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He J, Bai M, Xiao X, Qiu S, Chen W, Li J, Yu Y, Tian W. Intramolecular Cation-π Interactions Organize Bowl-Shaped, Luminescent Molecular Containers. Angew Chem Int Ed Engl 2024; 63:e202402697. [PMID: 38433608 DOI: 10.1002/anie.202402697] [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: 02/06/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Molecules with nonplanar architectures are highly desirable due to their unique topological structures and functions. We report here the synthesis of two molecular containers (1 ⋅ 3Br- and 1 ⋅ 3Cl-), which utilize intramolecular cation-π interactions to enforce macrocylic arrangements and exhibit high binding affinity and luminescent properties. Remarkably, the geometry of the cation-π interaction can be flexibly tailored to achieve a precise ring arrangement, irrespective of the angle of the noncovalent bonds. Additionally, the C-H⋅⋅⋅Br- hydrogen bonds within the container are also conducive to stabilizing the bowl-shaped conformation. These bowl-shaped conformations were confirmed both in solution through NMR spectroscopy and in the solid state by X-ray studies. 1 ⋅ 3Br- shows high binding affinity and selectivity: F->Cl-, through C-H⋅⋅⋅X- (X=F, Cl) hydrogen bonds. Additionally, these containers exhibited blue fluorescence in solution and yellow room-temperature phosphorescence (RTP) in the solid state. Our findings illustrate the utility of cation-π interactions in designing functional molecules.
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Affiliation(s)
- Jia He
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Minggui Bai
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Xuedong Xiao
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Shuai Qiu
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Wenzhuo Chen
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Jiaqi Li
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai, 200444, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
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Palica K, Deufel F, Skagseth S, Di Santo Metzler GP, Thoma J, Andersson Rasmussen A, Valkonen A, Sunnerhagen P, Leiros HKS, Andersson H, Erdelyi M. α-Aminophosphonate inhibitors of metallo-β-lactamases NDM-1 and VIM-2. RSC Med Chem 2023; 14:2277-2300. [PMID: 38020072 PMCID: PMC10650955 DOI: 10.1039/d3md00286a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 12/01/2023] Open
Abstract
The upswing of antibiotic resistance is an escalating threat to human health. Resistance mediated by bacterial metallo-β-lactamases is of particular concern as these enzymes degrade β-lactams, our most frequently prescribed class of antibiotics. Inhibition of metallo-β-lactamases could allow the continued use of existing β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems, whose applicability is becoming ever more limited. The design, synthesis, and NDM-1, VIM-2, and GIM-1 inhibitory activities (IC50 4.1-506 μM) of a series of novel non-cytotoxic α-aminophosphonate-based inhibitor candidates are presented herein. We disclose the solution NMR spectroscopic and computational investigation of their NDM-1 and VIM-2 binding sites and binding modes. Whereas the binding modes of the inhibitors are similar, VIM-2 showed a somewhat higher conformational flexibility, and complexed a larger number of inhibitor candidates in more varying binding modes than NDM-1. Phosphonate-type inhibitors may be potential candidates for development into therapeutics to combat metallo-β-lactamase resistant bacteria.
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Affiliation(s)
- Katarzyna Palica
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Fritz Deufel
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Susann Skagseth
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Gabriela Paula Di Santo Metzler
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Johannes Thoma
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Anna Andersson Rasmussen
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla Survontie 9B 40014 Finland
| | - Per Sunnerhagen
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Hanna Andersson
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
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Ding W, Zhao H, Chen Y, Lin S. New Strategies for Probing the Biological Functions of Protein Post-translational Modifications in Mammalian Cells with Genetic Code Expansion. Acc Chem Res 2023; 56:2827-2837. [PMID: 37793174 DOI: 10.1021/acs.accounts.3c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Protein post-translational modification (PTM) is a major mechanism for functional diversification of the human genome and plays a crucial role in almost every aspect of cellular processes, and the dysregulation of the protein PTM network has been associated with a variety of human diseases. Using high-resolution mass spectrometry, protein PTMs can be efficiently discovered and profiled under various biological and physiological conditions. However, it is often challenging to address the biological function of PTMs with biochemical and mutagenesis-based approaches. Specifically, this field lacks methods that allow gain-of-function studies of protein PTMs to understand their functional consequences in living cells. In this context, the genetic code expansion (GCE) strategy has made tremendous progress in the direct installation of PTMs and their analogs in the form of noncanonical amino acids (ncAAs) for gain-of-function investigations.In addition to studying the biological functions of known protein PTMs, the discovery of new protein PTMs is even more challenging due to the lack of chemical information for designing specific enrichment methods. Genetically encoded ncAAs in the proteome can be used as specific baits to enrich and subsequently identify new PTMs by mass spectrometry.In this Account, we discuss recent developments in the investigation of the biological functions of protein PTMs and the discovery of protein PTMs using new GCE strategies. First, we leveraged a chimeric design to construct several broadly orthogonal translation systems (OTSs). These broad OTSs can be engineered to efficiently incorporate different ncAAs in both E. coli and mammalian cells. With these broad OTSs, we accomplish the following: (1) We develop a computer-aided strategy for the design and genetic incorporation of length-tunable lipidation mimics. These lipidation mimics can fully recapitulate the biochemical properties of natural lipidation in membrane association for probing its biological functions on signaling proteins and in albumin binding for designing long-acting protein drugs. (2) We demonstrate that the binding affinity between histone methylations and their corresponding readers can be substantially increased with genetically encoded electron-rich Trp derivatives. These engineered affinity-enhanced readers can be applied to enrich, image, and profile the interactome of chromatin methylations. (3) We report the identification and verification of a novel type of protein PTM, aminoacylated lysine ubiquitination, using genetically encoded PTM ncAAs as chemical probes. This approach provides a general strategy for the identification of unknown PTMs by increasing the abundance of PTM bait probes.
