1
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Giugliano G, Gajo M, Marforio TD, Zerbetto F, Mattioli EJ, Calvaresi M. Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking. Chemistry 2024; 30:e202400871. [PMID: 38777795 DOI: 10.1002/chem.202400871] [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: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.
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Affiliation(s)
- Giulia Giugliano
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Margherita Gajo
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
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2
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Liang Q, Chi G, Cirqueira L, Zhi L, Marasco A, Pilati N, Gunthorpe MJ, Alvaro G, Large CH, Sauer DB, Treptow W, Covarrubias M. The binding and mechanism of a positive allosteric modulator of Kv3 channels. Nat Commun 2024; 15:2533. [PMID: 38514618 PMCID: PMC10957983 DOI: 10.1038/s41467-024-46813-8] [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: 04/10/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Small-molecule modulators of diverse voltage-gated K+ (Kv) channels may help treat a wide range of neurological disorders. However, developing effective modulators requires understanding of their mechanism of action. We apply an orthogonal approach to elucidate the mechanism of action of an imidazolidinedione derivative (AUT5), a highly selective positive allosteric modulator of Kv3.1 and Kv3.2 channels. AUT5 modulation involves positive cooperativity and preferential stabilization of the open state. The cryo-EM structure of the Kv3.1/AUT5 complex at a resolution of 2.5 Å reveals four equivalent AUT5 binding sites at the extracellular inter-subunit interface between the voltage-sensing and pore domains of the channel's tetrameric assembly. Furthermore, we show that the unique extracellular turret regions of Kv3.1 and Kv3.2 essentially govern the selective positive modulation by AUT5. High-resolution apo and bound structures of Kv3.1 demonstrate how AUT5 binding promotes turret rearrangements and interactions with the voltage-sensing domain to favor the open conformation.
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Affiliation(s)
- Qiansheng Liang
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Leonardo Cirqueira
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Lianteng Zhi
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Agostino Marasco
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Nadia Pilati
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Martin J Gunthorpe
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - Giuseppe Alvaro
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Charles H Large
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Werner Treptow
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Manuel Covarrubias
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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3
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Flood R, Cerofolini L, Fragai M, Crowley PB. Multivalent Calixarene Complexation of a Designed Pentameric Lectin. Biomacromolecules 2024; 25:1303-1309. [PMID: 38227741 PMCID: PMC10865345 DOI: 10.1021/acs.biomac.3c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonato-calix[8]arene (sclx8), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and 15N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein-calixarene interface observed to date. This system provides a platform for investigating multivalency.
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Affiliation(s)
- Ronan
J. Flood
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Linda Cerofolini
- Magnetic
Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| | - Peter B. Crowley
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
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4
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Volpi S, Doolan A, Baldini L, Casnati A, Crowley PB, Sansone F. Complex Formation between Cytochrome c and a Tetra-alanino-calix[4]arene. Int J Mol Sci 2022; 23:ijms232315391. [PMID: 36499717 PMCID: PMC9737847 DOI: 10.3390/ijms232315391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Owing to their remarkable features, calix[n]arenes are being exploited to study different aspects of molecular recognition, including protein complexation. Different complexation modes have been described, depending on the moieties that complement the aromatic cavity, allowing for function regulation and/or controlled assembly of the protein target. Here, a rigid cone calix[4]arene, bearing four anionic alanine units at the upper rim, was tested as a ligand for cytochrome c. Cocrystallization attempts were unfruitful, preventing a solid-state study of the system. Next, the complex was studied using NMR spectroscopy, which revealed the presence of two binding sites at lysine residues with dissociation constants (Kd) in the millimolar range.
