1
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Nazarova A, Shiabiev I, Shibaeva K, Mostovaya O, Mukhametzyanov T, Khannanov A, Evtugyn V, Zelenikhin P, Shi X, Shen M, Padnya P, Stoikov I. Thiacalixarene Carboxylic Acid Derivatives as Inhibitors of Lysozyme Fibrillation. Int J Mol Sci 2024; 25:4721. [PMID: 38731940 PMCID: PMC11083589 DOI: 10.3390/ijms25094721] [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: 03/28/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Amyloid fibroproliferation leads to organ damage and is associated with a number of neurodegenerative diseases affecting populations worldwide. There are several ways to protect against fibril formation, including inhibition. A variety of organic compounds based on molecular recognition of amino acids within the protein have been proposed for the design of such inhibitors. However, the role of macrocyclic compounds, i.e., thiacalix[4]arenes, in inhibiting fibrillation is still almost unknown. In the present work, the use of water-soluble thiacalix[4]arene derivatives for the inhibition of hen egg-white lysozyme (HEWL) amyloid fibrillation is proposed for the first time. The binding of HEWL by the synthesized thiacalix[4]arenes (logKa = 5.05-5.13, 1:1 stoichiometry) leads to the formation of stable supramolecular systems capable of stabilizing the protein structure and protecting against fibrillation by 29-45%. The macrocycle conformation has little effect on protein binding strength, and the native HEWL secondary structure does not change via interaction. The synthesized compounds are non-toxic to the A549 cell line in the range of 0.5-250 µg/mL. The results obtained may be useful for further investigation of the anti-amyloidogenic role of thiacalix[4]arenes, and also open up future prospects for the creation of new ways to prevent neurodegenerative diseases.
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Affiliation(s)
- Anastasia Nazarova
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Igor Shiabiev
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Ksenia Shibaeva
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Olga Mostovaya
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Timur Mukhametzyanov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Arthur Khannanov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Vladimir Evtugyn
- Interdisciplinary Center of Analytical Microscopy, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Pavel Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
- CQM—Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Mingwu Shen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Pavel Padnya
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Ivan Stoikov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
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2
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Lazar AN, Perret F, Perez-Lloret M, Michaud M, Coleman AW. Promises of anionic calix[n]arenes in life science: State of the art in 2023. Eur J Med Chem 2024; 264:115994. [PMID: 38070431 DOI: 10.1016/j.ejmech.2023.115994] [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: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
Because they hold together molecules by means of non-covalent interactions - relatively weak and thus, potentially reversible - the anionic calixarenes have become an interesting tool for efficiently binding a large range of ligands - from gases to large organic molecules. Being highly water soluble and conveniently biocompatible, they showed growing interest for many interdisciplinary fields, particularly in biology and medicine. Thanks to their intrinsic conical shape, they provide suitable platforms, from vesicles to bilayers. This is a valuable characteristic, as so they mimic the biologically functional architectures. The anionic calixarenes propose efficient alternatives for overcoming the limitations linked to drug delivery and bioavailability, as well as drug resistance along with limiting the undesirable side effects. Moreover, the dynamic non-covalent binding with the drugs enables predictable and on demand drug release, controlled by the stimuli present in the targeted environment. This particular feature instigated the use of these versatile, stimuli-responsive compounds for sensing biomarkers of diverse pathologies. The present review describes the recent achievements of the anionic calixarenes in the field of life science, from drug carriers to biomedical engineering, with a particular outlook on their applications for the diagnosis and treatment of different pathologies.
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Affiliation(s)
- Adina-N Lazar
- Univ Lyon, INSA-Lyon, CNRS UMR5259, LaMCoS, F-69621, France.
