51
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Mollica L, Giachin G. Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. J Chem Inf Model 2022; 63:531-545. [PMID: 36580661 PMCID: PMC9875307 DOI: 10.1021/acs.jcim.2c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Immunotherapy using antibodies to target the aggregation of flexible proteins holds promise for therapeutic interventions in neurodegenerative diseases caused by protein misfolding. Prions or PrPSc, the causal agents of transmissible spongiform encephalopathies (TSE), represent a model target for immunotherapies as TSE are prototypical protein misfolding diseases. The X-ray crystal structure of the wild-type (WT) human prion protein (HuPrP) bound to a camelid antibody fragment, denoted as Nanobody 484 (Nb484), has been previously solved. Nb484 was found to inhibit prion aggregation in vitro through a unique mechanism of structural stabilization of two disordered epitopes, that is, the palindromic motif (residues 113-120) and the β2-α2 loop region (residues 164-185). The study of the structural basis for antibody recognition of flexible proteins requires appropriate sampling techniques for the identification of conformational states occurring in disordered epitopes. To elucidate the Nb484-HuPrP recognition mechanisms, here we applied molecular dynamics (MD) simulations complemented with available NMR and X-ray crystallography data collected on the WT HuPrP to describe the conformational spaces occurring on HuPrP prior to Nb484 binding. We observe the experimentally determined binding competent conformations within the ensembles of pre-existing conformational states in solution before binding. We also described the Nb484 recognition mechanisms in two HuPrP carrying a polymorphism (E219K) and a TSE-causing mutation (V210I). Our hybrid approaches allow the identification of dynamic conformational landscapes existing on HuPrP and highly characterized by molecular disorder to identify physiologically relevant and druggable transitions.
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Affiliation(s)
- Luca Mollica
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan, Italy,
| | - Gabriele Giachin
- Department
of Chemical Sciences (DiSC), University
of Padua, 35131 Padova, Italy,
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52
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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53
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Wang X, Pavlović RZ, Finnegan TJ, Karmakar P, Moore CE, Badjić JD. Rapid Access to Chiral and Tripodal Cavitands from β-Pinene. Chemistry 2022; 28:e202202416. [PMID: 36168151 PMCID: PMC9797447 DOI: 10.1002/chem.202202416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 12/31/2022]
Abstract
We report Pd-catalyzed cyclotrimerization of (+)-α-bromoenone, obtained from monoterpene β-pinene, into an enantiopure cyclotrimer. This C3 symmetric compound has three bicyclo[3.1.1]heptane rings fused to its central benzene with each ring carrying a carbonyl group. The cyclotrimer undergoes diastereoselective threefold alkynylation with the lithium salts of five terminal alkynes (41-63 %, de=4-83 %). The addition enabled a rapid synthesis of a small library of novel chiral cavitands that, in shape, resemble a tripod stand. These molecular tripods include a tris-bicycloannelated benzene head attached to three alkyne legs twisted in one direction to form a nonpolar cavity with polar groups as feet. Tripods with methylpyridinium and methylisoquinolinium legs, respectively, form inclusion complexes with anti-inflammatory and chiral drugs (R)/(S)-ibuprofen and (R)/(S)-naproxen. The mode of binding shows drug molecules docked in the cavity of the host through ion-ion, cation-π, and C-H-π contacts that, in addition of desolvation, give rise to complexes having millimolar to micromolar stability in water. Our findings open the door to creating a myriad of enantiopure tripods with tunable functions that, in the future, might give novel chemosensors, catalysts or sequestering agents.
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Affiliation(s)
- Xiuze Wang
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Radoslav Z. Pavlović
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Tyler J. Finnegan
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Pratik Karmakar
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
- Department of ChemistryKing Mongkut's University of Technology Thonburi (KMUTT)126 Pracha Uthit Rd., Bang ModThung Khru, Bangkok10140Thailand
| | - Curtis E. Moore
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Jovica D. Badjić
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
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54
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Wei L, Sun T, Shi Z, Xu Z, Wen W, Jiang S, Zhao Y, Ma Y, Zhang YB. Guest-adaptive molecular sensing in a dynamic 3D covalent organic framework. Nat Commun 2022; 13:7936. [PMID: 36566293 DOI: 10.1038/s41467-022-35674-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Molecular recognition is an attractive approach to designing sensitive and selective sensors for volatile organic compounds (VOCs). Although organic macrocycles and cages have been well-developed for recognising organics by their adaptive pockets in liquids, porous solids for gas detection require a deliberate design balancing adaptability and robustness. Here we report a dynamic 3D covalent organic framework (dynaCOF) constructed from an environmentally sensitive fluorophore that can undergo concerted and adaptive structural transitions upon adsorption of gas and vapours. The COF is capable of rapid and reliable detection of various VOCs, even for non-polar hydrocarbon gas under humid conditions. The adaptive guest inclusion amplifies the host-guest interactions and facilitates the differentiation of organic vapours by their polarity and sizes/shapes, and the covalently linked 3D interwoven networks ensure the robustness and coherency of the materials. The present result paves the way for multiplex fluorescence sensing of various VOCs with molecular-specific responses.
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Affiliation(s)
- Lei Wei
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Tu Sun
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaolin Shi
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zezhao Xu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wen Wen
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Shan Jiang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China
| | - Yingbo Zhao
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China.
| | - Yanhang Ma
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China.
| | - Yue-Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China.