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Affiliation(s)
- Stefano Volpi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Aishling Doolan
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Laura Baldini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
- Correspondence:
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Peter B. Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
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5
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Abstract
ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystallization and X-ray structure determination as well as by solution state methods, NMR spectroscopy, isothermal titration calorimetry (ITC), and light scattering. Much of this work benefitted from collaboration, highlighted here. Our first breakthrough was the cocrystallization of cationic cytochrome c with sulfonato-calix[4]arene leading to a crystal structure defining three binding sites. Together with NMR studies, a dynamic complexation was deduced in which the calixarene explores the protein surface. Other cationic proteins were similarly amenable to cocrystallization with sulfonato-calix[4]arene, confirming calixarene-arginine/lysine encapsulation and consequent protein assembly. Calixarenes bearing anionic substituents such as sulfonate or phosphonate, but not carboxylate, have proven useful.Studies with larger calix[n]arenes (n = 6, 8) demonstrated the bigger better binder phenomenon with increased affinities and more interesting assemblies, including solution-state oligomerization and porous frameworks. While the calix[4]arene cavity accommodates a single cationic side chain, the larger macrocycles adopt different conformations, molding to the protein surface and accommodating several residues (hydrophobic, polar, and/or charged) in small cavities. In addition to accommodating protein features, the calixarene can bind exogenous components such as polyethylene glycol (PEG), metal ions, buffer, and additives. Ternary cocrystallization of cytochrome c, sulfonato-calix[8]arene, and spermine resulted in altered framework fabrication due to calixarene encapsulation of the tetraamine. Besides host-guest chemistry with exogenous components, the calixarene can also self-assemble, with numerous instances of macrocycle dimers.Calixarene complexation enables protein encapsulation, not merely side chain encapsulation. Cocrystal structures of sulfonato-calix[8]arene with cytochrome c or Ralstonia solanacearum lectin (RSL) provide evidence of encapsulation, with multiple calixarenes masking the same protein. NMR studies of cytochrome c and sulfonato-calix[8]arene are also consistent with multisite binding. In the case of RSL, a C3 symmetric trimer, up to six calixarenes bind the protein yielding a cubic framework mediated by calixarene dimers. Biomolecular calixarene complexation has evolved from molecular recognition to framework construction. This latter development contributes to the challenge in design and preparation of porous molecular materials. Cytochrome c and sulfonato-calix[8]arene form frameworks with >60% solvent in which the degree of porosity depends on the protein:calixarene ratio and the crystallization conditions. Recent developments with RSL led to three frameworks with varying porosity depending on the crystallization conditions, particularly the pH. NMR studies indicate a pH-triggered assembly in which two acidic residues appear to play key roles. The field of supramolecular protein chemistry is growing, and this Account aims to encourage new developments at the interface between biomolecular and synthetic/supramolecular chemistry.
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Affiliation(s)
- Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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6
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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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7
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Sbravati D, Bonardi A, Bua S, Angeli A, Ferraroni M, Nocentini A, Casnati A, Gratteri P, Sansone F, Supuran CT. Calixarenes Incorporating Sulfonamide Moieties: Versatile Ligands for Carbonic Anhydrases Inhibition. Chemistry 2021; 28:e202103527. [PMID: 34882858 DOI: 10.1002/chem.202103527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/10/2022]
Abstract
Carbonic anhydrases (CAs) continue to represent a relevant pharmaceutical target. The need of selective inhibitors and the involvement of these metalloenzymes in many multifaceted diseases boost the search for new ligands able to distinguish among the different CA isoforms, and for multifunctional systems simultaneously able to inhibit CAs and to interfere with other pathological events by interacting with additional targets. In this work, we successfully explored the possibility of preparing new CAs ligands by combining calixarenes with benzensulfonamide units. Inhibition tests towards three human CA isoforms evidenced, for some of the ligands, Ki values in the nanomolar range and promising selectivity. X-ray and molecular modeling studies provided information on the mode of binding of these calixarene derivatives. Thanks to the encouraging results and the structural features typical of the calixarene scaffold, it is then possible to plan for the future the design of multifunctional inhibitors for this class of widely spread enzymes.