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246, Univ. Lyon - CNRS - Univ. Claude Bernard Lyon 1 - CPE Lyon, 43 Boulevard du 11 Novembre 1918, Villeurbanne, 69622, Cedex, France.
| | - Marta Perez-Lloret
- School of Biological and Chemical Sciences, University of Galway, Ireland Galway, Ireland
| | - Mickael Michaud
- CIRI, Univ. Lyon1, Inserm, U1111, CNRS, UMR5308, ENS, Lyon, France
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3
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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4
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Selinger AJ, Hof F. Adaptive Supramolecular Networks: Emergent Sensing from Complex Systems. Angew Chem Int Ed Engl 2023; 62:e202312407. [PMID: 37699200 DOI: 10.1002/anie.202312407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Molecular differentiation by supramolecular sensors is typically achieved through sensor arrays, relying on the pattern recognition responses of large panels of isolated sensing elements. Here we report a new one-pot systems chemistry approach to differential sensing in biological solutions. We constructed an adaptive network of three cross-assembling sensor elements with diverse analyte-binding and photophysical properties. This robust sensing approach exploits complex interconnected sensor-sensor and sensor-analyte equilibria, producing emergent supramolecular and photophysical responses unique to each analyte. We characterize the basic mechanisms by which an adaptive network responds to analytes. The inherently data-rich responses of an adaptive network discriminate among very closely related proteins and protein mixtures without relying on designed protein recognition elements. We show that a single adaptive sensing solution provides better analyte discrimination using fewer response observations than a sensor array built from the same components. We also show the network's ability to adapt and respond to changing biological solutions over time.
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Affiliation(s)
- Allison J Selinger
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
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5
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Saldinger JC, Raymond M, Elvati P, Violi A. Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles. NATURE COMPUTATIONAL SCIENCE 2023; 3:393-402. [PMID: 38177838 DOI: 10.1038/s43588-023-00438-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/24/2023] [Indexed: 01/06/2024]
Abstract
Although challenging, the accurate and rapid prediction of nanoscale interactions has broad applications for numerous biological processes and material properties. While several models have been developed to predict the interaction of specific biological components, they use system-specific information that hinders their application to more general materials. Here we present NeCLAS, a general and efficient machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. NeCLAS outperforms current nanoscale prediction models for generic nanoparticles up to 10-20 nm, reproducing interactions for biological and non-biological systems. Two aspects contribute to these results: a low-dimensional representation of nanoparticles and molecules (to reduce the effect of data uncertainty), and environmental features (to encode the physicochemical neighborhood at multiple scales). This framework has several applications, from basic research to rapid prototyping and design in nanobiotechnology.
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Affiliation(s)
| | - Matt Raymond
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Paolo Elvati
- Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Angela Violi
- Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA.
- Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA.
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6
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Giner-Llorca M, Gallego del Sol F, Marcos JF, Marina A, Manzanares P. Rationally designed antifungal protein chimeras reveal new insights into structure-activity relationship. Int J Biol Macromol 2023; 225:135-148. [PMID: 36460243 DOI: 10.1016/j.ijbiomac.2022.11.280] [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: 09/27/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
Antifungal proteins (AFPs) are promising antimicrobial compounds that represent a feasible alternative to fungicides. Penicillium expansum encodes three phylogenetically distinct AFPs (PeAfpA, PeAfpB and PeAfpC) which show different antifungal profiles and fruit protection effects. To gain knowledge about the structural determinants governing their activity, we solved the crystal structure of PeAfpB and rationally designed five PeAfpA::PeAfpB chimeras (chPeAFPV1-V5). Chimeras showed significant differences in their antifungal activity. chPeAFPV1 and chPeAFPV2 improved the parental PeAfpB potency, and it was very similar to that of PeAfpA. chPeAFPV4 and chPeAFPV5 showed an intermediate profile of activity compared to the parental proteins while chPeAFPV3 was inactive towards most of the fungi tested. Structural analysis of the chimeras evidenced an identical scaffold to PeAfpB, suggesting that the differences in activity are due to the contributions of specific residues and not to induced conformational changes or structural rearrangements. Results suggest that mannoproteins determine protein interaction with the cell wall and its antifungal activity while there is not a direct correlation between binding to membrane phospholipids and activity. This work provides new insights about the relevance of sequence motifs and the feasibility of modifying protein specificity, opening the door to the rational design of chimeras with biotechnological applicability.