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Affiliation(s)
- Wenlong Ding
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hongxia Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Shaoxing Institute, Zhejiang University, Shaoxing 321000, China
| | - Shixian Lin
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Shaoxing Institute, Zhejiang University, Shaoxing 321000, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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Prakash M, Rudharachari Maiyelvaganan K, Lakshman NG, Mogren Al-Mogren M, Hochlaf M. Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces. Chemphyschem 2023; 24:e202300267. [PMID: 37283005 DOI: 10.1002/cphc.202300267] [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: 04/16/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.
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Affiliation(s)
- Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - K Rudharachari Maiyelvaganan
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - N Giri Lakshman
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - Muneerah Mogren Al-Mogren
- Department of Chemistry, College of Sciences, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454, Champs Sur Marne, France
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Spencer TA, Ditchfield R. Tryptophan Stabilization of a Biochemical Carbocation Evaluated by Analysis of π Complexes of 3-Ethylindole with the t-Butyl Cation. ACS OMEGA 2023; 8:26497-26507. [PMID: 37521644 PMCID: PMC10373456 DOI: 10.1021/acsomega.3c03259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Understanding how the highly unstable carbocation intermediates in terpenoid biosynthesis are stabilized and protected during their transient existence in enzyme active sites is an intriguing challenge which has to be addressed computationally. Our efforts have focused on evaluating the stabilization afforded via carbocation-π complexation between a biochemical carbocation and an aromatic amino acid residue. This has involved making measurements on an X-ray structure of an enzyme active site that shows a π donor proximate to a putative carbocation site and using these to build models which are analyzed computationally to provide an estimated stabilization energy (SE). Previously, we reported estimated SEs for several such carbocation-π complexes involving phenylalanine. Herein, we report the first such estimate involving tryptophan as the π donor. Because there was almost no published information about indole as a π-complexation donor, we first located computationally equilibrium π and σ complexes of 3-ethylindole with the t-butyl cation as relevant background information. Then, measurements on the X-ray structure of the enzyme CotB2 complexed with geranylgeranyl thiodiphosphate (GGSPP), specifically on the geometric relationship of the putative carbocation at C15 of GGSPP to W186, were used to build a model that afforded a computed SE of -15.3 kcal/mol.
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6
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Panwaria P, Das A. Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study. J Phys Chem A 2023; 127:3339-3346. [PMID: 37036493 DOI: 10.1021/acs.jpca.2c08641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA. Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat Commun 2023; 14:59. [PMID: 36599844 PMCID: PMC9813137 DOI: 10.1038/s41467-022-35761-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.
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Affiliation(s)
- Grace D Galles
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Colin J Clark
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Marcus L Hemshorn
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Shivani Manikandan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Frederico Fazan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Richard B Cooley
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Ryan A Mehl
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA.
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Li Z, Chan KC, Nickels JD, Cheng X. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B 2022; 126:8669-8679. [PMID: 36260486 PMCID: PMC10056799 DOI: 10.1021/acs.jpcb.2c04641] [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] [Indexed: 01/11/2023]
Abstract
Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
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Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
- Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio43210, United States
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Knox HJ, Rego Campello H, Lester HA, Gallagher T, Dougherty DA. Characterization of Binding Site Interactions and Selectivity Principles in the α3β4 Nicotinic Acetylcholine Receptor. J Am Chem Soc 2022; 144:16101-16117. [PMID: 36006801 DOI: 10.1021/jacs.2c06495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) play an important role in neurotransmission and are also involved in addiction and several disease states. There is significant interest in therapeutic targeting of nAChRs; however, achieving selectivity for one subtype over others has been a longstanding challenge, given the close structural similarities across the family. Here, we characterize binding interactions in the α3β4 nAChR subtype via structure-function studies involving noncanonical amino acid mutagenesis and two-electrode voltage clamp electrophysiology. We establish comprehensive binding models for both the endogenous neurotransmitter ACh and the smoking cessation drug cytisine. We also use a panel of C(10)-substituted cytisine derivatives to probe the effects of subtle changes in the ligand structure on binding. By comparing our results to those obtained for the well-studied α4β2 subtype, we identify several features of both the receptor and agonist structure that can be utilized to enhance selectivity for either α3β4 or α4β2. Finally, we characterize binding interactions of the α3β4-selective partial agonist AT-1001 to determine factors that contribute to its selectivity. These results shed new light on the design of selective nAChR-targeted ligands and can be used to inform the design of improved therapies with minimized off-target effects.
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Affiliation(s)
- Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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10
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Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
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11
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Structure and mechanism for iterative amide N-methylation in the biosynthesis of channel-forming peptide cytotoxins. Proc Natl Acad Sci U S A 2022; 119:e2116578119. [PMID: 35316135 PMCID: PMC9060474 DOI: 10.1073/pnas.2116578119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The channel-forming proteusins are bacterial helical peptides that allow permeation of positively charged ions to influence membrane potential and cellular physiology. We biochemically characterize the effect of two critical posttranslational modifications on the secondary structure of the peptide substrate. We determine how a methyl group can be added to the side chains of D-Asn residues in a peptide substrate and show how flanking residues influence selectivity. These studies should foster the development of small-molecule peptide ion channels as therapeutics. The polytheonamides are highly modified and potent, cytotoxic peptides with a unique β-helical structure (helical diameter ∼4 Å) that affords selective membrane permeation of monovalent cations. Toxicity has been linked to promiscuous ion-channel behavior in studies of the prototypical polytheonamide B. Specific structural features of the β-helical toxins include, among other modifications, Cα-epimerizations and Nγ-methylations, which have been highlighted as the early-stage modifications most critical for β-helix formation. Here, we interrogate Cα-epimerization and Nγ-methylation to understand the importance of these modifications for secondary structure. We characterize the mechanism of Nγ-methylations on the amide side chains of D-Asn, an enzymatic modification with little biochemical precedent. Crystal structures of the AerE methyltransferase in complex with its epimerized peptide substrate and S-adenosyl-homocysteine reveal features of substrate recognition and an unexpected metal-ion that may mediate methyl transfer to the poorly nucleophilic amide. These studies provide a framework for the engineering of novel β-helical peptides with ion and membrane selectivity.