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Affiliation(s)
- Davide Sbravati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Alessandro Bonardi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Silvia Bua
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Andrea Angeli
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Marta Ferraroni
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Paola Gratteri
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
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8
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein-protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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9
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10
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Baldini L, Casnati A, Sansone F. Multivalent and Multifunctional Calixarenes in Bionanotechnology. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Laura Baldini
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Alessandro Casnati
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Francesco Sansone
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
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11
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Yamini G, Nestorovich EM. Multivalent Inhibitors of Channel-Forming Bacterial Toxins. Curr Top Microbiol Immunol 2019; 406:199-227. [PMID: 27469304 PMCID: PMC6814628 DOI: 10.1007/82_2016_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rational design of multivalent molecules represents a remarkable modern tool to transform weak non-covalent interactions into strong binding by creating multiple finely-tuned points of contact between multivalent ligands and their supposed multivalent targets. Here, we describe several prominent examples where the multivalent blockers were investigated for their ability to directly obstruct oligomeric channel-forming bacterial exotoxins, such as the pore-forming bacterial toxins and B component of the binary bacterial toxins. We address problems related to the blocker/target symmetry match and nature of the functional groups, as well as chemistry and length of the linkers connecting the functional groups to their multivalent scaffolds. Using the anthrax toxin and AB5 toxin case studies, we briefly review how the oligomeric toxin components can be successfully disabled by the multivalent non-channel-blocking inhibitors, which are based on a variety of multivalent scaffolds.
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Affiliation(s)
- Goli Yamini
- Department of Biology, The Catholic University of America, Washington, D.C., 20064, USA
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12
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Salvio R, Volpi S, Folcarelli T, Casnati A, Cacciapaglia R. A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds. Org Biomol Chem 2019; 17:7482-7492. [DOI: 10.1039/c9ob01141b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Conjugated carbonyl units in a calixarene scaffold provide the right amount of flexibility for catalysis with a minimum entropic cost.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche
- Università “Tor Vergata”
- I-00133 Roma
- Italy
- ISB - CNR Sezione Meccanismi di Reazione
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | | | - Alessandro Casnati
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Roberta Cacciapaglia
- ISB - CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma
- Italy
- Dipartimento di Chimica
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13
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Hu X, Liu N, Yang H, Wu F, Chen X, Li C, Chen X. A reversible ion transportation switch of ON–OFF–ON type by a ligand-gated calix[6]arene channel. Chem Commun (Camb) 2019; 55:3008-3011. [DOI: 10.1039/c9cc00732f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calix[6]arene (CX6) was found to be an efficient ion transmembrane channel, which could be blocked by methylene blue (MB) through host–guest interactions.
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Affiliation(s)
- Xinyu Hu
- College of Mathematic and Electronic Information Engineering
- Wenzhou University
- Wenzhou 325035
- P. R. China
| | - Nannan Liu
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou 325035
- P. R. China
| | - Haishen Yang
- Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power
- Shanghai University of Electric Power
- Shanghai
- China
| | - Fen Wu
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou 325035
- P. R. China
| | - Xi Chen
- College of Mathematic and Electronic Information Engineering
- Wenzhou University
- Wenzhou 325035
- P. R. China
| | - Canpeng Li
- School of Chemical Science and Technology
- Yunnan University
- Kunming 650091
- P. R. China
| | - Xiaojing Chen
- College of Mathematic and Electronic Information Engineering
- Wenzhou University
- Wenzhou 325035
- P. R. China
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14
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15
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Signalling assemblies: the odds of symmetry. Biochem Soc Trans 2017; 45:599-611. [PMID: 28620024 DOI: 10.1042/bst20170009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 02/06/2023]
Abstract
The assembly of proteins into complexes is fundamental to nearly all biological signalling processes. Symmetry is a dominant feature of the structures of experimentally determined protein complexes, observed in the vast majority of homomers and many heteromers. However, some asymmetric structures exist, and asymmetry also often forms transiently, intractable to traditional structure determination methods. Here, we explore the role of protein complex symmetry and asymmetry in cellular signalling, focusing on receptors, transcription factors and transmembrane channels, among other signalling assemblies. We highlight a recurrent tendency for asymmetry to be crucial for signalling function, often being associated with activated states. We conclude with a discussion of how consideration of protein complex symmetry and asymmetry has significant potential implications and applications for pharmacology and human disease.