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55
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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56
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Jiao Y, Mao H, Qiu Y, Wu G, Chen H, Zhang L, Han H, Li X, Zhao X, Tang C, Chen XY, Feng Y, Stern CL, Wasielewski MR, Stoddart JF. Mechanical Bond-Assisted Full-Spectrum Investigation of Radical Interactions. J Am Chem Soc 2022; 144:23168-23178. [DOI: 10.1021/jacs.2c10882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yang Jiao
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Haochuan Mao
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Yunyan Qiu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Guangcheng Wu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hongliang Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
| | - Long Zhang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Han Han
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Xuesong Li
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Xingang Zhao
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chun Tang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Xiao-Yang Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Charlotte L. Stern
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Michael R. Wasielewski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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57
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Mamidi AS, Surolia A. Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins. PLoS Comput Biol 2022; 18:e1010661. [PMID: 36508460 PMCID: PMC9744295 DOI: 10.1371/journal.pcbi.1010661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/17/2022] [Indexed: 12/14/2022] Open
Abstract
The fundamental question on the mechanism of molecular recognition during ligand binding has attracted a lot of scientific scrutiny. The two competing theories of ligand binding-"induced fit" and "conformational selection" have been proposed to explain biomolecular recognition. Since exploring a family of proteins with similar structural architectures and conserved functional roles can provide valuable insight into the significance of molecular structure and function, we performed molecular dynamics simulations on the calreticulin family of proteins, which specifically recognize monoglucosylated N-glycan during the protein folding process. Atomistic simulations of lectins in free and bound forms demonstrated that they exist in several conformations spanning from favorable to unfavorable for glycan binding. Our analysis was confined to the carbohydrate recognition domain (CRD) of these lectins to demonstrate the degree of conservation in protein sequence and structure and relate them with their function. Furthermore, we computed the lectin-glycan binding affinity using the mmPBSA approach to identify the most favorable lectin conformation for glycan binding and compared the molecular interaction fields in terms of noncovalent bond interactions. We also demonstrated the involvement of Tyr and Trp residues in the CRD with the non-reducing end glucose and central mannose residues, which contribute to some of the specific interactions. Furthermore, we analyzed the conformational changes in the CRD through SASA, RMSFs and protein surface topography mapping of electrostatic and hydrophobic potentials. Our findings demonstrate a hybrid mechanism of molecular recognition, initially driven by conformational selection followed by glycan-induced fluctuations in the key residues to strengthen the glycan binding interactions.
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Affiliation(s)
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore–India
- * E-mail: (ASM); (AS)
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58
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Robinson HT, Haakansson CT, Corkish TR, Watson PD, McKinley AJ, Wild DA. Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes. Chemphyschem 2022; 24:e202200733. [PMID: 36504309 DOI: 10.1002/cphc.202200733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH3 Cl, CH2 Cl2 , CHCl3 , and CCl4 . The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.
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Affiliation(s)
- Hayden T Robinson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Christian T Haakansson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Timothy R Corkish
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Peter D Watson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom, OX1 3QZ
| | - Allan J McKinley
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Duncan A Wild
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,School of Science, Edith Cowan University, Joondalup, Western Australia, 6027
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59
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Wieland Goetzke F, Gropp C, Schwab A, Donckèle EJ, Thilgen C, Diederich F. Enantiopure Alleno‐Acetylenic Cage Receptors for Molecular Recognition in Aqueous Medium. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- F. Wieland Goetzke
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
| | - Cornelius Gropp
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
| | - Anatol Schwab
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
| | - Etienne J. Donckèle
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
| | - Carlo Thilgen
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 1–5/10 CH-8093 Zurich Switzerland
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60
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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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61
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Jiao Y, Stoddart J. Electron / hole catalysis: A versatile strategy for promoting chemical transformations. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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62
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Qin L, Xin X, Wang R, Lv H, Yang GY. Rational Design of Bromine-Modified Ir(III) Photosensitizer for Photocatalytic Hydrogen Generation. J Catal 2022. [DOI: 10.1016/j.jcat.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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63
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Kenny PW. Hydrogen-Bond Donors in Drug Design. J Med Chem 2022; 65:14261-14275. [DOI: 10.1021/acs.jmedchem.2c01147] [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)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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64
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Zhu Y, Hu X. Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27207124. [PMID: 36296718 PMCID: PMC9611543 DOI: 10.3390/molecules27207124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Protein kinases are key enzymes that catalyze the covalent phosphorylation of substrates via the transfer of the γ-phosphate of ATP, playing a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. Due to their pivotal cellular role, the aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Decades of intense development of protein kinase inhibitors (PKIs) resulted in 71 FDA-approved PKI drugs that target dozens of protein kinases for the treatment of various diseases. How do FDA-approved protein kinase inhibitor PKI drugs compete with ATP in their own binding pocket? This is the central question we attempt to address in this work. Based on modes of non-bonded interactions and their calculated interaction strengths by means of the advanced double hybrid DFT method B2PLYP, the molecular recognition of PKI drugs in the ATP-binding pockets was systematically analyzed. It was found that (1) all the FDA-approved PKI drugs studied here form one or more hydrogen bond(s) with the backbone amide N, O atoms in the hinge region of the ATP binding site, mimicking the adenine base; (2) all the FDA-approved PKI drugs feature two or more aromatic rings. The latter reach far and deep into the hydrophobic regions I and II, forming multiple CH-π interactions with aliphatic residues L(3), V(11), A(15), V(36), G(51), L(77) and π-π stacking interactions with aromatic residues F(47) and F(82), but ATP itself does not utilize these regions extensively; (3) all FDA-approved PKI drugs studied here have one thing in common, i.e., they frequently formed non-bonded interactions with a total of 12 residues L(3),V(11), A(15), K(17), E(24),V(36),T(45), F(47), G(51), L(77), D(81) and F(82) in the ATP binding. Many of those 12 commonly involved residues are highly conserved residues with important structural and catalytic functional roles. K(17) and E(24) are the two highly conserved residues crucial for the catalytic function of kinases. D(81) and F(82) belong to the DFG motif; T(45) was dubbed the gate keeper residue. F(47) is located on the hinge region and G(51) sits on the linker that connects the hinge to the αD-helix. It is this targeting of highly conserved residues in protein kinases that led to promiscuous PKI drugs that lack selectivity. Although the formation of hydrogen bond(s) with the backbone of the hinge gives PKI drugs the added binding affinity and the much-needed directionality, selectivity is sacrificed. That is why so many FDA-approved PKI drugs are known to have multiple targets. Moreover, off-target-mediated toxicity caused by a lack of selectivity was one of the major challenges facing the PKI drug discovery community. This work suggests a road map for future PKI drug design, i.e., targeting non-conserved residues in the ATP binding pocket to gain better selectivity so as to avoid off-target-mediated toxicity.