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12
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Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. J Am Chem Soc 2022; 144:2535-2545. [PMID: 35108000 PMCID: PMC8923077 DOI: 10.1021/jacs.1c09902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.
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Affiliation(s)
- Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Rodney Park
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
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13
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Yadav N, Dhilip Kumar TJ. Si doped T-graphene: a 2D lattice as an anode electrode in Na ion secondary batteries. NEW J CHEM 2022. [DOI: 10.1039/d2nj01009g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Heteroatom doping into 2-dimensional lattices of materials such as graphene brings revolutionary reform in the field of materials endowing the parent material with remarkable properties.
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Affiliation(s)
- Neha Yadav
- Quantum Dynamics Lab, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar 140001, India
| | - T. J. Dhilip Kumar
- Quantum Dynamics Lab, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar 140001, India
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14
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Simultaneous Interaction of Graphene Nanoflakes with Cations and Anions: A Cooperativity Study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Investigations on the role of cation-π interactions in active centers of superoxide dismutase. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2022. [DOI: 10.2298/jsc220109013s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this study, we have analysed the influence of cation-? interactions on
stability and properties of superoxide dismutase (SOD) active centres. The
number of interactions formed by arginine is higher than lysine in the
cationic group, while histidine is comparatively higher in the ? group. The
energy contribution resulting from most frequent cation-? interactions was
in the lower range of strong hydrogen bonds. The cation-? interactions
involving transition metal ions as cation have energy more negative than
-418.4 kJ mol-1. Stabilization centres for these proteins showed that all
residues involved in cation-? interactions were important in locating one or
more of such centres. The majority of the residues involved in cation-p
interactions were evolutionarily conserved and might have a significant
contribution towards the stability of SOD proteins. The results presented in
this work can be very useful for understanding the contribution of cation-?
interactions to the stability of SOD active canters.
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16
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Helfrich F, Scheidig AJ. Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. Acta Crystallogr D Struct Biol 2021; 77:1317-1335. [PMID: 34605434 PMCID: PMC8489232 DOI: 10.1107/s2059798321008937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
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Affiliation(s)
- F. Helfrich
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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17
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Cation-π Interactions and their Functional Roles in Membrane Proteins. J Mol Biol 2021; 433:167035. [PMID: 33957146 PMCID: PMC8338773 DOI: 10.1016/j.jmb.2021.167035] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 01/25/2023]
Abstract
Cation-π interactions arise as a result of strong attractive forces between positively charged entities and the π-electron cloud of aromatic groups. The physicochemical characteristics of cation-π interactions are particularly well-suited to the dual hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins bring molecular features into increasingly sharper view, cation-π interactions are gaining traction as essential contributors to membrane protein chemistry, function, and pharmacology. Here we review the physicochemical properties of cation-π interactions and present several prominent examples which demonstrate significant roles for this specialized biological chemistry.
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18
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Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM. Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1. ACS Chem Biol 2021; 16:1159-1163. [PMID: 34165961 DOI: 10.1021/acschembio.1c00326] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nuclear receptor-related 1 protein, Nurr1, is a transcription factor critical for the development and maintenance of dopamine-producing neurons in the substantia nigra pars compacta, a cell population that progressively loses the ability to make dopamine and degenerates in Parkinson's disease. Recently, we demonstrated that Nurr1 binds directly to and is regulated by the endogenous dopamine metabolite 5,6-dihydroxyindole (DHI). Unfortunately, DHI is an unstable compound, and thus a poor tool for studying Nurr1 function. Here, we report that 5-chloroindole, an unreactive analog of DHI, binds directly to the Nurr1 ligand binding domain with micromolar affinity and stimulates the activity of Nurr1, including the transcription of genes governing the synthesis and packaging of dopamine.
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19
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Mu L, Yang Y, Liu J, Du W, Chen J, Shi G, Fang H. Hydrated cation-π interactions of π-electrons with hydrated Li +, Na +, and K + cations. Phys Chem Chem Phys 2021; 23:14662-14670. [PMID: 34213518 DOI: 10.1039/d1cp01609a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.
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Affiliation(s)
- Liuhua Mu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Yang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China.
| | - Jian Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jige Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute and State Key Lab. Advanced Special Steel, Shanghai University, Shanghai 200444, China.
| | - Haiping Fang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China. and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
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20
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Ronchi E, Paradine SM, Jacobsen EN. Enantioselective, Catalytic Multicomponent Synthesis of Homoallylic Amines Enabled by Hydrogen-Bonding and Dispersive Interactions. J Am Chem Soc 2021; 143:7272-7278. [PMID: 33949857 PMCID: PMC8547772 DOI: 10.1021/jacs.1c03024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a one-step catalytic, enantioselective method for the preparation of homoallylic N-Boc amines directly from acetals. Reactive iminium ion intermediates are generated in situ through the combination of an acetal, a chiral thiourea catalyst, trialkylsilyl triflate, and N-Boc carbamate and are subsequently trapped by a variety of allylsilane nucleophiles. No homoallylic ether byproducts are detected, consistent with allylation of the iminium intermediate being highly favored over allylation of the intermediate oxocarbenium ion. Acetals derived from aromatic aldehydes possessing a variety of functional groups and substitution patterns yield homoallylic amines with excellent levels of enantiomeric enrichment. Experimental and computational data are consistent with an anchoring hydrogen-bond interaction between the protioiminium ion and the amide of the catalyst in the enantiodetermining transition state, and with stereodifferentiation achieved through specific noncovalent interactions (NCIs) with the catalyst pyrenyl moiety. Evidence is provided that the key NCI in the major pathway is a π-stacking interaction, contrasting with the cation-π interactions invoked in previously studied reactions promoted by the same family of aryl-pyrrolidino-H-bond-donor catalysts.