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Affiliation(s)
- Moisés Giner-Llorca
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain
| | - Francisca Gallego del Sol
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain
| | - Jose F Marcos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain.
| | - Paloma Manzanares
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain.
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7
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DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study. Int J Mol Sci 2023; 24:ijms24021208. [PMID: 36674720 PMCID: PMC9864379 DOI: 10.3390/ijms24021208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
PAF and related antifungal proteins are promising antimicrobial agents. They have highly stable folds around room temperature due to the presence of 3-4 disulfide bonds. However, unfolded states persist and contribute to the thermal equilibrium in aqueous solution, and low-populated states might influence their biological impact. To explore such equilibria during dimethyl sulfoxide (DMSO)-induced chemical unfolding, we studied PAF and its inactive variant PAFD19S using nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC). According to the NMR monitoring at 310 K, the folded structures disappear above 80 v/v% DMSO concentration, while the unfolding is completely reversible. Evaluation of a few resolved peaks from viscosity-compensated 15N-1H HSQC spectra of PAF yielded ∆G = 23 ± 7 kJ/M as the average value for NMR unfolding enthalpy. The NMR-based structures of PAF and the mutant in 50 v/v% DMSO/H2O mixtures were more similar in the mixed solvents then they were in water. The 15N NMR relaxation dynamics in the same mixtures verified the rigid backbones of the NMR-visible fractions of the proteins; still, enhanced dynamics around the termini and some loops were observed. DSC monitoring of the Tm melting point showed parabolic dependence on the DMSO molar fraction and suggested that PAF is more stable than the inactive PAFD19S. The DSC experiments were irreversible due to the applied broad temperature range, but still suggestive of the endothermic unfolding of PAF.
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8
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Synthesis, characterization, and computational study of aggregates from amphiphilic calix[6]arenes. Effect of encapsulation on degradation kinetics of curcumin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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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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10
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Flood R, Ramberg KO, Mengel DB, Guagnini F, Crowley PB. Protein Frameworks with Thiacalixarene and Zinc. CRYSTAL GROWTH & DESIGN 2022; 22:3271-3276. [PMID: 35529063 PMCID: PMC9073927 DOI: 10.1021/acs.cgd.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/10/2022] [Indexed: 05/15/2023]
Abstract
Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene (tsclx 4 ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx 4 -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c, each involving multinuclear zinc sites supported by the cone conformation of tsclx 4 . The tsclx 4 /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx 4 adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.
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11
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Role of Calixarene in Chemotherapy Delivery Strategies. Molecules 2021; 26:molecules26133963. [PMID: 34209495 PMCID: PMC8272165 DOI: 10.3390/molecules26133963] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/14/2023] Open
Abstract
Since cancer is a multifactorial disease with a high mortality rate, the study of new therapeutic strategies is one of the main objectives in modern research. Numerous chemotherapeutic agents, although widely used, have the disadvantage of being not very soluble in water or selective towards cancerous cells, with consequent side effects. Therefore, in recent years, a greater interest has emerged in innovative drug delivery systems (DDSs) such as calixarene, a third-generation supramolecular compound. Calixarene and its water-soluble derivatives show good biocompatibility and have low cytotoxicity. Thanks to their chemical–physical characteristics, calixarenes can be easily functionalized, and by itself can encapsulate host molecules forming nanostructures capable of releasing drugs in a controlled way. The encapsulation of anticancer drugs in a calixarene derivate improves their bioavailability and efficacy. Thus, the use of calixarenes as carriers of anticancer drugs could reduce their side effects and increase their affinity towards the target. This review summarizes the numerous research advances regarding the development of calixarene nanoparticles capable of encapsulating various anticancer drugs.