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Affiliation(s)
| | - Xiche Hu
- Correspondence: ; Tel.: +1-4195301513
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65
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Zetterberg FR, MacKinnon A, Brimert T, Gravelle L, Johnsson RE, Kahl-Knutson B, Leffler H, Nilsson UJ, Pedersen A, Peterson K, Roper JA, Schambye H, Slack RJ, Tantawi S. Discovery and Optimization of the First Highly Effective and Orally Available Galectin-3 Inhibitors for Treatment of Fibrotic Disease. J Med Chem 2022; 65:12626-12638. [PMID: 36154172 PMCID: PMC9574852 DOI: 10.1021/acs.jmedchem.2c00660] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 01/06/2023]
Abstract
Galectin-3 is a carbohydrate-binding protein central to regulating mechanisms of diseases such as fibrosis, cancer, metabolic, inflammatory, and heart disease. We recently found a high affinity (nM) thiodigalactoside GB0139 which currently is in clinical development (PhIIb) as an inhaled treatment of idiopathic pulmonary fibrosis. To enable treatment of systemically galectin-3 driven disease, we here present the first series of selective galectin-3 inhibitors combining high affinity (nM) with oral bioavailability. This was achieved by optimizing galectin-3 specificity and physical chemical parameters for a series of disubstituted monogalactosides. Further characterization showed that this class of compounds reduced profibrotic gene expression in liver myofibroblasts and displayed antifibrotic activity in CCl4-induced liver fibrosis and bleomycin-induced lung fibrosis mouse models. On the basis of the overall pharmacokinetic, pharmacodynamic, and safety profile, GB1211 was selected as the clinical candidate and is currently in phase IIa clinical trials as a potential therapy for liver cirrhosis and cancer.
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Affiliation(s)
- Fredrik R. Zetterberg
- Galecto
Biotech AB, Sahlgrenska
Science Park, Medicinaregatan 8 A, SE-413
46 Gothenburg, Sweden
| | - Alison MacKinnon
- Galecto
Biotech ApS, Nine Edinburgh
Bioquarter, 9 Little France Road, Edinburgh EH16 4UX, U.K.
| | - Thomas Brimert
- Red
Glead Discovery AB, Medicon
Village, SE-223 63 Lund, Sweden
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Lise Gravelle
- Galecto
Biotech ApS, Cobis Science
Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | | | - Barbro Kahl-Knutson
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Hakon Leffler
- Department
of Laboratory Medicine, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Galecto
Biotech AB, Sahlgrenska
Science Park, Medicinaregatan 8 A, SE-413
46 Gothenburg, Sweden
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Anders Pedersen
- Galecto
Biotech ApS, Cobis Science
Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | - Kristoffer Peterson
- Galecto
Biotech AB, Sahlgrenska
Science Park, Medicinaregatan 8 A, SE-413
46 Gothenburg, Sweden
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - James A. Roper
- Galecto
Biotech ApS, Stevenage
Bioscience Catalyst, Stevenage, SG1
2FX Hertfordshire, U.K.
| | - Hans Schambye
- Galecto
Biotech ApS, Cobis Science
Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | - Robert J. Slack
- Galecto
Biotech ApS, Stevenage
Bioscience Catalyst, Stevenage, SG1
2FX Hertfordshire, U.K.
| | - Susan Tantawi
- Galecto
Biotech ApS, Cobis Science
Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
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66
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Ostovan A, Arabi M, Wang Y, Li J, Li B, Wang X, Chen L. Greenificated Molecularly Imprinted Materials for Advanced Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2203154. [PMID: 35734896 DOI: 10.1002/adma.202203154] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Molecular imprinting technology (MIT) produces artificial binding sites with precise complementarity to substrates and thereby is capable of exquisite molecular recognition. Over five decades of evolution, it is predicted that the resulting host imprinted materials will overtake natural receptors for research and application purposes, but in practice, this has not yet been realized due to the unsustainability of their life cycles (i.e., precursors, creation, use, recycling, and end-of-life). To address this issue, greenificated molecularly imprinted polymers (GMIPs) are a new class of plastic antibodies that have approached sustainability by following one or more of the greenification principles, while also demonstrating more far-reaching applications compared to their natural counterparts. In this review, the most recent developments in the delicate design and advanced application of GMIPs in six fast-growing and emerging fields are surveyed, namely biomedicine/therapy, catalysis, energy harvesting/storage, nanoparticle detection, gas sensing/adsorption, and environmental remediation. In addition, their distinct features are highlighted, and the optimal means to utilize these features for attaining incredibly far-reaching applications are discussed. Importantly, the obscure technical challenges of the greenificated MIT are revealed, and conceivable solutions are offered. Lastly, several perspectives on future research directions are proposed.
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Affiliation(s)
- Abbas Ostovan
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Maryam Arabi
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yunqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinhua Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Bowei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaoyan Wang
- School of Pharmacy, Binzhou Medical University, Yantai, 264003, China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- School of Environmental & Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, China
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67
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King D, Wilson CR, Herron L, Deng CL, Mehdi S, Tiwary P, Hof F, Isaacs L. Molecular recognition of methylated amino acids and peptides by Pillar[6]MaxQ. Org Biomol Chem 2022; 20:7429-7438. [PMID: 36097881 PMCID: PMC9632254 DOI: 10.1039/d2ob01487d] [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: 11/21/2022]
Abstract
We report the molecular recognition properties of Pillar[n]MaxQ (P[n]MQ) toward a series of (methylated) amino acids, amino acid amides, and post-translationally modified peptides by a combination of 1H NMR, isothermal titration calorimetry, indicator displacement assays, and molecular dynamics simulations. We find that P6MQ is a potent receptor for N-methylated amino acid side chains. P6MQ recognized the H3K4Me3 peptide with Kd = 16 nM in phosphate buffered saline.
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Affiliation(s)
- David King
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
| | - Chelsea R Wilson
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada.
| | - Lukas Herron
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
| | - Shams Mehdi
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada.
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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68
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Chen J, Peng Q, Peng X, Zhang H, Zeng H. Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems. Chem Rev 2022; 122:14594-14678. [PMID: 36054924 DOI: 10.1021/acs.chemrev.2c00215] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.
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Affiliation(s)
- Jingsi Chen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Xuwen Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hao Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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69
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Zhai C, Isaacs L. New Synthetic Route to Water‐Soluble Prism[5]arene Hosts and Their Molecular Recognition Properties**. Chemistry 2022; 28:e202201743. [DOI: 10.1002/chem.202201743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Canjia Zhai
- Department of Chemistry and Biochemistry University of Maryland College Park 20742 Maryland USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry University of Maryland College Park 20742 Maryland USA
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70
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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71
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Stachowski TR, Vanarotti M, Seetharaman J, Lopez K, Fischer M. Water Networks Repopulate Protein-Ligand Interfaces with Temperature. Angew Chem Int Ed Engl 2022; 61:e202112919. [PMID: 35648650 PMCID: PMC9329195 DOI: 10.1002/anie.202112919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 12/14/2022]
Abstract
High-resolution crystal structures highlight the importance of water networks in protein-ligand interactions. However, as these are typically determined at cryogenic temperature, resulting insights may be structurally precise but not biologically accurate. By collecting 10 matched room-temperature and cryogenic datasets of the biomedical target Hsp90α, we identified changes in water networks that impact protein conformations at the ligand binding interface. Water repositioning with temperature repopulates protein ensembles and ligand interactions. We introduce Flipper conformational barcodes to identify temperature-sensitive regions in electron density maps. This revealed that temperature-responsive states coincide with ligand-responsive regions and capture unique binding signatures that disappear upon cryo-cooling. Our results have implications for discovering Hsp90 selective ligands, and, more generally, for the utility of hidden protein and water conformations in drug discovery.