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Affiliation(s)
| | | | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
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21
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Yadav N, Chakraborty B, Dhilip Kumar TJ. First-principles study of a 2-dimensional C-silicyne monolayer as a promising anode in Na/K ion secondary batteries. Phys Chem Chem Phys 2021; 23:11755-11763. [PMID: 33982721 DOI: 10.1039/d1cp01538a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
With the depleting resources of energy and increasing demand, the need for sustainable and renewable energy resources has become the need of the hour. The low storage capacity of current materials for Na/K ion batteries has led to the quest to identify suitable materials for an electrode with excellent electrochemical properties. In the present work, a systematic theoretical investigation of C-silicyne, a planar 2-dimensional hexagonal lattice, is performed to establish the geometric and thermal properties and stability. The electronic properties illustrate the metallic nature of C-silicyne, which is conserved even after the effective adsorption of Na/K ions on the surface of the monolayer. For the practical functionality, the storage capacity of C-silicyne is evaluated as 591 mA h g-1 for Na ions and 443 mA h g-1 for K ions. Moreover, the low diffusion barriers for the Na (0.57 eV) and K (0.34 eV) ions display their feasible movement across the monolayer as the electrochemical cycle progresses. The average working voltage is found to lie in the range of 0.1-1 V, which is required for the effective functioning of the anode in a Na/K ion battery. These results demonstrate the potential of C-silicyne as a material for the anode in Na/K ion batteries.
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Affiliation(s)
- Neha Yadav
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, 140001, India.
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India and Homi Bhabha National Institute, Mumbai, 400094, India
| | - T J Dhilip Kumar
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, 140001, India.
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22
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Kodama K, Takase F, Hirose T. Direct enantioseparation of axially chiral 1,1′-biaryl-2,2′-diols using amidine-based resolving agents. RSC Adv 2021; 11:18162-18170. [PMID: 35480945 PMCID: PMC9033420 DOI: 10.1039/d1ra03546k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022] Open
Abstract
Amidine-based optically active resolving agents for enantiomer separation of axially chiral 1,1′-biaryl-2,2′-diols have been developed. A strongly basic amidine bearing no substituents on its nitrogen atoms enables the formation of their diastereomeric salts upon being mixed with weakly acidic phenol derivatives. Enantiopure 1,1′-biaryl-2,2′-diols can be obtained in high yields after only one crystallization of their salts with the chiral amidine derived from dehydroabietic acid. X-ray crystallography revealed that the amidine moiety forms a salt with the phenol group and additional intermolecular NH/π interactions contribute to the efficient chiral recognition process. Enantioseparation of atropisomeric biphenols using a chiral amidine derived from dehydroabietic acid was reported. Only one crystallization of their mixture gave pure diastereomeric salts of biphenols from racemate.![]()
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Affiliation(s)
- Koichi Kodama
- Department of Applied Chemistry
- Graduate School of Science and Engineering
- Saitama University
- Japan
| | - Fusato Takase
- Department of Applied Chemistry
- Graduate School of Science and Engineering
- Saitama University
- Japan
| | - Takuji Hirose
- Department of Applied Chemistry
- Graduate School of Science and Engineering
- Saitama University
- Japan
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23
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Parameters for Irreversible Inactivation of Monoamine Oxidase. Molecules 2020; 25:molecules25245908. [PMID: 33322203 PMCID: PMC7763263 DOI: 10.3390/molecules25245908] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
The irreversible inhibitors of monoamine oxidases (MAO) slow neurotransmitter metabolism in depression and neurodegenerative diseases. After oxidation by MAO, hydrazines, cyclopropylamines and propargylamines form a covalent adduct with the flavin cofactor. To assist the design of new compounds to combat neurodegeneration, we have updated the kinetic parameters defining the interaction of these established drugs with human MAO-A and MAO-B and analyzed the required features. The Ki values for binding to MAO-A and molecular models show that selectivity is determined by the initial reversible binding. Common to all the irreversible inhibitor classes, the non-covalent 3D-chemical interactions depend on a H-bond donor and hydrophobic-aromatic features within 5.7 angstroms apart and an ionizable amine. Increasing hydrophobic interactions with the aromatic cage through aryl halogenation is important for stabilizing ligands in the binding site for transformation. Good and poor inactivators were investigated using visible spectroscopy and molecular dynamics. The initial binding, close and correctly oriented to the FAD, is important for the oxidation, specifically at the carbon adjacent to the propargyl group. The molecular dynamics study also provides evidence that retention of the allenyl imine product oriented towards FADH− influences the formation of the covalent adduct essential for effective inactivation of MAO.