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16
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Al-Sabi A, Daly D, Hoefer P, Kinsella GK, Metais C, Pickering M, Herron C, Kaza SK, Nolan K, Dolly JO. A Rational Design of a Selective Inhibitor for Kv1.1 Channels Prevalent in Demyelinated Nerves That Improves Their Impaired Axonal Conduction. J Med Chem 2017; 60:2245-2256. [PMID: 28225274 DOI: 10.1021/acs.jmedchem.6b01262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
K+ channels containing Kv1.1 α subunits, which become prevalent at internodes in demyelinated axons, may underlie their dysfunctional conduction akin to muscle weakness in multiple sclerosis. Small inhibitors were sought with selectivity for the culpable hyper-polarizing K+ currents. Modeling of interactions with the extracellular pore in a Kv1.1-deduced structure identified diaryldi(2-pyrrolyl)methane as a suitable scaffold with optimized alkyl ammonium side chains. The resultant synthesized candidate [2,2'-((5,5'(di-p-topyldiaryldi(2-pyrrolyl)methane)bis(2,2'carbonyl)bis(azanediyl)) diethaneamine·2HCl] (8) selectively blocked Kv1.1 channels (IC50 ≈ 15 μM) recombinantly expressed in mammalian cells, induced a positive shift in the voltage dependency of K+ current activation, and slowed its kinetics. It preferentially inhibited channels containing two or more Kv1.1 subunits regardless of their positioning in concatenated tetramers. In slices of corpus callosum from mice subjected to a demyelination protocol, this novel inhibitor improved neuronal conduction, highlighting its potential for alleviating symptoms in multiple sclerosis.
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Affiliation(s)
| | | | | | - Gemma K Kinsella
- School of Food Science and Environmental Health, College of Sciences and Health, Dublin Institute of Technology , Cathal Brugha Street, Dublin 1, Ireland
| | | | - Mark Pickering
- UCD School of Medicine, University College Dublin , Dublin, Ireland
| | - Caroline Herron
- School of Biomolecular and Biomed Science, Conway Institute , Belfield, Dublin 4, Ireland
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17
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Calixdrugs: calixarene-based clusters of established therapeutic drug agents. Mol Divers 2016; 20:781-7. [DOI: 10.1007/s11030-016-9667-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/12/2016] [Indexed: 11/27/2022]
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18
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Tommasone S, Talotta C, Gaeta C, Margarucci L, Monti MC, Casapullo A, Macchi B, Prete SP, Ladeira De Araujo A, Neri P. Biomolecular Fishing for Calixarene Partners by a Chemoproteomic Approach. Angew Chem Int Ed Engl 2015; 54:15405-9. [DOI: 10.1002/anie.201508651] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Stefano Tommasone
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Carmen Talotta
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Carmine Gaeta
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Luigi Margarucci
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Agostino Casapullo
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
| | - Beatrice Macchi
- Dipartimento di Medicina dei Sistemi, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Roma (Italy)
| | - Salvatore Pasquale Prete
- Dipartimento di Medicina dei Sistemi, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Roma (Italy)
| | - Adriana Ladeira De Araujo
- Department of Pathology, Laboratory of Dermatology and Immunodeficiencies, Medical School, University of Sao Paulo (Brasil)
| | - Placido Neri
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno, Italy)
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19
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Tommasone S, Talotta C, Gaeta C, Margarucci L, Monti MC, Casapullo A, Macchi B, Prete SP, Ladeira De Araujo A, Neri P. Biomolecular Fishing for Calixarene Partners by a Chemoproteomic Approach. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Nissinkorn Y, Lahav‐Mankovski N, Rabinkov A, Albeck S, Motiei L, Margulies D. Sensing Protein Surfaces with Targeted Fluorescent Receptors. Chemistry 2015; 21:15981-7. [DOI: 10.1002/chem.201502069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yael Nissinkorn
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Naama Lahav‐Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Aharon Rabinkov
- Department of Biological Services, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
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21
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Giuliani M, Morbioli I, Sansone F, Casnati A. Moulding calixarenes for biomacromolecule targeting. Chem Commun (Camb) 2015; 51:14140-59. [PMID: 26286064 DOI: 10.1039/c5cc05204a] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
After their successful use as a preorganized platform for the preparation of receptors for metal ions and small neutral molecules over the last 15 years, calixarenes are enjoying a renaissance of popularity as scaffolds for ligands that are able to efficiently and selectively target macromolecules such as proteins/enzymes, nucleic acids and lipids. This feature article summarizes the peculiar factors characterizing the calixarene structure and properties, as well as outlines the main rules that can be used to turn such macrocycles into efficient and successful ligands for these classes of biomacromolecules. Factors that affect the multivalent properties of calixarenes, such as the size, conformation and stereochemical presentation of binding groups or their amphiphilicity and hybrid character, are described in detail with the use of a few selected examples from the literature. Perspectives and applications of these ligands in bionanotechnology and nanomedicine, such as protein sensing and inhibition, gene-delivery, targeted drug-delivery and cell imaging, are also discussed.