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Affiliation(s)
- Timothy R. Stachowski
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Murugendra Vanarotti
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Jayaraman Seetharaman
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Karlo Lopez
- School of Natural SciencesMathematicsand EngineeringCalifornia State UniversityBakersfieldCA 93311USA
| | - Marcus Fischer
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTN 38105USA
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72
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El‐Nahass MN, Youssif MM, El‐Daly HA, Fayed TA. Naked‐eye colorimetric and optical assay of heavy metals based on nano‐architectured prototype of organically functionalized mesoporous titania grafted with 4‐Chloro‐2‐(4'‐methyl‐benzothiazol‐2'‐ylazo)‐phenol. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marwa N. El‐Nahass
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Mahmoud M. Youssif
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Hosny A. El‐Daly
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Tarek A. Fayed
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
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73
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Cai H, Wu YX, Lu Z, Luo D, Sun JX, Wu GW, Li M, Wei YB, Zhong LM, Li D. Mimicking DNA Periodic Docking Grooves for Adaptive Identification of l-/d-Tryptophan in a Biological Metal-Organic Framework. J Am Chem Soc 2022; 144:9559-9563. [PMID: 35604644 DOI: 10.1021/jacs.2c03326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bioinspired metal-organic frameworks (MOFs) serve as suitable crystalline models for recognition and sensing of biomolecules mimicking natural processes, providing new ideas and concepts for cutting-edge biomedical applications. Here, we have successfully prepared a robust biological metal-organic framework with periodic docking grooves resembling the major and minor grooves in the DNA double helix structure, which can be used as unique recognition sites for selectively identifying l-/d-tryptophan (l-/d-Trp). Notably, successful encapsulation of Trp could be observed by single-crystal X-ray diffraction for the first time. Trp has matched size and shape to fit snugly into the major groove. Combined with isothermal titration calorimetry, it was found that ZnBTCHx could spontaneously capture l-/d-Trp through two different thermodynamic pathways: enthalpy-driven for encapsulating l-Trp and entropy-driven for uptaking d-Trp. Furthermore, molecular dynamics and density functional theory verified the role of hydrogen bonding and π-π/C-H···π interactions in the host-guest interface. This work provides unique insight for the construction of bionic models to mimic the natural binding properties, which is of great significance for the fields of pharmaceutical chemistry and biomedical science.
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Affiliation(s)
- Hong Cai
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, P.R. China
| | - Yu-Xin Wu
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, P.R. China
| | - Zhou Lu
- Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Co-ordination Materials and Applications, Jinan University, Guangzhou 510632, P.R. China
| | - Jing-Xuan Sun
- Department of Chemistry, Shantou University, Shantou 515063, P.R. China
| | - Guang-Wei Wu
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, P.R. China
| | - Mian Li
- Department of Chemistry, Shantou University, Shantou 515063, P.R. China
| | - Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Co-ordination Materials and Applications, Jinan University, Guangzhou 510632, P.R. China
| | - Li-Ming Zhong
- School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, P.R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Co-ordination Materials and Applications, Jinan University, Guangzhou 510632, P.R. China
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74
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput Biol 2022; 18:e1009783. [PMID: 35653385 PMCID: PMC9197077 DOI: 10.1371/journal.pcbi.1009783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/14/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available at https://github.com/n-szulc/fingeRNAt.
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75
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Stachowski TR, Vanarotti M, Seetharaman J, Lopez K, Fischer M. Water Networks Repopulate Protein‐Ligand Interfaces With Temperature. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Timothy R Stachowski
- St Jude Children's Research Hospital Chemical Biology & Therapeutics UNITED STATES
| | - Murugendra Vanarotti
- St Jude Children's Research Hospital Chemical Biology & Therapeutics UNITED STATES
| | | | - Karlo Lopez
- California State University - Bakersfield School of Natural Sciences, Mathematics, and Engineering UNITED STATES
| | - Marcus Fischer
- St. Jude Children's Research Hospital Chemical Biology & Therapeutics 262 Danny Thomas Place 38105 Memphis UNITED STATES
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76
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DiMaggio D, Brockett AT, Shuster M, Murkli S, Zhai C, King D, O'Dowd B, Cheng M, Brady K, Briken V, Roesch MR, Isaacs L. Anthracene-Walled Acyclic CB[n] Receptors: in vitro and in vivo Binding Properties toward Drugs of Abuse. ChemMedChem 2022; 17:e202200046. [PMID: 35238177 PMCID: PMC9119912 DOI: 10.1002/cmdc.202200046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/01/2022] [Indexed: 11/07/2022]
Abstract
We report studies of the interaction of six acyclic CB[n]-type receptors toward a panel of drugs of abuse by a combination of isothermal titration calorimetry and 1 H NMR spectroscopy. Anthracene walled acyclic CB[n] host (M3) displays highest binding affinity toward methamphetamine (Kd =15 nM) and fentanyl (Kd =4 nM). Host M3 is well tolerated by Hep G2 and HEK 293 cells up to 100 μM according to MTS metabolic and adenylate kinase release assays. An in vivo maximum tolerated dose study with Swiss Webster mice showed no adverse effects at the highest dose studied (44.7 mg kg-1 ). Host M3 is not mutagenic based on the Ames fluctuation test and does not inhibit the hERG ion channel. In vivo efficacy studies showed that pretreatment of mice with M3 significantly reduces the hyperlocomotion after treatment with methamphetamine, but M3 does not function similarly when administered 30 seconds after methamphetamine.