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Mockler NM, Engilberge S, Rennie ML, Raston CL, Crowley PB. Protein-macrocycle framework engineering: supramolecular copolymerisation with two disparate calixarenes. Supramol Chem 2021. [DOI: 10.1080/10610278.2021.1935946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Niamh M. Mockler
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Colin L Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Bedford Park SA Adelaide, Australia
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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13
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Consoli GML, Tosto R, Baglieri A, Petralia S, Campagna T, Di Natale G, Zimbone S, Giuffrida ML, Pappalardo G. Novel Peptide-Calix[4]arene Conjugate Inhibits Aβ Aggregation and Rescues Neurons from Aβ's Oligomers Cytotoxicity In Vitro. ACS Chem Neurosci 2021; 12:1449-1462. [PMID: 33844495 PMCID: PMC9535895 DOI: 10.1021/acschemneuro.1c00117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
Alzheimer’s
disease (AD) is a progressive neurodegenerative
condition affecting people in the elderly. Targeting aggregation of
β-amyloid peptides (Aβ) is considered a promising approach
for the therapeutic treatment of the disease. Peptide based inhibitors
of β-amyloid fibrillation are emerging as safe drug candidates
as well as interesting compounds for early diagnosis of AD. Peptide
conjugation via covalent bond with functional moieties enables the
resultant hybrid system to acquire desired functions. Here we report
the synthesis, the structural characterization, and the Aβ42 interaction of a p-amino-calix[4]arene
derivative bearing a GPGKLVFF peptide pendant at the lower rim. We
demonstrate that the p-amino-calix[4]arene–GPGKLVFF
conjugate alters the Aβ42 aggregation pathways by
preventing Aβ42’s conformational transition
from random coil to β-sheet with concomitant changes of the
aggregation kinetic profile as evidenced by circular dichroism (CD),
thioflavin T (ThT), and dynamic light scattering (DLS) measurements,
respectively. High resolution mass spectrometry (HR-MS) confirmed
a direct interaction of the p-amino-calix[4]arene–GPGKLVFF
conjugate with Aβ42 monomer which provided insight
into a possible working mechanism, whereas the alteration of the Aβ42’s fibrillary architecture, by the calix-peptide conjugate,
was further validated by atomic force microscopy (AFM) imaging. Finally,
the herein proposed compound was shown to be effective against Aβ42 oligomers’ toxicity in differentiated neuroblastoma
cells, SH-SY5Y.
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Affiliation(s)
| | - Rita Tosto
- International PhD School of Chemical Sciences, University of Catania, V.le A. Doria 6, 95125 Catania, Italy
- CNR-Institute of Crystallography, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ausilia Baglieri
- CNR-Institute of Biomolecular Chemistry, Via P. Gaifami 18, 95126 Catania, Italy
| | - Salvatore Petralia
- Department of Drug Sciences and Health, University of Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Tiziana Campagna
- CNR-Institute of Crystallography, Via P. Gaifami 18, 95126 Catania, Italy
| | - Giuseppe Di Natale
- CNR-Institute of Crystallography, Via P. Gaifami 18, 95126 Catania, Italy
| | - Stefania Zimbone
- CNR-Institute of Crystallography, Via P. Gaifami 18, 95126 Catania, Italy
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14
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Mockler N, Ramberg KO, Guagnini F, Raston CL, Crowley PB. Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with α-Helical Recognition Properties. CRYSTAL GROWTH & DESIGN 2021; 21:1424-1427. [PMID: 34054353 PMCID: PMC8154262 DOI: 10.1021/acs.cgd.0c01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Water-soluble, anionic calix[n]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene (sclx 8 ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger receptor would have increased capacity for protein masking/encapsulation. A cocrystal structure of p-benzyl-sulfonato-calix[8]arene (b-sclx 8 ) and cytochrome c (cyt c) revealed a surprising assembly. A pseudorotaxane comprising a stack of three b-sclx 8 molecules threaded by polyethylene glycol (PEG) was bound to the protein. The trimeric b-sclx 8 stack, a tubelike structure with a highly charged surface, mediated assembly via a new mode of protein recognition. The calixarene stack presents four hydrophobic grooves, each of which binds to one cyt c by accommodating the N-terminal α-helix. This unprecedented binding mode suggests new possibilities for supramolecular protein chemistry.
