 34487128 DOI: 10.1039/d1cc04644f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A double-helical supramolecular structure was formed by self-assembly of 1,1'-binaphthyl-based bisguanidines and bisphosphoric acids. Interestingly the homochiral (S,S) + (S,S)-pair forms a left-handed double-helix, while the heterochiral (S,S) + (R,R)-pair forms a non-helical dimer.
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Affiliation(s)
- Maike Thiele
- Faculty of Chemistry, Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
| | - Frescilia Octa-Smolin
- Faculty of Chemistry, Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
| | - Simon Thölke
- Faculty of Chemistry, Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
| | - Christoph Wölper
- Faculty of Chemistry, Inorganic Chemistry, University of Duisburg-Essen, Germany
| | - Jürgen Linders
- Faculty of Chemistry, Physical Chemistry, University of Duisburg-Essen, Germany
| | - Christian Mayer
- Faculty of Chemistry, Physical Chemistry, University of Duisburg-Essen, Germany
| | - Gebhard Haberhauer
- Faculty of Chemistry, Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
| | - Jochen Niemeyer
- Faculty of Chemistry, Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
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25
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Li Z, Siddique I, Hadrović I, Kirupakaran A, Li J, Zhang Y, Klärner FG, Schrader T, Bitan G. Lysine-selective molecular tweezers are cell penetrant and concentrate in lysosomes. Commun Biol 2021; 4:1076. [PMID: 34521989 PMCID: PMC8440717 DOI: 10.1038/s42003-021-02603-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/24/2021] [Indexed: 11/09/2022] Open
Abstract
Lysine-selective molecular tweezers are promising drug candidates against proteinopathies, viral infection, and bacterial biofilm. Despite demonstration of their efficacy in multiple cellular and animal models, important questions regarding their mechanism of action, including cell penetrance and intracellular distribution, have not been answered to date. The main impediment to answering these questions has been the low intrinsic fluorescence of the main compound tested to date, called CLR01. Here, we address these questions using new fluorescently labeled molecular tweezers derivatives. We show that these compounds are internalized in neurons and astrocytes, at least partially through dynamin-dependent endocytosis. In addition, we demonstrate that the molecular tweezers concentrate rapidly in acidic compartments, primarily lysosomes. Accumulation of molecular tweezers in lysosomes may occur both through the endosomal-lysosomal pathway and via the autophagy-lysosome pathway. Moreover, by visualizing colocalization of molecular tweezers, lysosomes, and tau aggregates we show that lysosomes likely are the main site for the intracellular anti-amyloid activity of molecular tweezers. These findings have important implications for the mechanism of action of molecular tweezers in vivo, explaining how administration of low doses of the compounds achieves high effective concentrations where they are needed, and supporting the development of these compounds as drugs for currently cureless proteinopathies.
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Affiliation(s)
- Zizheng Li
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Inesa Hadrović
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Abbna Kirupakaran
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jiwen Li
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ye Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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26
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Brenner S, Braun B, Read C, Weil T, Walther P, Schrader T, Münch J, von Einem J. The Molecular Tweezer CLR01 Inhibits Antibody-Resistant Cell-to-Cell Spread of Human Cytomegalovirus. Viruses 2021; 13:v13091685. [PMID: 34578265 PMCID: PMC8472163 DOI: 10.3390/v13091685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Human cytomegalovirus (HCMV) uses two major ways for virus dissemination: infection by cell-free virus and direct cell-to-cell spread. Neutralizing antibodies can efficiently inhibit infection by cell-free virus but mostly fail to prevent cell-to-cell transmission. Here, we show that the ‘molecular tweezer’ CLR01, a broad-spectrum antiviral agent, is not only highly active against infection with cell-free virus but most remarkably inhibits antibody-resistant direct cell-to-cell spread of HCMV. The inhibition of cell-to-cell spread by CLR01 was not limited to HCMV but was also shown for the alphaherpesviruses herpes simplex viruses 1 and 2 (HSV-1, -2). CLR01 is a rapid acting small molecule that inhibits HCMV entry at the attachment and penetration steps. Electron microscopy of extracellular virus particles indicated damage of the viral envelope by CLR01, which likely impairs the infectivity of virus particles. The rapid inactivation of viral particles by CLR01, the viral envelope as the main target, and the inhibition of virus entry at different stages are presumably the key to inhibition of cell-free virus infection and cell-to-cell spread by CLR01. Importance: While cell-free spread enables the human cytomegalovirus (HCMV) and other herpesviruses to transmit between hosts, direct cell-to-cell spread is thought to be more relevant for in vivo dissemination within infected tissues. Cell-to-cell spread is resistant to neutralizing antibodies, thus contributing to the maintenance of virus infection and virus dissemination in the presence of an intact immune system. Therefore, it would be therapeutically interesting to target this mode of spread in order to treat severe HCMV infections and to prevent dissemination of virus within the infected host. The molecular tweezer CLR01 exhibits broad-spectrum antiviral activity against a number of enveloped viruses and efficiently blocks antibody-resistant cell-to-cell spread of HCMV, thus representing a novel class of small molecules with promising antiviral activity.