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Affiliation(s)
- Delaney DiMaggio
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Adam T Brockett
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland, College Park, MD 20742, USA
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Canjia Zhai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - David King
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Brona O'Dowd
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Kimberly Brady
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Matthew R Roesch
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland, College Park, MD 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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77
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Wang X, Quan M, Yao H, Pang XY, Ke H, Jiang W. Switchable bifunctional molecular recognition in water using a pH-responsive Endo-functionalized cavity. Nat Commun 2022; 13:2291. [PMID: 35484144 PMCID: PMC9051166 DOI: 10.1038/s41467-022-30012-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
The construction of water-soluble synthetic hosts with a stimuli-responsive endo-functionalized cavity is challenging. These hosts feature a switchable cavity and may bring new properties to the fields of self-assembly, molecular machines, and biomedical sciences. Herein, we report a pair of water-soluble naphthotubes with a pH-responsive endo-functionalized cavity. The inward-directing secondary amine group of the hosts can be protonated and deprotonated. Thus, the hosts have different cavity features at the two states and show drastically different binding preference and selectivity in water. We reveal that the binding difference of the two host states is originated from the differences in charge repulsion, hydrogen bonding and the hydrophobic effects. Moreover, the guest binding can be easily switched in a ternary mixture with two guest molecules by adjusting the pH value of the solution. These pH-responsive hosts may be used for the construction of smart self-assembly systems and water-soluble molecular machines.
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Affiliation(s)
- Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Mao Quan
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Huan Yao
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Xin-Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Hua Ke
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China.
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78
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El‐Nahass MN, Fayed TA, El‐Daly HA, Youssif MM. Benzothiazole azo‐derivatives as colorimetric probes for optical recognition of different metal ions and anions. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marwa N. El‐Nahass
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Tarek A. Fayed
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Hosny A. El‐Daly
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
| | - Mahmoud M. Youssif
- Department of Chemistry, Faculty of Science Tanta University Tanta Egypt
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79
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Chen J, Wang H, Zheng Y, Zhang X, Xu X, Gou Q. Sp 2- and sp 3-C⋯O tetrel bonds in the 3-oxetanone homodimer. Phys Chem Chem Phys 2022; 24:8992-8998. [PMID: 35380142 DOI: 10.1039/d2cp00703g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures and non-covalent interactions at play in the 3-oxetanone homodimer have been investigated using a pulsed jet Fourier transform microwave spectrometer supplemented with quantum chemical calculations. Two isomers were identified in the pulsed jet. With the analyses of non-covalent intermolecular interactions including the quantum theory of atoms, Johnson's non-covalent interactions and natural bond orbital, the observed global minimum is stabilized by a combination of one sp2-C⋯O tetrel bond and a network of multiple C-H⋯O weak hydrogen bonds. The second isomer is characterized by carbonyl-carbonyl interactions, with the formation of one sp2- and one sp3-C⋯O tetrel bond. The conformational population of the two observed isomers in the supersonic expansion was estimated to be NCE1/NCC1 ≈ 7/5.
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Affiliation(s)
- Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 550000, Guizhou, China.,Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Hao Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Xinyue Zhang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Xuefang Xu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China. .,Chongqing Key Laboratory of Theoretical and Computational Chemistry, Daxuecheng South Rd. 55, 401331, Chongqing, China
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80
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Juanes M, Saragi RT, Pérez C, Enríquez L, Jaraíz M, Lesarri A. Torsional chirality and molecular recognition: the homo and heterochiral dimers of thenyl and furfuryl alcohol. Phys Chem Chem Phys 2022; 24:8999-9006. [PMID: 35380144 DOI: 10.1039/d2cp00479h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Furfuryl alcohol and thenyl alcohol contain a labile torsional chiral center, producing transiently chiral enantiomers interconverting in the nanosecond time-scale. We explored chiral molecular recognition using the weakly-bound intermolecular dimers of both alcohols, freezing stereomutation. Supersonic jet broadband microwave spectroscopy revealed homo and heterochiral diastereoisomers for each alcohol dimer and the structural characteristics of the clusters. All dimers are primarily stabilized by a moderately intense O-H⋯O hydrogen bond, but differ in the secondary interactions, which introduce additional hydrogen bonds either to the ring oxygen in furfuryl alcohol or to the π ring system in thenyl alcohol. Density-functional calculations (B2PLYP-D3(BJ)/def2-TZVP) show no clear preferences for a particular stereochemistry in the dimers, with relative energies of the order 1-2 kJ mol-1. The study suggests opportunities for the investigation of chiral recognition in molecules with torsional barriers in between transient and permanent interconversion regimes.
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Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Cristóbal Pérez
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
| | - Lourdes Enríquez
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain
| | - Martín Jaraíz
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain.
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81
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Abstract
Molecular recognition1-4 and supramolecular assembly5-8 cover a broad spectrum9-11 of non-covalently orchestrated phenomena between molecules. Catalysis12 of such processes, however, unlike that for the formation of covalent bonds, is limited to approaches13-16 that rely on sophisticated catalyst design. Here we establish a simple and versatile strategy to facilitate molecular recognition by extending electron catalysis17, which is widely applied18-21 in synthetic covalent chemistry, into the realm of supramolecular non-covalent chemistry. As a proof of principle, we show that the formation of a trisradical complex22 between a macrocyclic host and a dumbbell-shaped guest-a molecular recognition process that is kinetically forbidden under ambient conditions-can be accelerated substantially on the addition of catalytic amounts of a chemical electron source. It is, therefore, electrochemically possible to control23 the molecular recognition temporally and produce a nearly arbitrary molar ratio between the substrates and complexes ranging between zero and the equilibrium value. Such kinetically stable supramolecular systems24 are difficult to obtain precisely by other means. The use of the electron as a catalyst in molecular recognition will inspire chemists and biologists to explore strategies that can be used to fine-tune non-covalent events, control assembly at different length scales25-27 and ultimately create new forms of complex matter28-30.
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82
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Francke R. Self-assembly of molecules triggered by electricity. Nature 2022; 603:229-230. [PMID: 35264746 DOI: 10.1038/d41586-022-00640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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83
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Ghosh R, Singh S, Mukherjee D, Mondal S, Das M, Pal U, Adhikari A, Bhushan A, Bose S, Bhattacharyya SS, Pal D, Saha-Dasgupta T, Bhattacharyya M, Bhattacharyya D, Mallick AK, Das R, Pal SK. Host-assisted delivery of a model drug to genomic DNA: Key information from ultrafast spectroscopy and in silico study. Chembiochem 2022; 23:e202200109. [PMID: 35225409 DOI: 10.1002/cbic.202200109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 11/10/2022]
Abstract
Intended drug delivery to a target without adverse effect is one of the major criteria for its acceptance in real use. Herein, we have made an attempt to explore the delivery efficacy of SDS surfactant in a monomer and micellar stage during the delivery of model drug, Toluidine Blue (TB) from micellar cavity to DNA. Molecular recognition of pre-micellar SDS encapsulated TB with DNA occurs at a rate constant (k1~652 s-1). On the contrary, no significant release of encapsulated TB at micellar concentration was observed within the experimental time frame. This originated from the higher binding affinity of TB towards the nano cavity of SDS at micellar concentration which doesn't allow the delivery of TB from the nano cavity of SDS micelle to DNA. Thus, molecular recognition controls the extent of DNA recognition by TB which in turn modulates the rate of delivery of TB from SDS in a concentration dependent morphology.