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Affiliation(s)
- Niamh
M. Mockler
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Kiefer O. Ramberg
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Francesca Guagnini
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Colin L. Raston
- Flinders
Institute for Nanoscale Science and Technology, College of Science
and Engineering, Flinders University, Bedford Park, South 5042, Australia
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
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15
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Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene. J Struct Biol 2021; 213:107711. [PMID: 33631304 DOI: 10.1016/j.jsb.2021.107711] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/14/2022]
Abstract
Controlled protein assembly holds great potential in the fabrication of biohybrid materials. However, the structural diversity and complexity of proteins present an obstacle to controlled assembly. Supramolecular chemistry is a possible solution as it offers tools to mediate self-assembly with molecular precision. This paper deals with the calixarene- and zinc-mediated assembly and crystallization of the histidine-rich Penicillium chrysogenum antifungal protein B (PAFB). We report crystal structures of pure PAFB, PAFB in complex with Zn2+, and the ternary complex of PAFB, Zn2+ and sulfonato-calix[8]arene (sclx8). A comparison of the three crystal structures revealed the structural plasticity of PAFB. While the flexible and highly anionic sclx8 resulted in large molecular weight aggregates of PAFB in solution, diffraction-quality crystals of PAFB-sclx8 were not obtained. We report crystals of PAFB-Zn2+-sclx8 in which a trinuclear zinc cluster occurred adjacent to a calixarene binding site. Interestingly, the combination of sclx8 complexation and zinc coordination resulted in a porous framework with channels of circa 2 nm diameter. Detailed analysis of the crystal structure highlighted novel molecular recognition features. This research enriches the set of supramolecular interactions available to promote protein assembly.
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16
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Hämisch B, Pollak R, Ebbinghaus S, Huber K. Thermodynamic Analysis of the Self‐Assembly of Pseudo Isocyanine Chloride in the Presence of Crowding Agents. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Roland Pollak
- Physical and Theoretical Chemistry TU Braunschweig 38106 Braunschweig Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry TU Braunschweig 38106 Braunschweig Germany
| | - Klaus Huber
- Physical Chemistry Paderborn University 33098 Paderborn Germany
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17
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Ramberg KO, Engilberge S, Guagnini F, Crowley PB. Protein recognition by cucurbit[6]uril: high affinity N-terminal complexation. Org Biomol Chem 2021; 19:837-844. [PMID: 33406171 DOI: 10.1039/d0ob02356f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The donut-shaped cucurbit[n]urils (Qn, n = 6-8) are rigid macrocyclic receptors with widespread use in protein recognition. To date, most applications have centred on the encapsulation of N-terminal aromatic residues by Q7 or Q8. Less attention has been placed on Q6, which can recognize lysine side chains due to its high affinity for alkylamines. In this work, we investigated protein-Q6 complexation by using NMR spectroscopy. Attempts to crystallize protein-Q6 complexes were thwarted by the crystallization of Q6. We studied four proteins that vary in size, net charge, and lysine content. In addition to Q6 interactions with specific Lys or dimethylated Lys residues, we report striking evidence for N-terminal recognition. High affinity (micromolar) binding occurred with the N-terminal Met-Lys motif present in one of the four model proteins. Engineering this feature into another model protein yielded a similar high affinity site. We also present evidence for Q8 binding at this N-terminal feature. These data expand the cucurbituril toolkit for protein sensing.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
| | - Francesca Guagnini
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
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18
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Ramberg KO, Engilberge S, Skorek T, Crowley PB. Facile Fabrication of Protein-Macrocycle Frameworks. J Am Chem Soc 2021; 143:1896-1907. [PMID: 33470808 PMCID: PMC8154523 DOI: 10.1021/jacs.0c10697] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Precisely defined protein aggregates,
as exemplified by crystals,
have applications in functional materials. Consequently, engineered
protein assembly is a rapidly growing field. Anionic calix[n]arenes
are useful scaffolds that can mold to cationic proteins and induce
oligomerization and assembly. Here, we describe protein-calixarene
composites obtained via cocrystallization of commercially available
sulfonato-calix[8]arene (sclx8) with the symmetric and “neutral” protein RSL. Cocrystallization
occurred across a wide range of conditions and protein charge states,
from pH 2.2–9.5, resulting in three crystal forms. Cationization
of the protein surface at pH ∼ 4 drives calixarene complexation
and yielded two types of porous frameworks with pore diameters >3
nm. Both types of framework provide evidence of protein encapsulation
by the calixarene. Calixarene-masked proteins act as nodes within
the frameworks, displaying octahedral-type coordination in one case.