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24
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25
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Xing H, Andrud KW, Soti F, Rouchaud A, Jahn SC, Lu Z, Cho YH, Habibi S, Corsino P, Slavov S, Rocca JR, Lindstrom JM, Lukas RJ, Kem WR. A Methyl Scan of the Pyrrolidinium Ring of Nicotine Reveals Significant Differences in Its Interactions with α7 and α4 β2 Nicotinic Acetylcholine Receptors. Mol Pharmacol 2020; 98:168-180. [PMID: 32474444 DOI: 10.1124/mol.119.118786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/06/2020] [Indexed: 01/15/2023] Open
Abstract
The two major nicotinic acetylcholine receptors (nAChRs) in the brain are the α4β2 and α7 subtypes. A "methyl scan" of the pyrrolidinium ring was used to detect differences in nicotine's interactions with these two receptors. Each methylnicotine was investigated using voltage-clamp and radioligand binding techniques. Methylation at each ring carbon elicited unique changes in nicotine's receptor interactions. Replacing the 1'-N-methyl with an ethyl group or adding a second 1'-N-methyl group significantly reduced interaction with α4β2 but not α7 receptors. The 2'-methylation uniquely enhanced binding and agonist potency at α7 receptors. Although 3'- and 5'-trans-methylations were much better tolerated by α7 receptors than α4β2 receptors, 4'-methylation decreased potency and efficacy at α7 receptors much more than at α4β2 receptors. Whereas cis-5'-methylnicotine lacked agonist activity and displayed a low affinity at both receptors, trans-5'-methylnicotine retained considerable α7 receptor activity. Differences between the two 5'-methylated analogs of the potent pyridyl oxymethylene-bridged nicotine analog A84543 were consistent with what was found for the 5'-methylnicotines. Computer docking of the methylnicotines to the Lymnaea acetylcholine binding protein crystal structure containing two persistent waters predicted most of the changes in receptor affinity that were observed with methylation, particularly the lower affinities of the cis-methylnicotines. The much smaller effects of 1'-, 3'-, and 5'-methylations and the greater effects of 2'- and 4'-methylations on nicotine α7 nAChR interaction might be exploited for the design of new drugs based on the nicotine scaffold. SIGNIFICANCE STATEMENT: Using a comprehensive "methyl scan" approach, we show that the orthosteric binding sites for acetylcholine and nicotine in the two major brain nicotinic acetylcholine receptors interact differently with the pyrrolidinium ring of nicotine, and we suggest reasons for the higher affinity of nicotine for the heteromeric receptor. Potential sites for nicotine structure modification were identified that may be useful in the design of new drugs targeting these receptors.
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Affiliation(s)
- Hong Xing
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Kristin W Andrud
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Ferenc Soti
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Anne Rouchaud
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Stephan C Jahn
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Ziang Lu
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Yeh-Hyon Cho
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Sophia Habibi
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Patrick Corsino
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Svetoslav Slavov
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - James R Rocca
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Jon M Lindstrom
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - Ron J Lukas
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
| | - William R Kem
- Department of Pharmacology and Therapeutics (H.X., K.W.A., F.S., A.R., S.C.J., Z.L., Y.-H.C., S.H., P.C., W.R.K.) and AMRIS, McKnight Brain Institute (J.R.R.), College of Medicine, University of Florida, Gainesville, Florida; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas (S.S.); Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania (J.M.L.); and Division of Neurobiology, Barrow Neurologic Institute, Phoenix, Arizona (R.J.L.)
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26
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Van Den Broeck E, Verbraeken B, Dedecker K, Cnudde P, Vanduyfhuys L, Verstraelen T, Van Hecke K, Jerca VV, Catak S, Hoogenboom R, Van Speybroeck V. Cation−π Interactions Accelerate the Living Cationic Ring-Opening Polymerization of Unsaturated 2-Alkyl-2-oxazolines. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Elias Van Den Broeck
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Bart Verbraeken
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
| | - Karen Dedecker
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Pieter Cnudde
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Louis Vanduyfhuys
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-S3, B-9000 Ghent, Belgium
| | - Valentin Victor Jerca
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
- Centre for Organic Chemistry “Costin D. Nenitzescu”, Romanian Academy, 202B Spl. Independentei CP 35-108, Bucharest 060023, Romania
| | - Saron Catak
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
- Department of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
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27
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Mikhailov GP. Modeling of the Interaction of Cations of Alkali Metals with a Fragment of Graphene in the Environment of Benzene. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2020. [DOI: 10.1134/s1990793120010108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Ferretti A, d’Ischia M, Prampolini G. Benchmarking Cation−π Interactions: Assessment of Density Functional Theory and Möller–Plesset Second-Order Perturbation Theory Calculations with Optimized Basis Sets (mp2mod) for Complexes of Benzene, Phenol, and Catechol with Na+, K+, Rb+, and Cs+. J Phys Chem A 2020; 124:3445-3459. [DOI: 10.1021/acs.jpca.0c02090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Marco d’Ischia
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, I-80126 Napoli, Italy
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29
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Krone MW, Albanese KI, Leighton GO, He CQ, Lee GY, Garcia-Borràs M, Guseman AJ, Williams DC, Houk KN, Brustad EM, Waters ML. Thermodynamic consequences of Tyr to Trp mutations in the cation-π-mediated binding of trimethyllysine by the HP1 chromodomain. Chem Sci 2020; 11:3495-3500. [PMID: 34109021 PMCID: PMC8152637 DOI: 10.1039/d0sc00227e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Evolution has converged on cation–π interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation–π interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation–π interaction is about −5 kcal mol−1 stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation–π interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy–entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation–π interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains. In this work, we experimentally validate that tryptophan provides the strongest cation–π binding interaction among aromatic amino acids and also lend insight into the importance of residue identity in trimethyllysine recognition by reader proteins.![]()
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Affiliation(s)
- Mackenzie W Krone
- University of North Carolina at Chapel Hill 131 South Road, Campus Box 3290 Chapel Hill NC 27599 USA
| | - Katherine I Albanese
- University of North Carolina at Chapel Hill 131 South Road, Campus Box 3290 Chapel Hill NC 27599 USA
| | - Gage O Leighton
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill 120 Mason Farm Rd, Campus Box 7260 Chapel Hill NC 27599 USA
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, University of California at Los Angeles 607 Charles E. Young Drive East, Box 951569 Los Angeles CA 90095-1569 USA
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California at Los Angeles 607 Charles E. Young Drive East, Box 951569 Los Angeles CA 90095-1569 USA
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California at Los Angeles 607 Charles E. Young Drive East, Box 951569 Los Angeles CA 90095-1569 USA
| | - Alex J Guseman
- University of North Carolina at Chapel Hill 131 South Road, Campus Box 3290 Chapel Hill NC 27599 USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill Campus Box 7525, Brinkhous-Bullitt Building Chapel Hill NC 27599 USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill 450 West Drive Chapel Hill NC 27599 USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California at Los Angeles 607 Charles E. Young Drive East, Box 951569 Los Angeles CA 90095-1569 USA
| | - Eric M Brustad
- University of North Carolina at Chapel Hill 131 South Road, Campus Box 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- University of North Carolina at Chapel Hill 131 South Road, Campus Box 3290 Chapel Hill NC 27599 USA
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30
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Spencer TA, Ditchfield R. A simpler method affords evaluation of π stabilization by phenylalanine of several biochemical carbocations. Org Biomol Chem 2020; 18:7597-7607. [DOI: 10.1039/d0ob01565b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple models based on measurements taken from X-ray structures of relevant active sites are used to evaluate π stabilization by phenylalanine of several biochemical carbocations.