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Affiliation(s)
- Ria Ghosh
- S N Bose National Centre for Basic Sciences, CBMS, Block JD, Sector 3, Salt lake,, 700106, Kolkata, INDIA
| | - Soumendra Singh
- S N Bose National Centre for Basic Sciences, Technical Research Centre, Block JD, Sector 3, Salt Lake, 700106, Kolkata, INDIA
| | - Dipanjan Mukherjee
- S N Bose National Centre for Basic Sciences, CBMS, Block JD, Sector 3, Salt lake, 700106, Kolkata, INDIA
| | - Susmita Mondal
- S N Bose National Centre for Basic Sciences, CBMS, Block JD, Sector 3, Salt lake, 700106, Kolkata, INDIA
| | - Monojit Das
- Vidyasagar University, Zoology, 7221102, Midnapore, INDIA
| | - Uttam Pal
- S N Bose National Centre for Basic Sciences, Technical Research Centre, Block JD, Sector 3, Salt Lake, 700106, Kolkata, INDIA
| | - Aniruddha Adhikari
- S N Bose National Centre for Basic Sciences, CBMS, Block JD, Sector 3, Salt lake, 700106, Kolkata, INDIA
| | - Aman Bhushan
- Thapar University: Thapar Institute of Engineering and Technology, Biotechnology, Bhadson Road, Patiala, Punjab, 147004, Patiala, INDIA
| | - Surajit Bose
- KSDJ Dental College and Hospital, Oral and Maxillofacial Pathology, 700002, Kolkata, INDIA
| | | | - Debasish Pal
- Uluberia College, Zoology, 711315, Howrah, INDIA
| | - Tanusri Saha-Dasgupta
- S N Bose National Centre for Basic Sciences, CMPS, Block JD, Sector 3, Salt Lake, 700106, Kolkata, INDIA
| | - Maitree Bhattacharyya
- University of Calcutta, Biochemistry, 35, Ballygunge Circular Rd, Ballygunge, 700019, Kolkata, INDIA
| | - Debasis Bhattacharyya
- Nilratan Sircar Medical College and Hospital, Gynecology and Obstetrics, 138, AJC Bose Road, Sealdah, Raja Bazar,, 700014, Kolkata, INDIA
| | - Asim Kumar Mallick
- Nilratan Sircar Medical College and Hospital, Pediatric Medicine, 138, AJC Bose Road, Sealdah, Raja Bazar, 700014, Kolkata, INDIA
| | - Ranjan Das
- West Bengal State University, Chemistry, 700126, Kolkata, INDIA
| | - Samir Kumar Pal
- SNBNCBS, CBMS, Block JD, Sector III, Salt Lake City, 700098, Kolkata, INDIA
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84
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Xiong W, Liu X, Qi Q, Ji H, Liu F, Zhong C, Liu S, Tian T, Zhou X. Supramolecular CRISPR-OFF switches with host-guest chemistry. Nucleic Acids Res 2022; 50:1241-1255. [PMID: 35100423 PMCID: PMC8860601 DOI: 10.1093/nar/gkac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) technology is a powerful tool in biology and medicine. However, the safety and application of this technology is hampered by excessive activity of CRISPR machinery. It is particularly important to develop methods for switching off CRISPR activity in human cells. The current study demonstrates the concept of supramolecular CRISPR-OFF switches by employing host-guest chemistry. We demonstrate that the CRISPR systems show considerable tolerance to adamantoylation on guide RNAs (gRNAs), whereas supramolecular complexation tremendously affects the function of adamantoyl gRNAs. Host-guest chemistry is demonstrated to be novel and effective tools to reduce unwanted excessive activities of CRISPR complexes in human cells. This work indicates considerable potential of supramolecular strategy for controlling and enhancing CRISPR systems.
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Affiliation(s)
- Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Huimin Ji
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Fengbo Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Cheng Zhong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Simin Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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85
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Stanojlovic V, Müller A, Moazzam A, Hinterholzer A, Ożga K, Berlicki Ł, Schubert M, Cabrele C. A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. Chembiochem 2022; 23:e202100604. [PMID: 34856053 PMCID: PMC9299858 DOI: 10.1002/cbic.202100604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Indexed: 11/09/2022]
Abstract
The β-hairpin is a structural element of native proteins, but it is also a useful artificial scaffold for finding lead compounds to convert into peptidomimetics or non-peptide structures for drug discovery. Since linear peptides are synthetically more easily accessible than cyclic ones, but are structurally less well-defined, we propose XWXWXpPXK(/R)X(R) as an acyclic but still rigid β-hairpin scaffold that is robust enough to accommodate different types of side chains, regardless of the secondary-structure propensity of the X residues. The high conformational stability of the scaffold results from tight contacts between cross-strand cationic and aromatic side chains, combined with the strong tendency of the d-Pro-l-Pro dipeptide to induce a type II' β-turn. To demonstrate the robustness of the scaffold, we elucidated the NMR structures and performed molecular dynamics (MD) simulations of a series of peptides displaying mainly non-β-branched, poorly β-sheet-prone residues at the X positions. Both the NMR and MD data confirm that our acyclic β-hairpin scaffold is highly versatile as regards the amino-acid composition of the β-sheet face opposite to the cationic-aromatic one.