The other framework formed millimeter-scale crystals within hours,
without the need for precipitants or specialized equipment. NMR experiments
revealed macrocycle-modulated side chain pKa values and suggested a mechanism for pH-triggered assembly.
The same low pH framework was generated at high pH with a permanently
cationic arginine-enriched RSL variant. Finally, in addition to protein
framework fabrication, sclx8 enables de novo structure determination.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Tomasz Skorek
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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19
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Bartocci A, Gillet N, Jiang T, Szczepaniak F, Dumont E. Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C. J Phys Chem B 2020; 124:11371-11378. [PMID: 33270456 DOI: 10.1021/acs.jpcb.0c08482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies [comparison between the molecular mechanics Poisson-Boltzmann surface area analysis and the isothermal titration calorimetry measurements]. The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically driven association and notably the role of arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of a hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way toward an automated procedure to predict the supramolecular protein-cage association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.
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Affiliation(s)
- Alessio Bartocci
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Natacha Gillet
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Tao Jiang
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Florence Szczepaniak
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Elise Dumont
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.,Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
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20
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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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21
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Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
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Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
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22
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Gorbunov A, Iskandarova A, Puchnin K, Nenajdenko V, Kovalev V, Vatsouro I. A route to virtually unlimited functionalization of water-soluble p-sulfonatocalix[4]arenes. Chem Commun (Camb) 2020; 56:4122-4125. [PMID: 32166302 DOI: 10.1039/d0cc01196g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The functionality of p-sulfonatocalix[4]arenes can be easily extended using the propargylation/CuAAC reaction sequence, which allows the introduction of up to four substituted triazole units to the narrow rims of the macrocycles while maintaining their cone shapes and water solubility and, thus, biomedical applicability.
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Affiliation(s)
- Alexander Gorbunov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Anna Iskandarova
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Kirill Puchnin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Valentine Nenajdenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Vladimir Kovalev
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Ivan Vatsouro
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
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23
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Two small, cysteine-rich and cationic antifungal proteins from Penicillium chrysogenum: A comparative study of PAF and PAFB. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183246. [PMID: 32142818 PMCID: PMC7138148 DOI: 10.1016/j.bbamem.2020.183246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Penicillium chrysogenum Q176 secretes the antimicrobial proteins (AMPs) PAF and PAFB, which share a compact disulfide-bond mediated, β-fold structure rendering them highly stable. These two AMPs effectively inhibit the growth of human pathogenic fungi in micromolar concentrations and exhibit antiviral potential without causing cytotoxic effects on mammalian cells in vitro and in vivo. The antifungal mechanism of action of both AMPs is closely linked to - but not solely dependent on - the lipid composition of the fungal cell membrane and requires a strictly regulated protein uptake into the cell, indicating that PAF and PAFB are not canonical membrane active proteins. Variations in their antifungal spectrum and their killing dynamics point towards a divergent mode of action related to their physicochemical properties and surface charge distribution. In this review, we relate characteristic features of PAF and PAFB to the current knowledge about other AMPs of different sources. In addition, we present original data that have never been published before to substantiate our assumptions and provide evidences that help to explain and understand better the mechanistic function of PAF and PAFB. Finally, we underline the promising potential of PAF and PAFB as future antifungal therapeutics. Penicillium chrysogenum secretes the small, cysteine-rich proteins PAF and PAFB. Both exhibit antifungal activity, but with differences in their mode of action. Structure, membrane interaction and cellular uptake determine their function. PAF and PAFB are well tolerated by mammalian cells. They promise applicability in medicine, plant protection and food industry.
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24
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Abstract
The articles in crystal engineering and structural chemistry in IUCrJ published from 2019 onwards reflect the breadth and outreach of this new and important subject.