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Affiliation(s)
- Sina Brenner
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.B.); (B.B.); (C.R.)
| | - Berenike Braun
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.B.); (B.B.); (C.R.)
| | - Clarissa Read
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.B.); (B.B.); (C.R.)
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany;
| | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (T.W.); (J.M.)
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany;
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany;
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (T.W.); (J.M.)
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (S.B.); (B.B.); (C.R.)
- Correspondence: ; Tel.: +49-(0)731-500-65104; Fax: +49-(0)731-500-65102
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27
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Michalak M, Bisek B, Nowacki M, Górecki M. Base-Catalyzed, Solvent-Free Synthesis of Rigid V-Shaped Epoxydibenzo[ b, f][1,5]diazocines. J Org Chem 2021; 86:8955-8969. [PMID: 34161097 PMCID: PMC8279491 DOI: 10.1021/acs.joc.1c00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A novel method for
the synthesis of epoxydibenzo[b,f][1,5]diazocines exhibiting a V-shaped molecular
architecture is reported. The unique approach is based on unprecedented
base-catalyzed, solvent-free autocondensation and cross-condensation
of fluorinated o-aminophenones. The structure of
the newly synthesized diazocines was confirmed independently by X-ray
analysis and chiroptical methods. The rigidity of the diazocine scaffold
allowed for the separation of the racemate into single enantiomers
that proved to be thermally stable up to 140 °C. Furthermore,
the inertness of the diazocine scaffold was demonstrated by performing
a series of typical transformations, including transition metal-catalyzed
reactions, proceeding without affecting the bis-hemiaminal subunit.
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Affiliation(s)
- Michał Michalak
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Bartosz Bisek
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michał Nowacki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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28
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Ibáñez S, Peris E. Shape-Adaptability and Redox-Switching Properties of a Di-Gold Metallotweezer. Chemistry 2021; 27:9661-9665. [PMID: 33844341 PMCID: PMC8362111 DOI: 10.1002/chem.202100794] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/24/2022]
Abstract
The use of a carbazolyl-connected di-gold(I) metallotweezer for the encapsulation of several electron-poor organic substrates, and a planar Au(III) complex containing a CNC pincer ligand, is described. The binding affinity of the receptor depends on the electron-deficient character of the planar guest, with larger association constants found for the more electron-poor guests. The X-ray diffraction molecular structures of two host:guest adducts show that the host approaches its arms in order to facilitate the optimum interaction with the surface of the planar guests, in a clear example of an guest-induced fit conformational arrangement. The electrochemical studies of the encapsulation of N,N'-dimethyl-naphthalenetetracarboxy diimide (NTCDI) show that the redox active guest is released from the receptor upon one electron reduction, thus constituting an example of redox-switchable binding.