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Affiliation(s)
- Marta Giuliani
- Dip. to di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy.
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22
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Ali M, Daze KD, Strongin DE, Rothbart SB, Rincon-Arano H, Allen HF, Li J, Strahl BD, Hof F, Kutateladze TG. Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes. J Biol Chem 2015; 290:22919-30. [PMID: 26229108 DOI: 10.1074/jbc.m115.669333] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Indexed: 11/06/2022] Open
Abstract
Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes, including transcriptional activation and repression, DNA damage repair, cell differentiation, and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated lysine 4 of histone H3 in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying the biological roles of methyllysine readers in epigenetic signaling.
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Affiliation(s)
- Muzaffar Ali
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Kevin D Daze
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Daniel E Strongin
- the Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Scott B Rothbart
- the Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Hector Rincon-Arano
- the Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Hillary F Allen
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Janessa Li
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Brian D Strahl
- the Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Fraser Hof
- the Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada,
| | - Tatiana G Kutateladze
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045,
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23
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Kubota R, Hamachi I. Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells. Chem Soc Rev 2015; 44:4454-71. [DOI: 10.1039/c4cs00381k] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review describes the recognition and sensing techniques of proteins and their building blocks by use of small synthetic binders.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
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24
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Rescifina A, Zagni C, Mineo PG, Giofrè SV, Chiacchio U, Tommasone S, Talotta C, Gaeta C, Neri P. DNA Recognition with Polycyclic-Aromatic-Hydrocarbon-Presenting Calixarene Conjugates. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Carta V, Pangerl M, Baur R, Puthenkalam R, Ernst M, Trauner D, Sigel E. A pentasymmetric open channel blocker for Cys-loop receptor channels. PLoS One 2014; 9:e106688. [PMID: 25184303 PMCID: PMC4153658 DOI: 10.1371/journal.pone.0106688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/31/2014] [Indexed: 11/30/2022] Open
Abstract
γ-Aminobutyric acid type A receptors (GABAA receptors) are chloride ion channels composed of five subunits, mediating fast synaptic and tonic inhibition in the mammalian brain. These receptors show near five-fold symmetry that is most pronounced in the second trans-membrane domain M2 lining the Cl- ion channel. To take advantage of this inherent symmetry, we screened a variety of aromatic anions with matched symmetry and found an inhibitor, pentacyanocyclopentdienyl anion (PCCP-) that exhibited all characteristics of an open channel blocker. Inhibition was strongly dependent on the membrane potential. Through mutagenesis and covalent modification, we identified the region α1V256-α1T261 in the rat recombinant GABAA receptor to be important for PCCP- action. Introduction of positive charges into M2 increased the affinity for PCCP- while PCCP- prevented the access of a positively charged molecule into M2. Interestingly, other anion selective cys-loop receptors were also inhibited by PCCP-, among them the Drosophila RDL GABAA receptor carrying an insecticide resistance mutation, suggesting that PCCP- could serve as an insecticide.