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Affiliation(s)
- Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
- Correspondence e-mail:
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25
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Affiliation(s)
- Yuliya Razuvayeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Ruslan Kashapov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Lucia Zakharova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Kazan, Russia
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26
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Ramanujam V, Shen Y, Ying J, Mobli M. Residual Dipolar Couplings for Resolving Cysteine Bridges in Disulfide-Rich Peptides. Front Chem 2020; 7:889. [PMID: 32039137 PMCID: PMC6987419 DOI: 10.3389/fchem.2019.00889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Disulfide bridges in proteins are formed by the oxidation of pairs of cysteine residues. These cross-links play a critical role in stabilizing the 3D-structure of small disulfide rich polypeptides such as hormones and venom toxins. The arrangement of the multiple disulfide bonds directs the peptide fold into distinct structural motifs that have evolved for resistance against biochemical and physical insults. These structural scaffolds have, therefore, proven to be very attractive in bioengineering efforts to develop novel biologics with applications in health and agriculture. Structural characterization of small disulfide rich peptides (DRPs) presents unique challenges when using commonly applied biophysical methods. NMR is the most commonly used method for studying such molecules, where the relatively small size of these molecules results in highly precise structural ensembles defined by a large number of distance and dihedral angle restraints per amino acid. However, in NMR the sulfur atoms that are involved in three of the five dihedral angles in a disulfide bond cannot be readily measured. Given the central role of disulfide bonds in the structure of these molecules, it is unclear what the inherent resolution of such NMR structures is when using traditional NMR methods. Here, we use an extensive set of long-range residual dipolar couplings (RDCs) to assess the resolution of the NMR structure of a disulfide-rich peptide. We find that structures based primarily on NOEs, yield ensembles that are equivalent to a crystallographic resolution of 2-3 Å in resolution, and that incorporation of RDCs reduces this to ~1-1.5 Å resolution. At this resolution the sidechain of ordered amino acids can be defined accurately, allowing the geometry of the cysteine bridges to be better defined, and allowing for disulfide-bond connectivities to be determined with high confidence. The observed improvements in resolution when using RDCs is remarkable considering the small size of these peptides.
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Affiliation(s)
- Venkatraman Ramanujam
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
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27
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Vandebroek L, Noguchi H, Kamata K, Tame JRH, Van Meervelt L, Parac-Vogt TN, Voet ARD. Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry. Chem Commun (Camb) 2020; 56:11601-11604. [DOI: 10.1039/d0cc05071g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A symmetric designer protein forms hybrid complexes with different polyoxometalates and may serve as a building block for porous frameworks.
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Affiliation(s)
- Laurens Vandebroek
- Laboratory for Bioinorganic Chemistry
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
- Biomolecular Architecture
| | - Hiroki Noguchi
- Laboratory for Biomolecular Modelling and Design
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Kenichi Kamata
- Drug Design Laboratory
- Yokohama City University 1-7-29
- Yokohama
- Japan
| | | | - Luc Van Meervelt
- Biomolecular Architecture
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Tatjana N. Parac-Vogt
- Laboratory for Bioinorganic Chemistry
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Arnout R. D. Voet
- Laboratory for Biomolecular Modelling and Design
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
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28
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Alex JM, McArdle P, Crowley PB. Supramolecular stacking in a high Z′ calix[8]arene–porphyrin assembly. CrystEngComm 2020. [DOI: 10.1039/c9ce01646e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A co-crystal structure of sulfonato-calix[8]arene (sclx8) and trimethylanilinium-porphyrin (tmap) at 1.0 Å resolution is reported.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Patrick McArdle
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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29
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Guagnini F, Engilberge S, Ramberg KO, Pérez J, Crowley PB. Engineered assembly of a protein–cucurbituril biohybrid. Chem Commun (Camb) 2020; 56:360-363. [DOI: 10.1039/c9cc07198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Additional Q7 binding sites drive protein aggregation in solution and statistical disorder in the crystalline biohybrid suggest new possibilities for protein-based materials.