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Affiliation(s)
- Susana Ibáñez
- Institute of Advanced Materials (INAM), Centro de Innovación en Química Avanzada (ORFEO-CINQA).Universitat Jaume I.Av. Vicente Sos Baynat s/nCastellón1271Spain
| | - Eduardo Peris
- Institute of Advanced Materials (INAM), Centro de Innovación en Química Avanzada (ORFEO-CINQA).Universitat Jaume I.Av. Vicente Sos Baynat s/nCastellón1271Spain
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29
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Binding Properties of a Dinuclear Zinc(II) Salen-Type Molecular Tweezer with a Flexible Spacer in the Formation of Lewis Acid-Base Adducts with Diamines. INORGANICS 2021. [DOI: 10.3390/inorganics9060049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this paper we report the binding properties, by combined 1H NMR, optical absorption, and fluorescence studies, of a molecular tweezer composed of two Zn(salen)-type Schiff-base units connected by a flexible spacer, towards a series of ditopic diamines having a strong Lewis basicity, with different chain length and rigidity. Except for the 1,2-diaminoethane, in all other cases the formation of stable 1:1 Lewis acid-base adducts with large binding constants is demonstrated. For α,ω-aliphatic diamines, binding constants progressively increase with the increasing length of the alkyl chain, thanks to the flexible nature of the spacer and the parallel decreased conformational strain upon binding. Stable adducts are also found even for short diamines with rigid molecular structures. Given their preorganized structure, these latter species are not subjected to loss of degrees of freedom. The binding characteristics of the tweezer have been exploited for the colorimetric and fluorometric selective and sensitive detection of piperazine.
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30
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Kumar V, Holtum T, Voskuhl J, Giese M, Schrader T, Schlücker S. Prospects of ultraviolet resonance Raman spectroscopy in supramolecular chemistry on proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119622. [PMID: 33743304 DOI: 10.1016/j.saa.2021.119622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Ultraviolet resonance Raman scattering (UVRR) has been frequently used for studying peptide and protein structure and dynamics, while applications in supramolecular chemistry are quite rare. Since UVRR offers the additional advantages of chromophore selectivity and high sensitivity compared with conventional non-resonant Raman scattering, it is ideally suited for label-free probing of relatively small artificial/supramolecular ligands exhibiting electronic resonances in the UV. In this perspective article, we first summarize results of UVRR spectroscopy in supramolecular chemistry in the context of peptide/protein recognition. We focus on selected artificial ligands which were rationally designed as selective carboxylate binders (guanidiniocarbonyl pyrrole, GCP, and guanidiniocarbonyl indole, GCI) and selective lysine binder (molecular tweezer, CLR01), respectively, via a combination of non-covalent interactions involving electrostatics, hydrogen bonding, and hydrophobic effects/van der Waals forces. Current limitations of applying UVRR as a universally applicable method for label-free and site-specific probing of molecular recognition between supramolecular ligands and proteins are highlighted. We then propose solutions to overcome these limitations for transforming UVRR spectroscopy into a generic tool in supramolecular chemistry on proteins, with an emphasis on mono- and multivalent GCP- and GCI-based ligands. Finally, we outline specific cases of supramolecular ligands such as molecular tweezers where alternative approaches such as laser-based mid-IR spectroscopy are required since UVRR can intrinsically not provide the required molecular information.
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Affiliation(s)
- Vikas Kumar
- Department of Chemistry (Physical Chemistry), Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany.
| | - Tim Holtum
- Department of Chemistry (Physical Chemistry), Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Jens Voskuhl
- Department of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Michael Giese
- Department of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Thomas Schrader
- Department of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sebastian Schlücker
- Department of Chemistry (Physical Chemistry), Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany.
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31
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Sandoval IM, Marmion DJ, Meyers KT, Manfredsson FP. Gene Therapy to Modulate Alpha-Synuclein in Synucleinopathies. JOURNAL OF PARKINSONS DISEASE 2021; 11:S189-S197. [PMID: 34092656 PMCID: PMC8543271 DOI: 10.3233/jpd-212679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The protein alpha-Synuclein (α-Syn) is a key contributor to the etiology of Parkinson’s disease (PD) with aggregation, trans-neuronal spread, and/or depletion of α-Syn being viewed as crucial events in the molecular processes that result in neurodegeneration. The exact succession of pathological occurrences that lead to neuronal death are still largely unknown and are likely to be multifactorial in nature. Despite this unknown, α-Syn dose and stability, autophagy-lysosomal dysfunction, and inflammation, amongst other cellular impairments, have all been described as participatory events in the neurodegenerative process. To that end, in this review we discuss the logical points for gene therapy to intervene in α-Syn-mediated disease and review the preclinical body of work where gene therapy has been used, or could conceptually be used, to ameliorate α-Syn induced neurotoxicity. We discuss gene therapy in the traditional sense of modulating gene expression, as well as the use of viral vectors and nanoparticles as methods to deliver other therapeutic modalities.