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Affiliation(s)
- Vesna Stanojlovic
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Anna Müller
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Ali Moazzam
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
- School of ChemistryCollege of ScienceUniversity of TehranP.O. Box 14155–6619TehranIran
| | - Arthur Hinterholzer
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Katarzyna Ożga
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Łukasz Berlicki
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Mario Schubert
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Chiara Cabrele
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
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86
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Li Q, Chang J, Shi H, Niu T, Dong H, Mu H. Cyanide detection using a highly selective fluorescent and colorimetrical double channel probe incorporating hybrid naphthopyran–benzothiazole in an aqueous solution. Supramol Chem 2022. [DOI: 10.1080/10610278.2022.2035386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Qiao Li
- College of Chemical Engineering, Lanzhou University of Arts and Science, Lanzhou, China
| | - Jing Chang
- Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, China
| | - Haixiong Shi
- College of Chemical Engineering, Lanzhou University of Arts and Science, Lanzhou, China
| | - Teng Niu
- College of Chemical Engineering, Lanzhou University of Arts and Science, Lanzhou, China
| | - Hongru Dong
- College of Chemical Engineering, Lanzhou University of Arts and Science, Lanzhou, China
| | - Hongmei Mu
- Department of Environment and Chemistry, Lanzhou Resources & Environment Voc-Tech College, Lanzhou, China
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87
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Mazumdar P, Choudhury D. Study of the alkyl-π interaction between methane and few substituted pyrimidine systems using DFT, AIM and NBO calculations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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88
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He W, Wang Q, Tian X, Pan G. Recapitulating dynamic ECM ligand presentation at biomaterial interfaces: Molecular strategies and biomedical prospects. EXPLORATION (BEIJING, CHINA) 2022; 2:20210093. [PMID: 37324582 PMCID: PMC10191035 DOI: 10.1002/exp.20210093] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
The extracellular matrix (ECM) provides not only physical support for the tissue structural integrity, but also dynamic biochemical cues capable of regulating diverse cell behaviors and functions. Biomaterial surfaces with dynamic ligand presentation are capable of mimicking the dynamic biochemical cues of ECM, showing ECM-like functions to modulate cell behaviors. This review paper described an overview of present dynamic biomaterial interfaces by focusing on currently developed molecular strategies for dynamic ligand presentation. The paradigmatic examples for each strategy were separately discussed. In addition, the regulation of some typical cell behaviors on these dynamic biointerfaces including cell adhesion, macrophage polarization, and stem cell differentiation, and their potential applications in pathogenic cell isolation, single cell analysis, and tissue engineering are highlighted. We hope it would not only clarify a clear background of this field, but also inspire to exploit novel molecular strategies and more applications to match the increasing demand of manipulating complex cellular processes in biomedicine.
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Affiliation(s)
- Wenbo He
- Institute for Advanced MaterialsSchool of Materials Science and EngineeringJiangsu UniversityZhenjiangP. R. China
| | - Qinghe Wang
- Institute for Advanced MaterialsSchool of Materials Science and EngineeringJiangsu UniversityZhenjiangP. R. China
| | - Xiaohua Tian
- Institute for Advanced MaterialsSchool of Materials Science and EngineeringJiangsu UniversityZhenjiangP. R. China
- School of Chemistry and Chemical EngineeringJiangsu UniversityZhenjiangP. R. China
| | - Guoqing Pan
- Institute for Advanced MaterialsSchool of Materials Science and EngineeringJiangsu UniversityZhenjiangP. R. China
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89
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Abstract
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His3-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pKa of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
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90
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Deng CL, Cheng M, Zavalij PY, Isaacs L. Thermodynamics of Pillararene•Guest Complexation: Blinded Dataset for the SAMPL9 Challenge. NEW J CHEM 2022; 46:995-1002. [PMID: 35250257 PMCID: PMC8896905 DOI: 10.1039/d1nj05209h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report an investigation of the complexation between a water soluble pillararene host (WP6) and a panel of hydrophobic cationic guests (G1 - G20) by a combination of 1H NMR spectroscopy and isothermal titration calorimetry in phosphate buffered saline. We find that WP6 forms 1:1 complexes with Ka values in the 104 - 109 M-1 range driven by favorable enthalpic contributions. This thermodynamic dataset serves as blinded data for the SAMPL9 challenge.
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Affiliation(s)
- Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Peter Y Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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91
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Vial L, Perret F, Leclaire J. Dyn[
n
]arenes: Versatile Platforms To Study the Interplay between Covalent and Noncovalent Bonds. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Laurent Vial
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | - Julien Leclaire
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
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92
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Kim H, Lee D. Cascade proton relays facilitate electron transfer across hydrogen‐bonding network. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Heechan Kim
- Department of Chemistry Seoul National University Seoul South Korea
| | - Dongwhan Lee
- Department of Chemistry Seoul National University Seoul South Korea
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93
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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94
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Lazić A, Radovanović L, Gak Simić K, Rogan J, Janjić G, Trišović N, Đorđević I. Unravelling conformational and crystal packing preferences of cyclohexane-5-spirohydantoin derivatives incorporating a halogenated benzoyl group. CrystEngComm 2022. [DOI: 10.1039/d2ce00376g] [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
The conformational and supramolecular diversity of spirohydantoins have been investigated.
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Affiliation(s)
- Anita Lazić
- Innovation Centre of the Faculty of Technology and Metallurgy, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Lidija Radovanović
- Innovation Centre of the Faculty of Technology and Metallurgy, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Kristina Gak Simić
- Innovation Centre of the Faculty of Technology and Metallurgy, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Jelena Rogan
- University of Belgrade, Faculty of Technology and Metallurgy, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Goran Janjić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11001 Belgrade, Serbia
| | - Nemanja Trišović
- University of Belgrade, Faculty of Technology and Metallurgy, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Ivana Đorđević
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11001 Belgrade, Serbia
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95
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Kikkawa Y, Nagasaki M, Koyama E, Ito S, Tsuzuki S. Halogen bond-directed self-assembly in bicomponent blends at the solid/liquid interface: Effect of the alkyl chain substitution position. Phys Chem Chem Phys 2022; 24:17088-17097. [DOI: 10.1039/d2cp02206k] [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
The fabrication of well-organised molecular assemblies on surfaces is fundamental for the creation of functional molecular systems applicable to nanoelectronics and molecular devices. In this study, we investigated the effect...