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Affiliation(s)
- Valentina Carta
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Michael Pangerl
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Munich, Germany
| | - Roland Baur
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Roshan Puthenkalam
- Department of Biochemistry and Molecular Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Margot Ernst
- Department of Biochemistry and Molecular Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Munich, Germany
| | - Erwin Sigel
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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26
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Mutihac L, Varduca Enache I, Diacu E, Mutihac RC, Vicens J. Anion influence on extraction and transport of amino acid methyl esters by functionalised calix[4]arene. Supramol Chem 2014. [DOI: 10.1080/10610278.2013.863315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Lucia Mutihac
- Department of Analytical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Ioana Varduca Enache
- Department of Analytical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Elena Diacu
- Department of Analytical Chemistry, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Polizu 1, 011061 Bucharest, Romania
| | - Radu-Cristian Mutihac
- Laboratory for Physics and Chemistry of Interfaces, Department of Microsystems Engineering-IMTEK, University of Freiburg, Freiburg, Germany
| | - Jacques Vicens
- IPHC-ULP-ECPM-CNRS, Laboratory of Molecular Conception, University of Strasbourg, 25, rue Becquerel, F-67087 Strasbourg, France
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27
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Kokhan O, Ponomarenko N, Pokkuluri PR, Schiffer M, Tiede DM. Multimerization of solution-state proteins by tetrakis(4-sulfonatophenyl)porphyrin. Biochemistry 2014; 53:5070-9. [PMID: 25028772 DOI: 10.1021/bi500278g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Surface binding and interactions of anionic porphyins bound to cationic proteins have been studied for nearly three decades and are relevant as models for protein surface molecular recognition and photoinitiated electron transfer. However, interpretation of data in nearly all reports explicitly or implicitly assumed interaction of porphyrin with monodisperse proteins in solutions. In this report, using small-angle X-ray scattering with solution phase samples, we demonstrate that horse heart cytochrome (cyt) c, triheme cytochrome c7 PpcA from Geobacter sulfurreducens, and hen egg lysozyme multimerize in the presence of zinc tetrakis(4-sulfonatophenyl)porphyrin (ZnTPPS). Multimerization of cyt c showed a pH dependence with a stronger apparent binding affinity under alkaline conditions and was weakened in the presence of a high salt concentration. Ferric-cyt c formed complexes larger than those formed by ferro-cyt c. Free base TPPS and FeTPPS facilitated formation of complexes larger than those of ZnTPPS. No increase in protein aggregation state for cationic proteins was observed in the presence of cationic porphyrins. All-atom molecular dynamics simulations of cyt c and PpcA with free base TPPS corroborated X-ray scattering results and revealed a mechanism by which the tetrasubstituted charged porphyrins serve as bridging ligands nucleating multimerization of the complementarily charged protein. The final aggregation products suggest that multimerization involves a combination of electrostatic and hydrophobic interactions. The results demonstrate an overlooked complexity in the design of multifunctional ligands for protein surface recognition.
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Affiliation(s)
- Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Lemont, Illinois 60439, United States
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28
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Abstract
The tandem PHD (plant homeodomain) fingers of the CHD4 (chromodomain helicase DNA-binding protein 4) ATPase are epigenetic readers that bind either unmodified histone H3 tails or H3K9me3 (histone H3 trimethylated at Lys⁹). This dual function is necessary for the transcriptional and chromatin remodelling activities of the NuRD (nucleosome remodelling and deacetylase) complex. In the present paper, we show that calixarene-based supramolecular hosts disrupt binding of the CHD4 PHD2 finger to H3K9me3, but do not affect the interaction of this protein with the H3K9me0 (unmodified histone H3) tail. A similar inhibitory effect, observed for the association of chromodomain of HP1γ (heterochromatin protein 1γ) with H3K9me3, points to a general mechanism of methyl-lysine caging by calixarenes and suggests a high potential for these compounds in biochemical applications. Immunofluorescence analysis reveals that the supramolecular agents induce changes in chromatin organization that are consistent with their binding to and disruption of H3K9me3 sites in living cells. The results of the present study suggest that the aromatic macrocyclic hosts can be used as a powerful new tool for characterizing methylation-driven epigenetic mechanisms.
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29
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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30
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Dantas JM, Morgado L, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:750-60. [PMID: 24530867 DOI: 10.1016/j.bbabio.2014.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 11/25/2022]
Abstract
The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Carlos A Salgueiro
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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31
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A stimuli-responsive nanopore based on a photoresponsive host-guest system. Sci Rep 2013; 3:1662. [PMID: 23588705 PMCID: PMC3627192 DOI: 10.1038/srep01662] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/27/2013] [Indexed: 12/17/2022] Open
Abstract
The open-close states of the ion channels in a living system are regulated by multiple stimuli such as ligand, pH, potential and light. Functionalizing natural channels by using synthetic chemistry would provide biological nanopores with novel properties and applications. Here we use para-sulfonato-calix[4]arene-based host-guest supramolecular system to develop artificial gating mechanisms aiming at regulating wild-type α-HL commanded by both ligand and light stimuli. Using the gating property of α-hemolysin, we studied the host-guest interactions between para-sulfonato-calix[4]arene and 4, 4'-dipyridinium-azobenzene at the single-molecule level. Subsequently, we have extended the application of this gating system to the real-time study of light-induced molecular shuttle based on para-sulfonato-calix[4]arene and 4, 4'-dipyridinium-azobenzene at the single-molecule level. These experiments provide a more efficient method to develop a general tool to analyze the individual motions of supramolecular systems by using commercially available α-HL nanopores.