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Affiliation(s)
- Ivette M Sandoval
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - David J Marmion
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Kimberly T Meyers
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
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32
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Xu J, Zheng T, Huang X, Wang Y, Yin G, Du W. Procyanidine resists the fibril formation of human islet amyloid polypeptide. Int J Biol Macromol 2021; 183:1067-1078. [PMID: 33965498 DOI: 10.1016/j.ijbiomac.2021.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is widely studied due to its close correlation with the pathogenic mechanism of type II diabetes mellitus (T2DM). Bioflavonoids have been used in the neurodegeneration and diabetes studies. However, the structure-activity relationship remains unclear in many of these compounds. In this work, we performed diverse biophysical and biochemical methods to explore the inhibition of procyanidine on hIAPP and compared with that on amyloid-β (Aβ) protein which is linked to Alzheimer's disease (AD). The procyanidine effectively inhibited the aggregation of hIAPP and Aβ through hydrophobic and hydrogen bonding interactions, it dissolved the aged fibrils into nanoscale particles. The compound also ameliorated the cytotoxicity and the membrane leakage by reducing the peptide oligomerization. The procyanidine showed better binding affinity and inhibitory effects on peptide aggregation and upregulated the cell viability to hIAPP than to Aβ, which could be a prospective inhibitor against hIAPP. This work also offered a possible strategy for T2DM and AD treatments.
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Affiliation(s)
- Jufei Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Ting Zheng
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiangyi Huang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Yanan Wang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Guowei Yin
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China.
| | - Weihong Du
- Department of Chemistry, Renmin University of China, Beijing 100872, China.
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33
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Malishev R, Salinas N, Gibson J, Eden AB, Mieres-Perez J, Ruiz-Blanco YB, Malka O, Kolusheva S, Klärner FG, Schrader T, Sanchez-Garcia E, Wang C, Landau M, Bitan G, Jelinek R. Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
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Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nir Salinas
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Angela Bailey Eden
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
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34
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Erkelenz M, Kosinski R, Sritharan O, Giesler H, Saccà B, Schlücker S. Site-specific facet protection of gold nanoparticles inside a 3D DNA origami box: a tool for molecular plasmonics. Chem Commun (Camb) 2021; 57:3151-3153. [PMID: 33634818 DOI: 10.1039/d0cc07712g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bare gold nanocubes and nanospheres with different sizes are incorporated into a rationally designed 3D DNA origami box. The encaged particles expose a gold surface accessible for subsequent site-specific functionalization, for example, for applications in molecular plasmonics such as SERS or SEF.
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Affiliation(s)
- Michael Erkelenz
- Department of Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE) and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany.
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35
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Hisamatsu Y, Otani K, Takase H, Umezawa N, Higuchi T. Fluorescence Response and Self-Assembly of a Tweezer-Type Synthetic Receptor Triggered by Complexation with Heme and Its Catabolites. Chemistry 2021; 27:6489-6499. [PMID: 33026121 DOI: 10.1002/chem.202003872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Indexed: 11/11/2022]
Abstract
There is increasing interest in the development and applications of synthetic receptors that recognize target biomolecules in aqueous media. We have developed a new tweezer-type synthetic receptor that gives a significant fluorescence response upon complexation with heme in aqueous solution at pH 7.4. The synthetic receptor consists of a tweezer-type heme recognition site and sulfo-Cy5 as a hydrophilic fluorophore. The receptor-heme complex exhibits a supramolecular amphiphilic character that facilitates the formation of self-assembled aggregates, and both the tweezer moiety and the sulfo-Cy5 moiety are important for this property. The synthetic receptor also exhibits significant fluorescence responses to biliverdin and bilirubin, but shows very weak fluorescence responses to flavin mononucleotide, folic acid, and nicotinamide adenine dinucleotide, which contain smaller π-scaffolds.