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96
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Zhou C, Hermes MR, Wu D, Bao JJ, Pandharkar R, King DS, Zhang D, Scott TR, Lykhin AO, Gagliardi L, Truhlar DG. Electronic structure of strongly correlated systems: recent developments in multiconfiguration pair-density functional theory and multiconfiguration nonclassical-energy functional theory. Chem Sci 2022; 13:7685-7706. [PMID: 35865899 PMCID: PMC9261488 DOI: 10.1039/d2sc01022d] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/01/2022] [Indexed: 12/25/2022] Open
Abstract
Strong electron correlation plays an important role in transition-metal and heavy-metal chemistry, magnetic molecules, bond breaking, biradicals, excited states, and many functional materials, but it provides a significant challenge for modern electronic structure theory. The treatment of strongly correlated systems usually requires a multireference method to adequately describe spin densities and near-degeneracy correlation. However, quantitative computation of dynamic correlation with multireference wave functions is often difficult or impractical. Multiconfiguration pair-density functional theory (MC-PDFT) provides a way to blend multiconfiguration wave function theory and density functional theory to quantitatively treat both near-degeneracy correlation and dynamic correlation in strongly correlated systems; it is more affordable than multireference perturbation theory, multireference configuration interaction, or multireference coupled cluster theory and more accurate for many properties than Kohn–Sham density functional theory. This perspective article provides a brief introduction to strongly correlated systems and previously reviewed progress on MC-PDFT followed by a discussion of several recent developments and applications of MC-PDFT and related methods, including localized-active-space MC-PDFT, generalized active-space MC-PDFT, density-matrix-renormalization-group MC-PDFT, hybrid MC-PDFT, multistate MC-PDFT, spin–orbit coupling, analytic gradients, and dipole moments. We also review the more recently introduced multiconfiguration nonclassical-energy functional theory (MC-NEFT), which is like MC-PDFT but allows for other ingredients in the nonclassical-energy functional. We discuss two new kinds of MC-NEFT methods, namely multiconfiguration density coherence functional theory and machine-learned functionals. This feature article overviews recent work on active spaces, matrix product reference states, treatment of quasidegeneracy, hybrid theory, density-coherence functionals, machine-learned functionals, spin–orbit coupling, gradients, and dipole moments.![]()
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Affiliation(s)
- Chen Zhou
- Department of Chemistry, Chemical Theory Center, Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
| | - Matthew R. Hermes
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dihua Wu
- Department of Chemistry, Chemical Theory Center, Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
| | - Jie J. Bao
- Department of Chemistry, Chemical Theory Center, Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
| | - Riddhish Pandharkar
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Daniel S. King
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dayou Zhang
- Department of Chemistry, Chemical Theory Center, Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
| | - Thais R. Scott
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Aleksandr O. Lykhin
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
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97
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Krishnapriya VU, Suresh CH. The use of electrostatic potential at nuclei in the analysis of halogen bonding. NEW J CHEM 2022. [DOI: 10.1039/d2nj00256f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular electrostatic potential data at interacting nuclei provide strong evidence of bond formation in many intermolecular halogen bonded complexes.
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Affiliation(s)
- Vilakkathala U. Krishnapriya
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
| | - Cherumuttathu H. Suresh
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
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98
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Lalisse RF, Pavlović RZ, Hadad CM, Badjić JD. A computational study of competing conformational selection and induced fit in an abiotic system. Phys Chem Chem Phys 2021; 24:507-511. [PMID: 34904140 DOI: 10.1039/d1cp05253e] [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
Host-guest complexations can be described by two competing mechanisms, conformational selection (CS) and induced fit (IF). In this work, we used a combination of nudged elastic band (NEB), adaptive steered molecular dynamics (ASMD), and density functional theory (DFT, with a correction for dispersion) to study the dynamics of the pathways (IF/CS) by which two conformers of basket B(+) and B(-) interconvert and trap CX4 guests (X = Cl and Br). While the results from NEB/DFT studies disclosed host-guest noncovalent contacts reducing the basket's conformational dynamics, ASMD methodology suggested an associative mechanism for the guest complexation. With theory in excellent agreement with experiments, NEB and ASMD emerge as the methods of choice for studying dynamics of supramolecular systems.
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Affiliation(s)
- Remy F Lalisse
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Radoslav Z Pavlović
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Christopher M Hadad
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Jovica D Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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99
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Wang P, Liu K, Ma H, Nian H, Li Y, Li Q, Cheng L, Cao L. Synthesis and aqueous anion recognition of an imidazolium-based nonacationic cup. Chem Commun (Camb) 2021; 57:13377-13380. [PMID: 34821898 DOI: 10.1039/d1cc05603d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An imidazolium-based nonacationic cup (1·9X; X = PF6- or Cl-) was synthesized via step-by-step SN2 reactions without using any template. The water-soluble 1·9Cl- as a molecular container can encapsulate anionic nucleoside triphosphate and dinucleotide molecules (e.g., ATP and NADH) inside its cavity through hydrogen bonds and electrostatic interactions in aqueous solution.
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Affiliation(s)
- Pinpin Wang
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, P. R. China.,College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Kai Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, P. R. China
| | - Huanqing Ma
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Hao Nian
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Yawen Li
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Qingfang Li
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Lin Cheng
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Liping Cao
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, P. R. China.
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100
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Brockett AT, Deng C, Shuster M, Perera S, DiMaggio D, Cheng M, Murkli S, Briken V, Roesch MR, Isaacs L. In Vitro and In Vivo Sequestration of Methamphetamine by a Sulfated Acyclic CB[n]-Type Receptor. Chemistry 2021; 27:17476-17486. [PMID: 34613641 PMCID: PMC8665056 DOI: 10.1002/chem.202102919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Indexed: 01/26/2023]
Abstract
We report the synthesis of two new acyclic sulfated acyclic CB[n]-type receptors (TriM0 and Me4 TetM0) and investigations of their binding properties toward a panel of drugs of abuse (1-13) by a combination of 1 H NMR spectroscopy and isothermal titration calorimetry. TetM0 is the most potent receptor with Ka ≥106 M-1 toward methamphetamine, fentanyl, MDMA and mephedrone. TetM0 is not cytotoxic toward HepG2 and HEK 293 cells below 100 μM according to MTS metabolic and adenylate kinase release assays and is well tolerated in vivo when dosed at 46 mg kg-1 . TetM0 does not inhibit the hERG ion channel and is not mutagenic based on the Ames fluctuation test. Finally, in vivo efficacy studies show that the hyperlocomotion of mice treated with methamphetamine can be greatly reduced by treatment with TetM0 up to 5 minutes later. TetM0 has potential as a broad spectrum in vivo sequestrant for drugs of abuse.
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Affiliation(s)
- Adam T Brockett
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland at College Park, College Park, MD 20742, United States
| | - Chunlin Deng
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, United States
| | - Suvenika Perera
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Delaney DiMaggio
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, United States
| | - Matthew R Roesch
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland at College Park, College Park, MD 20742, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
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