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Affiliation(s)
- Thomas A. Spencer
- Department of Chemistry
- 6128 Burke Laboratory
- Dartmouth College
- Hanover
- USA
| | - Robert Ditchfield
- Department of Chemistry
- 6128 Burke Laboratory
- Dartmouth College
- Hanover
- USA
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31
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Sajid H, Ayub K, Arshad M, Mahmood T. Highly selective acridinium based cyanine dyes for the detection of DNA base pairs (adenine, cytosine, guanine and thymine). COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112509] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Crnjar A, Comitani F, Melis C, Molteni C. Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution. Interface Focus 2019; 9:20180067. [PMID: 31065340 PMCID: PMC6501341 DOI: 10.1098/rsfs.2018.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
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Affiliation(s)
- Alessandro Crnjar
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudio Melis
- Universitá degli Studi di Cagliari, Complesso Universitario di Monserrato, Dipartimento di Fisica, S.P. Monserrato-Sestu Km 0,700, Monserrato (CA) 09042, Italy
| | - Carla Molteni
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
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33
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Rezhdo A, Islam M, Huang M, Van Deventer JA. Future prospects for noncanonical amino acids in biological therapeutics. Curr Opin Biotechnol 2019; 60:168-178. [PMID: 30974337 DOI: 10.1016/j.copbio.2019.02.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/22/2019] [Indexed: 12/12/2022]
Abstract
There is growing evidence that noncanonical amino acids (ncAAs) can be utilized in the creation of biological therapeutics ranging from protein conjugates to cell-based therapies. However, when does genetically encoding ncAAs yield biologics with unique properties compared to other approaches? In this review, we attempt to answer this question in the broader context of therapeutic development, emphasizing advances within the past two years. In several areas, ncAAs add valuable routes to therapeutically relevant entities, but application-specific needs ultimately determine whether ncAA-mediated or alternative solutions are preferred. Looking forward, using ncAAs to perform 'protein medicinal chemistry,' in which atomic-level changes to proteins dramatically enhance therapeutic properties, is a promising emerging area. Further upgrades to the performance of ncAA incorporation technologies will be essential to realizing the full potential of ncAAs in biological therapeutics.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States; Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States.
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34
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Mikhailov GP. Analysis of the Electron Density Laplacian of Lithium Complexes of Polycyclic Aromatic Hydrocarbons. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428018110222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Perez-Borrajero C, Lin CSH, Okon M, Scheu K, Graves BJ, Murphy ME, McIntosh LP. The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor. J Mol Biol 2019; 431:593-614. [DOI: 10.1016/j.jmb.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
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36
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Zhu Y, Rebek Jr J, Yu Y. Cyclizations catalyzed inside a hexameric resorcinarene capsule. Chem Commun (Camb) 2019; 55:3573-3577. [DOI: 10.1039/c9cc01611b] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The self-assembled, hydrogen-bonded hexameric resorcin[4]arene capsule represents one of the most readily accessible host systems for the study of container catalysis.
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Affiliation(s)
- Yujie Zhu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry
- College of Science
- Shanghai University
- Shanghai 200444
- China
| | - Julius Rebek Jr
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry
- College of Science
- Shanghai University
- Shanghai 200444
- China
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry
- College of Science
- Shanghai University
- Shanghai 200444
- China
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37
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Featherstone J, Chong T, Martens JK, Oomens J, McMahon TB. Inverse Sandwich Cyclopentadienyl Complexes of Sodium in the Gas Phase. J Phys Chem A 2018; 122:8659-8664. [DOI: 10.1021/acs.jpca.8b09366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua Featherstone
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tom Chong
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jonathan K. Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH Amsterdam, The Netherlands
| | - Terrance B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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38
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Yourdkhani S, Chojecki M, Korona T. Interaction of Non-polarizable Cations with Azaborine Isomers and Their Mono-Substituted Derivatives: Position, Induction, and Non-Classical Effects Matter. Chemphyschem 2018; 19:3092-3106. [DOI: 10.1002/cphc.201800691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3, CZ- 12116 Prague 2 Czech Republic
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Michał Chojecki
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Tatiana Korona
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
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39
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Hong S, Wang Y, Park SY, Lee H. Progressive fuzzy cation-π assembly of biological catecholamines. SCIENCE ADVANCES 2018; 4:eaat7457. [PMID: 30202784 PMCID: PMC6128673 DOI: 10.1126/sciadv.aat7457] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/30/2018] [Indexed: 05/21/2023]
Abstract
Biological functions depend on biomolecular assembly processes. Assemblies of lipid bilayers, actins, microtubules, or chromosomes are indispensable for cellular functions. These hierarchical assembly processes are reasonably predictable by understanding chemical structures of the defined building blocks and their interactions. However, biopigment assembly is rather fuzzy and unpredictable because a series of covalently coupled intermediates from catecholamine oxidation pathways progressively form a higher-level hierarchy. This study reports a different yet unexplored type of assembly process named "cation-π progressive assembly." We demonstrated for the first time that the cation-π is the primary mechanism for intermolecular assembly in dopamine-melanin biopigment. We also found that the self-assembled products physically grow and chemically gain new functions "progressively" over time in which cation-π plays important roles. The progressive assembly explains how biological systems produce wide spectra of pigment colors and broad wavelength absorption through energy-efficient processes. Furthermore, we also demonstrate surface-independent wettability control using cation-π progressive assembly.