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Affiliation(s)
- Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Koki Otani
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Hiroshi Takase
- Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
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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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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Rahman MU, Rehman AU, Arshad T, Chen HF. Disaggregation mechanism of prion amyloid for tweezer inhibitor. Int J Biol Macromol 2021; 176:510-519. [PMID: 33607137 DOI: 10.1016/j.ijbiomac.2021.02.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/08/2021] [Accepted: 02/13/2021] [Indexed: 02/07/2023]
Abstract
The aggregation of amyloid has been an important event in the pathology of amyloidogenicity. A number of small molecules have been designed for Amyloidosis treatment. Molecular tweezer CLR01, a potential drug for misfolded β-amyloids inhibition, was reportedly bind directly to Lysine residues and interrupt oligomerization. However, the disaggregation mechanism of amyloid for this inhibitor is unclear. Here we used long timescale of molecular dynamic simulation to reveal the mechanism of disaggregation for pentamer prion amyloid. Molecular docking and molecular dynamics simulation demonstrate that CLR01 is attached with Lysine222 nitrogen by π-cation interaction of its nine aromatic rings and formation of salt bridge/hydrogen bond of one of the two rotatable peripheral anionic phosphate groups. Upon CLR01 binding, we found a major shifting occurs in initial conformation of the oligomer and stretch out the N-terminal chain A from the rest of the amyloid which seems to be the first stage of disaggregated the fibrils slowly yet efficiently. Moreover, the CLR01 remodelled the pentamer Prion220-272 into a compact structure which might be the resistant conformation for further oligomerization. Our work will contribute to better understand the interaction and deterioration mechanism of molecular tweezer for prions and similar amyloids, and offer significant insights into therapeutic development for Amyloidosis treatment.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Bioinformation Technology, Shanghai 200235, China.
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Di J, Siddique I, Li Z, Malki G, Hornung S, Dutta S, Hurst I, Ishaaya E, Wang A, Tu S, Boghos A, Ericsson I, Klärner FG, Schrader T, Bitan G. The molecular tweezer CLR01 improves behavioral deficits and reduces tau pathology in P301S-tau transgenic mice. ALZHEIMERS RESEARCH & THERAPY 2021; 13:6. [PMID: 33397489 PMCID: PMC7784007 DOI: 10.1186/s13195-020-00743-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Molecular tweezers (MTs) are broad-spectrum inhibitors of abnormal protein aggregation. A lead MT, called CLR01, has been demonstrated to inhibit the aggregation and toxicity of multiple amyloidogenic proteins in vitro and in vivo. Previously, we evaluated the effect of CLR01 in the 3 × Tg mouse model of Alzheimer's disease, which overexpresses mutant human presenilin 1, amyloid β-protein precursor, and tau and found that subcutaneous administration of the compound for 1 month led to a robust reduction of amyloid plaques, neurofibrillary tangles, and microgliosis. CLR01 also has been demonstrated to inhibit tau aggregation in vitro and tau seeding in cell culture, yet because in Alzheimer's disease (AD) and in the 3 × Tg model, tau hyperphosphorylation and aggregation are thought to be downstream of Aβ insults, the study in this model left open the question whether CLR01 affected tau in vivo directly or indirectly. METHODS To determine if CLR01 could ameliorate tau pathology directly in vivo, we tested the compound similarly using the P301S-tau (line PS19) mouse model. Mice were administered 0.3 or 1.0 mg/kg per day CLR01 and tested for muscle strength and behavioral deficits, including anxiety- and disinhibition-like behavior. Their brains then were analyzed by immunohistochemical and biochemical assays for pathological forms of tau, neurodegeneration, and glial pathology. RESULTS CLR01 treatment ameliorated muscle-strength deterioration, anxiety-, and disinhibition-like behavior. Improved phenotype was associated with decreased levels of pathologic tau forms, suggesting that CLR01 exerts a direct effect on tau in vivo. Limitations of the study included a relatively short treatment period of the mice at an age in which full pathology is not yet developed. In addition, high variability in this model lowered the statistical significance of the findings of some outcome measures. CONCLUSIONS The findings suggest that CLR01 is a particularly attractive candidate for the treatment of AD because it targets simultaneously the two major pathogenic proteins instigating and propagating the disease, amyloid β-protein (Aβ), and tau, respectively. In addition, our study suggests that CLR01 can be used for the treatment of other tauopathies in the absence of amyloid pathology.