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32
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Kong L, Harrington L, Li Q, Cheley S, Davis BG, Bayley H. Single-molecule interrogation of a bacterial sugar transporter allows the discovery of an extracellular inhibitor. Nat Chem 2013; 5:651-9. [DOI: 10.1038/nchem.1695] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 05/24/2013] [Indexed: 11/09/2022]
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33
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Molecular tweezers modulate 14-3-3 protein–protein interactions. Nat Chem 2013; 5:234-9. [DOI: 10.1038/nchem.1570] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/10/2013] [Indexed: 12/12/2022]
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35
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Derbel N, Clarot I, Mourer M, Regnouf-de-Vains JB, Ruiz-López MF. Intramolecular interactions versus hydration effects on p-guanidinoethyl-phenol structure and pKa values. J Phys Chem A 2012; 116:9404-11. [PMID: 22931189 DOI: 10.1021/jp3069893] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We analyze the structure, hydration, and pK(a) values of p-guanidinoethyl-phenol through a combined experimental and theoretical study. These issues are relevant to understand the mechanism of action of the tetrameric form, the antibacterial compound tetra-p-guanidinoethyl-calix[4]arene (Cx1). The investigated system can also be useful to model other pharmaceutical drugs bearing a guanidine function in the vicinity of an ionizable group and the effect of arginine on the pK(a) of vicinal ionizable residues (in particular tyrosine) in peptides. The p-guanidinoethyl-phenol monomer (mCx1) has two ionizable groups. One important particularity of this system is that it exhibits high molecular flexibility that potentially leads to enhanced stabilization in folded structures by direct, strong Coulombic interactions between the ionizable groups. The first pK(a) corresponding to ionization of the -OH group has experimentally been shown to be only slightly different from usual values in substituted phenols. However, because of short-range Coulombic interactions, the role of intramolecular interactions and solvation effects on the acidities of this compound is expected to be important and it has been analyzed here on the basis of theoretical calculations. We use a discrete-continuum solvation model together with quantum-mechanical calculations at the B3LYP level of theory and the extended 6-311+G(2df,2p) basis set. Both intra- and intermolecular effects are very large (~70 kcal/mol) but exhibit an almost perfect compensation, thus explaining that the actual pK(a) of mCx1 is close to free phenol. The same compensation of environmental effects applies to the second pK(a) that concerns the guanidinium group. Such a pK(a) could not be determined experimentally with standard titration techniques and in fact the theoretical study predicts a value of 14.2, that is, one unit above the pK(a) of the parent ethyl-guanidinium molecule.
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Affiliation(s)
- Najoua Derbel
- LSAMA, University of Tunis - El Manar, Campus Universitaire, 2092, Tunis, Tunisia.
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McGovern RE, Fernandes H, Khan AR, Power NP, Crowley PB. Protein camouflage in cytochrome c–calixarene complexes. Nat Chem 2012; 4:527-33. [DOI: 10.1038/nchem.1342] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/22/2012] [Indexed: 01/06/2023]
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Giant regular polyhedra from calixarene carboxylates and uranyl. Nat Commun 2012; 3:785. [PMID: 22510690 PMCID: PMC3337980 DOI: 10.1038/ncomms1793] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/19/2012] [Indexed: 11/08/2022] Open
Abstract
Self-assembly of large multi-component systems is a common strategy for the bottom-up construction of discrete, well-defined, nanoscopic-sized cages. Icosahedral or pseudospherical viral capsids, built up from hundreds of identical proteins, constitute typical examples of the complexity attained by biological self-assembly. Chemical versions of the so-called 5 Platonic regular or 13 Archimedean semi-regular polyhedra are usually assembled combining molecular platforms with metals with commensurate coordination spheres. Here we report novel, self-assembled cages, using the conical-shaped carboxylic acid derivatives of calix[4]arene and calix[5]arene as ligands, and the uranyl cation UO(2)2+ as a metallic counterpart, which coordinates with three carboxylates at the equatorial plane, giving rise to hexagonal bipyramidal architectures. As a result, octahedral and icosahedral anionic metallocages of nanoscopic dimensions are formed with an unusually small number of components.