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Affiliation(s)
- Seonki Hong
- Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology, 333 Techno Jungang-daero, Hyeonpung-myeon, Dalseong-gun, Daegu 42988, Republic of Korea
- Corresponding author. (H.L.); (S.H.)
| | - Younseon Wang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sung Young Park
- Department of Chemical and Biological Engineering, Korea National University of Transportation, Chungju 380-702, Republic of Korea
| | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Corresponding author. (H.L.); (S.H.)
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40
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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41
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Combs SA, Mueller BK, Meiler J. Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. J Chem Inf Model 2018; 58:1021-1036. [PMID: 29641200 DOI: 10.1021/acs.jcim.7b00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.
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Affiliation(s)
- Steven A Combs
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
| | - Benjamin K Mueller
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
| | - Jens Meiler
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
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42
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Monn JA, Henry SS, Massey SM, Clawson DK, Chen Q, Diseroad BA, Bhardwaj RM, Atwell S, Lu F, Wang J, Russell M, Heinz BA, Wang XS, Carter JH, Getman BG, Adragni K, Broad LM, Sanger HE, Ursu D, Catlow JT, Swanson S, Johnson BG, Shaw DB, McKinzie DL, Hao J. Synthesis and Pharmacological Characterization of C4 β-Amide-Substituted 2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylates. Identification of (1 S,2 S,4 S,5 R,6 S)-2-Amino-4-[(3-methoxybenzoyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid (LY2794193), a Highly Potent and Selective mGlu 3 Receptor Agonist. J Med Chem 2018; 61:2303-2328. [PMID: 29350927 DOI: 10.1021/acs.jmedchem.7b01481] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multiple therapeutic opportunities have been suggested for compounds capable of selective activation of metabotropic glutamate 3 (mGlu3) receptors, but small molecule tools are lacking. As part of our ongoing efforts to identify potent, selective, and systemically bioavailable agonists for mGlu2 and mGlu3 receptor subtypes, a series of C4β-N-linked variants of (1 S,2 S,5 R,6 S)-2-amino-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid 1 (LY354740) were prepared and evaluated for both mGlu2 and mGlu3 receptor binding affinity and functional cellular responses. From this investigation we identified (1 S,2 S,4 S,5 R,6 S)-2-amino-4-[(3-methoxybenzoyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid 8p (LY2794193), a molecule that demonstrates remarkable mGlu3 receptor selectivity. Crystallization of 8p with the amino terminal domain of hmGlu3 revealed critical binding interactions for this ligand with residues adjacent to the glutamate binding site, while pharmacokinetic assessment of 8p combined with its effect in an mGlu2 receptor-dependent behavioral model provides estimates for doses of this compound that would be expected to selectively engage and activate central mGlu3 receptors in vivo.
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43
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Ivanova B, Spiteller M. Cation-π-complex of Ag(I) ion with 1H-indole-5-carboxylic acid – Structural analysis and energetics of the M–L bonds. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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44
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Dujardin M, Cantrelle FX, Lippens G, Hanoulle X. Interaction study between HCV NS5A-D2 and NS5B using 19F NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 70:67-76. [PMID: 29218486 DOI: 10.1007/s10858-017-0159-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
The non structural protein 5A (NS5A) regulates the replication of the hepatitis C viral RNA through a direct molecular interaction of its domain 2 (NS5A-D2) with the RNA dependent RNA polymerase NS5B. Because of conflicting data in the literature, we study here this molecular interaction using fluorinated versions of the NS5A-D2 protein derived from the JFH1 Hepatitis C Virus strain. Two methods to prepare fluorine-labelled NS5A-D2 involving the biosynthetic incorporation of a 19F-tryptophan using 5-fluoroindole and the posttranslational introduction of fluorine by chemical conjugation of 2-iodo-N-(trifluoromethyl)acetamide with the NS5A-D2 cysteine side chains are presented. The dissociation constants (KD) between NS5A-D2 and NS5B obtained with these two methods are in good agreement, and yield values comparable to those derived previously from a surface plasmon resonance study. We compare benefits and limitations of both labeling methods to study the interaction between an intrinsically disordered protein and a large molecular target by 19F NMR.
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Affiliation(s)
- Marie Dujardin
- Université de Lille, CNRS, UMR 8576 - UGSF, 59000, Lille, France
| | | | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, UPS 135 avenue de Rangueil, 31077, Toulouse, France
| | - Xavier Hanoulle
- Université de Lille, CNRS, UMR 8576 - UGSF, 59000, Lille, France.
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Baril SA, Koenig AL, Krone MW, Albanese KI, Qixin He C, Lee GY, Houk KN, Waters ML, Brustad EM. Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis. J Am Chem Soc 2017; 139:17253-17256. [PMID: 29111699 PMCID: PMC6040664 DOI: 10.1021/jacs.7b09223] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.