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Affiliation(s)
- Jing Di
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Zizheng Li
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ghattas Malki
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Simon Hornung
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA.,Present Address: Division of Peptide Biochemistry, Technical University of Munich, Freising, Germany
| | - Suman Dutta
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ian Hurst
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ella Ishaaya
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Austin Wang
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Sally Tu
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ani Boghos
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ida Ericsson
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA. .,Brain Research Institute, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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Ruks T, Loza K, Heggen M, Prymak O, Sehnem AL, Oliveira CLP, Bayer P, Beuck C, Epple M. Peptide-Conjugated Ultrasmall Gold Nanoparticles (2 nm) for Selective Protein Targeting. ACS APPLIED BIO MATERIALS 2021. [DOI: 10.1021/acsabm.0c01424] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Tatjana Ruks
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Kateryna Loza
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Marc Heggen
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Oleg Prymak
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Andre Luiz Sehnem
- Institute of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo 05508-090, Brazil
| | - Cristiano L. P. Oliveira
- Institute of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo 05508-090, Brazil
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
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41
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Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
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42
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van der Meer SB, Hadrovic I, Meiners A, Loza K, Heggen M, Knauer SK, Bayer P, Schrader T, Beuck C, Epple M. New Tools to Probe the Protein Surface: Ultrasmall Gold Nanoparticles Carry Amino Acid Binders. J Phys Chem B 2020; 125:115-127. [DOI: 10.1021/acs.jpcb.0c09846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Selina Beatrice van der Meer
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Inesa Hadrovic
- Organic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Kateryna Loza
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Marc Heggen
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Shirley K. Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Thomas Schrader
- Organic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
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Kawahata M, Tominaga M, Komatsu A, Hyodo T, Yamaguchi K. Structural elucidation of liquid cyclooctatetraene and cyclooctadienes in inclusion crystals. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Xu J, Zheng T, Zhao C, Huang X, Du W. Resistance of nepetin and its analogs on the fibril formation of human islet amyloid polypeptide. Int J Biol Macromol 2020; 166:435-447. [PMID: 33127549 DOI: 10.1016/j.ijbiomac.2020.10.202] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/10/2020] [Accepted: 10/24/2020] [Indexed: 12/17/2022]
Abstract
The self-aggregation of human islet amyloid polypeptide (hIAPP) into toxic oligomers and fibrils is closely linked to the pathogenesis of type II diabetes mellitus. Inhibitors can resist hIAPP misfolding, and the resistance can be considered an alternative therapeutic strategy for this disease. Flavones have been applied in the field of diabetes research, however, the inhibition mechanism of many compounds on the fibril formation of related pathogenic peptides remains unclear. In this work, four flavones, namely, nepetin (1), genkwanin (2), luteolin (3), and apigenin (4), were used to impede the peptide aggregation of hIAPP and compared with that on Aβ protein, which is correlated with Alzheimer's disease. Results indicated that the four flavones effectively inhibited the aggregation of the two peptides and mostly dispersed the mature fibrils to monomers. The interactions of flavones with the two peptides demonstrated a spontaneous and exothermic reaction through predominant hydrophobic and hydrogen bonding interactions. The binding affinities of 1 and 3 were stronger than those of 2 and 4 possibly because of the difference in the substituent groups of these molecules. These flavones could also decrease membrane leakage and upregulate cell viability by reducing the formation of toxic oligomers. Moreover, the performance of these flavones in terms of binding affinity, cellular viability, and decreased oligomerization was better on hIAPP than on Aβ. This work offered valuable data about these flavones as prospective therapeutic agents against relevant diseases.
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Affiliation(s)
- Jufei Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Ting Zheng
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Cong Zhao
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiangyi Huang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Weihong Du
- Department of Chemistry, Renmin University of China, Beijing 100872, China.