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Conley MP, Valero J, de Mendoza J. Guanidinium-Based Receptors for Oxoanions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hu W, Blecking C, Kralj M, Šuman L, Piantanida I, Schrader T. Dimeric calixarenes: a new family of major-groove binders. Chemistry 2012; 18:3589-97. [PMID: 22336964 DOI: 10.1002/chem.201100634] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 11/26/2011] [Indexed: 01/26/2023]
Abstract
A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl-protected calix[4]arene tetramines in relatively short synthetic sequences (3-5 steps). The compounds attach themselves to double-stranded nucleic acids in a noncovalent fashion, with micro- to nanomolar affinities. Guanidinium headgroups with their extended hydrogen-bonding "fingers" are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K(d))<AT-rich (1 μM)<GC-rich DNA double strands (100-10 nM). Ethidium bromide displacement studies confirm this order. CE(50) values are remarkably low (1-4 μM), and are more than 300 times lower than that of spermine, which is a typical backbone binder. Stoichiometries are rather high (one calixarene dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye-loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A-form to a perfect B-signature, providing further experimental evidence for major-groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte-Carlo simulations on 1:1 complexes in water.
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Affiliation(s)
- Wenbin Hu
- Department of Chemistry, Universität Duisburg-Essen, Universitätsstr. 7, 45117 Essen, Germany
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Dutt S, Wilch C, Schrader T. Artificial synthetic receptors as regulators of protein activity. Chem Commun (Camb) 2011; 47:5376-83. [DOI: 10.1039/c0cc05812b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superimposed snapshots of a MD simulation for the ternary complex between G6PD, a molecular clip and included NADP+ cofactor.
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Affiliation(s)
- Som Dutt
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Constanze Wilch
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Thomas Schrader
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
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Baldini L, Sansone F, Scaravelli F, Casnati A, Ungaro R. Proximal and distal N,C-linked tetra-peptidocalix[4]arenes as bifunctional receptors: synthesis, conformation and preliminary binding studies. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.506548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Laura Baldini
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Francesco Sansone
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Federico Scaravelli
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Alessandro Casnati
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Rocco Ungaro
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
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Wich P, Schmuck C. Reversible and Noncompetitive Inhibition of β-Tryptase by Protein Surface Binding of Tetravalent Peptide Ligands Identified from a Combinatorial Split-Mix Library. Angew Chem Int Ed Engl 2010; 49:4113-6. [DOI: 10.1002/anie.200907221] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wich P, Schmuck C. Reversible and Noncompetitive Inhibition of β-Tryptase by Protein Surface Binding of Tetravalent Peptide Ligands Identified from a Combinatorial Split-Mix Library. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907221] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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RETRACTED: Carboxylated calixarenes bind strongly to CD69 and protect CD69+ killer cells from suicidal cell death induced by tumor cell surface ligands. Bioorg Med Chem 2010; 18:1434-40. [DOI: 10.1016/j.bmc.2010.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/06/2010] [Accepted: 01/07/2010] [Indexed: 12/28/2022]
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Sansone F, Baldini L, Casnati A, Ungaro R. Calixarenes: from biomimetic receptors to multivalent ligands for biomolecular recognition. NEW J CHEM 2010. [DOI: 10.1039/c0nj00285b] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Rebek J. Molecular recognition and self-assembly special feature: Introduction to the molecular recognition and self-assembly special feature. Proc Natl Acad Sci U S A 2009; 106:10423-4. [PMID: 19567839 PMCID: PMC2705568 DOI: 10.1073/pnas.0905341106] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Julius Rebek
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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