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Affiliation(s)
| | | | - Kiefer O. Ramberg
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Javier Pérez
- Synchrotron SOLEIL
- L’Orme des Merisiers
- 91192 Gif-sur-Yvette Cedex
- France
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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30
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Alex JM, Brancatelli G, Volpi S, Bonaccorso C, Casnati A, Geremia S, Crowley PB. Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org Biomol Chem 2020; 18:211-214. [DOI: 10.1039/c9ob02275a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| | - Giovanna Brancatelli
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Carmela Bonaccorso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- Catania
- Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
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31
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Seyfi R, Kahaki FA, Ebrahimi T, Montazersaheb S, Eyvazi S, Babaeipour V, Tarhriz V. Antimicrobial Peptides (AMPs): Roles, Functions and Mechanism of Action. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09946-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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32
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Engilberge S, Rennie ML, Dumont E, Crowley PB. Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. ACS NANO 2019; 13:10343-10350. [PMID: 31490058 DOI: 10.1021/acsnano.9b04115] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This "switch" calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein "pillar", resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host-guest interactions.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Martin L Rennie
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , 69342 Lyon , France
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
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33
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Setner B, Szumna A. Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media - circular dichroism and diffusion studies of chirality transfer and solvent dependence. Beilstein J Org Chem 2019; 15:1913-1924. [PMID: 31501658 PMCID: PMC6720235 DOI: 10.3762/bjoc.15.187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 11/23/2022] Open
Abstract
Directional self‐assembly of conformationally well-defined complexes in polar environment is still a major challenge in supramolecular chemistry. In the present study we demonstrate that resorcin[4]arene sulfonic acid (RSA) interacts with chiral amines (amino acid derivatives and aminocavitands) to form inclusion complexes and capsules based on electrostatic interactions. The complexes were characterized by circular dichroism and DOSY NMR spectroscopy. Chirality transfer from amines onto a resorcinarene skeleton was manifested by the appearance of signals in CD spectra and diastereotopic splitting in NMR spectra. The complexes proved to be thermodynamically stable in methanol, but DMSO and methanol/water mixtures were found to be highly disintegrative for these complexes. This result is quite non-intuitive and worth attention in the context of formation of supramolecular complexes in polar environment, for which DMSO is most often a first-choice solvent.
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Affiliation(s)
- Bartosz Setner
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Engilberge S, Rennie ML, Crowley PB. Calixarene capture of partially unfolded cytochrome c. FEBS Lett 2019; 593:2112-2117. [PMID: 31254353 DOI: 10.1002/1873-3468.13512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/20/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
Supramolecular receptors such as water-soluble calixarenes are in development as 'molecular glues' for protein assembly. Here, we obtained cocrystals of sulfonato-calix[6]arene (sclx6 ) and yeast cytochrome c (cytc) in the presence of imidazole. A crystal structure at 2.65 Å resolution reveals major structural rearrangement and disorder in imidazole-bound cytc. The largest protein-calixarene interface involves 440 Å2 of the protein surface with key contacts at Arg13, Lys73, and Lys79. These lysines participate in alkaline transitions of cytc and are part of Ω-loop D, which is substantially restructured in the complex with sclx6 . The structural modification also includes Ω-loop C, which is disordered (residues 41-55 inclusive). These results suggest the possibility of using supramolecular scaffolds to trap partially disordered proteins.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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Rennie ML, Crowley PB. A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold. Chemphyschem 2019; 20:1011-1017. [DOI: 10.1002/cphc.201900153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
- Present address: Institute of Molecular Cell and System BiologyUniversity of Glasgow University Avenue Glasgow UK
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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Alex JM, Corvaglia V, Hu X, Engilberge S, Huc I, Crowley PB. Crystal structure of a protein–aromatic foldamer composite: macromolecular chiral resolution. Chem Commun (Camb) 2019; 55:11087-11090. [DOI: 10.1039/c9cc05330a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A protein–foldamer crystal structure illustrates protein assembly by a sulfonated aromatic oligoamide, and chiral resolution of the foldamer helix handedness.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Valentina Corvaglia
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | - Xiaobo Hu
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | | | - Ivan Huc
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
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