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Lieblein T, Zangl R, Martin J, Hoffmann J, Hutchison MJ, Stark T, Stirnal E, Schrader T, Schwalbe H, Morgner N. Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer's disease related oligomers. eLife 2020; 9:59306. [PMID: 33095161 PMCID: PMC7682991 DOI: 10.7554/elife.59306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 01/24/2023] Open
Abstract
The formation of oligomers of the amyloid-β peptide plays a key role in the onset of Alzheimer's disease. We describe herein the investigation of disease-relevant small amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing functionally relevant structural attributes. In particular, we can show that amyloid-β oligomers develop in two distinct arrangements leading to either neurotoxic oligomers and fibrils or non-toxic amorphous aggregates. Comprehending the key-attributes responsible for those pathways on a molecular level is a pre-requisite to specifically target the peptide's tertiary structure with the aim to promote the emergence of non-toxic aggregates. Here, we show for two fibril inhibiting ligands, an ionic molecular tweezer and a hydrophobic peptide that despite their different interaction mechanisms, the suppression of the fibril pathway can be deduced from the disappearance of the corresponding structure of the first amyloid-β oligomers.
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Affiliation(s)
- Tobias Lieblein
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Rene Zangl
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Janosch Martin
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Jan Hoffmann
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Marie J Hutchison
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Tina Stark
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Elke Stirnal
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Thomas Schrader
- University of Duisburg-Essen, Institute of Organic Chemistry, Essen, Germany
| | - Harald Schwalbe
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Nina Morgner
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
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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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Weil T, Groß R, Röcker A, Bravo-Rodriguez K, Heid C, Sowislok A, Le MH, Erwin N, Dwivedi M, Bart SM, Bates P, Wettstein L, Müller JA, Harms M, Sparrer K, Ruiz-Blanco YB, Stürzel CM, von Einem J, Lippold S, Read C, Walther P, Hebel M, Kreppel F, Klärner FG, Bitan G, Ehrmann M, Weil T, Winter R, Schrader T, Shorter J, Sanchez-Garcia E, Münch J. Supramolecular Mechanism of Viral Envelope Disruption by Molecular Tweezers. J Am Chem Soc 2020; 142:17024-17038. [PMID: 32926779 PMCID: PMC7523239 DOI: 10.1021/jacs.0c06400] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Broad-spectrum
antivirals are powerful weapons against dangerous
viruses where no specific therapy exists, as in the case of the ongoing
SARS-CoV-2 pandemic. We discovered that a lysine- and arginine-specific
supramolecular ligand (CLR01) destroys enveloped viruses, including
HIV, Ebola, and Zika virus, and remodels amyloid fibrils in semen
that promote viral infection. Yet, it is unknown how CLR01 exerts
these two distinct therapeutic activities. Here, we delineate a novel
mechanism of antiviral activity by studying the activity of tweezer
variants: the “phosphate tweezer” CLR01, a “carboxylate
tweezer” CLR05, and a “phosphate clip” PC. Lysine
complexation inside the tweezer cavity is needed to antagonize amyloidogenesis
and is only achieved by CLR01. Importantly, CLR01 and CLR05 but not
PC form closed inclusion complexes with lipid head groups of viral
membranes, thereby altering lipid orientation and increasing surface
tension. This process disrupts viral envelopes and diminishes infectivity
but leaves cellular membranes intact. Consequently, CLR01 and CLR05
display broad antiviral activity against all enveloped viruses tested,
including herpesviruses, Measles virus, influenza, and SARS-CoV-2.
Based on our mechanistic insights, we potentiated the antiviral, membrane-disrupting
activity of CLR01 by introducing aliphatic ester arms into each phosphate
group to act as lipid anchors that promote membrane targeting. The
most potent ester modifications harbored unbranched C4 units, which
engendered tweezers that were approximately one order of magnitude
more effective than CLR01 and nontoxic. Thus, we establish the mechanistic
basis of viral envelope disruption by specific tweezers and establish
a new class of potential broad-spectrum antivirals with enhanced activity.