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Affiliation(s)
- Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amber L. Koenig
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mackenzie W. Krone
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Tiekink ER. Supramolecular assembly based on “emerging” intermolecular interactions of particular interest to coordination chemists. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.01.009] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Goins CM, Dajnowicz S, Thanna S, Sucheck SJ, Parks JM, Ronning DR. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives. ACS Infect Dis 2017; 3:378-387. [PMID: 28285521 DOI: 10.1021/acsinfecdis.7b00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was cocrystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, noncatalytic Cys209 residue forming a selenenylsulfide bond. Continuous difference density for both thiol modifiers allowed for the assessment of interactions that influence ebselen binding and inhibitor orientation that were unobserved in previous Ag85C ebselen structures. The kinact/KI values for ebselen, adamantyl ebselen, and azido ebselen support the importance of observed constructive chemical interactions with Arg239 for increased in vitro efficacy toward Ag85C. To better understand the in vitro kinetic properties of these ebselen derivatives, the energetics of specific protein-inhibitor interactions and relative reaction free energies were calculated for ebselen and both derivatives using density functional theory. These studies further support the different in vitro properties of ebselen and two select ebselen derivatives from our previously published ebselen library with respect to kinetics and protein-inhibitor interactions. In both structures, the α9 helix was displaced farther from the enzyme active site than the previous Ag85C ebselen structure, resulting in the restructuring of a connecting loop and imparting a conformational change to residues believed to play a role in substrate binding specific to Ag85C. These notable structural changes directly affect protein stability, reducing the overall melting temperature by up to 14.5 °C, resulting in the unfolding of protein at physiological temperatures. Additionally, this structural rearrangement due to covalent allosteric modification creates a sizable solvent network that encompasses the active site and extends to the modified Cys209 residue. In all, this study outlines factors that influence enzyme inhibition by ebselen and its derivatives while further highlighting the effects of the covalent modification of Cys209 by said inhibitors on the structure and stability of Ag85C. Furthermore, the results suggest a strategy for developing new classes of Ag85 inhibitors with increased specificity and potency.
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Affiliation(s)
- Christopher M. Goins
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Steven Dajnowicz
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sandeep Thanna
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Steven J. Sucheck
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics,
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Donald R. Ronning
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
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48
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Secondary Ammonium Agonists Make Dual Cation-π Interactions in α4β2 Nicotinic Receptors. eNeuro 2017; 4:eN-NWR-0032-17. [PMID: 28589175 PMCID: PMC5458768 DOI: 10.1523/eneuro.0032-17.2017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 11/21/2022] Open
Abstract
A cation-π interaction between the ammonium group of an agonist and a conserved tryptophan termed TrpB is a near universal feature of agonist binding to nicotinic acetylcholine receptors (nAChRs). TrpB is one of five residues that form the aromatic box of the agonist binding site, and for the prototype agonists ACh and nicotine, only TrpB makes a functional cation-π interaction. We report that, in addition to TrpB, a significant cation-π interaction is made to a second aromatic, TyrC2, by the agonists metanicotine, TC299423, varenicline, and nornicotine. A common structural feature of these agonists, and a distinction from ACh and nicotine, is a protonated secondary amine that provides the cation for the cation-π interaction. These results indicate a distinction in binding modes between agonists with subtly different structures that may provide guidance for the development of subtype-selective agonists of nAChRs.
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Liu Y, Miao K, Dunham NP, Liu H, Fares M, Boal AK, Li X, Zhang X. The Cation-π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification. Biochemistry 2017; 56:1585-1595. [PMID: 28221782 PMCID: PMC5362743 DOI: 10.1021/acs.biochem.7b00056] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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The design of fluorogenic
probes for a Halo tag is highly desirable
but challenging. Previous work achieved this goal by controlling the
chemical switch of spirolactones upon the covalent conjugation between
the Halo tag and probes or by incorporating a “channel dye”
into the substrate binding tunnel of the Halo tag. In this work, we
have developed a novel class of Halo-tag fluorogenic probes that are
derived from solvatochromic fluorophores. The optimal probe, harboring
a benzothiadiazole scaffold, exhibits a 1000-fold fluorescence enhancement
upon reaction with the Halo tag. Structural, computational, and biochemical
studies reveal that the benzene ring of a tryptophan residue engages
in a cation−π interaction with the dimethylamino electron-donating
group of the benzothiadiazole fluorophore in its excited state. We
further demonstrate using noncanonical fluorinated tryptophan that
the cation−π interaction directly contributes to the
fluorogenicity of the benzothiadiazole fluorophore. Mechanistically,
this interaction could contribute to the fluorogenicity by promoting
the excited-state charge separation and inhibiting the twisting motion
of the dimethylamino group, both leading to an enhanced fluorogenicity.
Finally, we demonstrate the utility of the probe in no-wash direct
imaging of Halo-tagged proteins in live cells. In addition, the fluorogenic
nature of the probe enables a gel-free quantification of fusion proteins
expressed in mammalian cells, an application that was not possible
with previously nonfluorogenic Halo-tag probes. The unique mechanism
revealed by this work suggests that incorporation of an excited-state
cation−π interaction could be a feasible strategy for
enhancing the optical performance of fluorophores and fluorogenic
sensors.
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Affiliation(s)
| | | | | | - Hongbin Liu
- Department of Chemistry, University of Washington , Seattle, Washington 98105, United States
| | | | | | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98105, United States
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50
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Parui S, Manna RN, Jana B. Destabilization of Hydrophobic Core of Chicken Villin Headpiece in Guanidinium Chloride Induced Denaturation: Hint of π-Cation Interaction. J Phys Chem B 2016; 120:9599-607. [DOI: 10.1021/acs.jpcb.6b06325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
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