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Affiliation(s)
- Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Annika Röcker
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Kenny Bravo-Rodriguez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christian Heid
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Andrea Sowislok
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - My-Hue Le
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Nelli Erwin
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Mridula Dwivedi
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Stephen M Bart
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Konstantin Sparrer
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Sina Lippold
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Clarissa Read
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany.,Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Marco Hebel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Florian Kreppel
- Center for Biomedical Education and Research, University of Witten/Herdecke, Stockumer Strasse 10, 58453 Witten, Germany
| | | | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Michael Ehrmann
- Microbiology II, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - James Shorter
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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CLR01 protects dopaminergic neurons in vitro and in mouse models of Parkinson's disease. Nat Commun 2020; 11:4885. [PMID: 32985503 PMCID: PMC7522721 DOI: 10.1038/s41467-020-18689-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
Parkinson’s disease (PD) affects millions of patients worldwide and is characterized by alpha-synuclein aggregation in dopamine neurons. Molecular tweezers have shown high potential as anti-aggregation agents targeting positively charged residues of proteins undergoing amyloidogenic processes. Here we report that the molecular tweezer CLR01 decreased aggregation and toxicity in induced pluripotent stem cell-derived dopaminergic cultures treated with PD brain protein extracts. In microfluidic devices CLR01 reduced alpha-synuclein aggregation in cell somas when axonal terminals were exposed to alpha-synuclein oligomers. We then tested CLR01 in vivo in a humanized alpha-synuclein overexpressing mouse model; mice treated at 12 months of age when motor defects are mild exhibited an improvement in motor defects and a decreased oligomeric alpha-synuclein burden. Finally, CLR01 reduced alpha-synuclein-associated pathology in mice injected with alpha-synuclein aggregates into the striatum or substantia nigra. Taken together, these results highlight CLR01 as a disease-modifying therapy for PD and support further clinical investigation. CLR01 is a molecular tweezer that inhibits protein aggregation. Here the authors show that CLR01 protects dopaminergic neurons in vitro and in vivo in human neurons and in mouse models showing potential as a disease-modifying therapy for Parkinson’s disease.
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Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
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50
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Mason AJ, Hurst I, Malik R, Siddique I, Solomonov I, Sagi I, Klärner FG, Schrader T, Bitan G. Different Inhibitors of Aβ42-Induced Toxicity Have Distinct Metal-Ion Dependency. ACS Chem Neurosci 2020; 11:2243-2255. [PMID: 32559370 DOI: 10.1021/acschemneuro.0c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oligomers of amyloid β-protein (Aβ) are thought to be the proximal toxic agents initiating the neuropathologic process in Alzheimer's disease (AD). Therefore, targeting the self-assembly and oligomerization of Aβ has been an important strategy for designing AD therapeutics. In parallel, research into the metallobiology of AD has shown that Zn2+ can strongly modulate the aggregation of Aβ in vitro and both promote and inhibit the neurotoxicity of Aβ, depending on the experimental conditions. Thus, successful inhibitors of Aβ self-assembly may have to inhibit the toxicity not only of Aβ oligomers themselves but also of Aβ-Zn2+ complexes. However, there has been relatively little research investigating the effects of Aβ self-assembly and toxicity inhibitors in the presence of Zn2+. Our group has characterized previously a series of Aβ42 C-terminal fragments (CTFs), some of which have been shown to inhibit Aβ oligomerization and neurotoxicity. Here, we asked whether three CTFs shown to be potent inhibitors of Aβ42 toxicity maintained their activity in the presence of Zn2+. Biophysical analysis showed that the CTFs had different effects on oligomer, β-sheet, and fibril formation by Aβ42-Zn2+ complexes. However, cell viability experiments in differentiated PC-12 cells incubated with Aβ42-Zn2+ complexes in the absence or presence of these CTFs showed that the CTFs completely lost their inhibitory activity in the presence of Zn2+ even when applied at 10-fold excess relative to Aβ42. In light of these results, we tested another inhibitor, the molecular tweezer CLR01, which coincidentally had been shown to have a high affinity for Zn2+, suggesting that it could disrupt both Aβ42 oligomerization and Aβ42-Zn2+ complexation. Indeed, we found that CLR01 effectively inhibited the toxicity of Aβ42-Zn2+ complexes. Moreover, it did so at a lower concentration than needed for inhibiting the toxicity of Aβ42 alone. In agreement with these results, CLR01 inhibited β-sheet and fibril formation in Aβ42-Zn2+ complexes. Our data suggest that, for the development of efficient therapeutic agents, inhibitors of Aβ self-assembly and toxicity should be examined in the presence of relevant metal ions and that molecular tweezers may be particularly attractive candidates for therapy development.
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Affiliation(s)
- Ashley J. Mason
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ian Hurst
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
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