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Yuan T, Wang L, Chen L, Zhong J, Lin Y, Wang Y, Lin C, Fan H. Combinatorial preparation and structural characterization of anthocyanins and aglycones from Purple-heart Radish for evaluation of physicochemical stability and pancreatic lipase inhibitory activity. Food Chem 2024; 446:138832. [PMID: 38412808 DOI: 10.1016/j.foodchem.2024.138832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
In this study, an efficient approach to preparation of different anthocyanins from Purple-heart Radish was developed by combining microwave-assisted extraction (MAE), macroporous resin purification (MRP) and ultrasound-assisted acid hydrolysis (UAAH) for evaluation of physicochemical stability and pancreatic lipase (PL) inhibitory activity. By optimization of MAE, MRP and UAAH processes, the anthocyanins reached the yield of 6.081 ± 0.106 mg/g, the purity of 78.54 ± 0.62 % (w/w) and the content of 76.29 ± 1.31 % (w/w), respectively. With high-resolution UHPLC-Q-Orbitrap/MS, 15 anthocyanins were identified as pelargonins with diverse glucosides and confirmed by pelargonidin standard. By glycosylation, pelargonins exhibited higher stability in different pH, temperature, light, metal ions environments than that of pelargonidin. However, PL inhibitory assay, kinetic analysis and molecular docking demonstrated that pelargonidin had higher PL inhibitory activity than pelargonins even though with similar binding sites and a dose-effect relationship. The above results revealed that the effect of glycosylation and deglycosylation on PL inhibitory activity and physicochemical stability.
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Affiliation(s)
- Tiefeng Yuan
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China national Analytical Center), Guangzhou, 510070, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Liping Wang
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China national Analytical Center), Guangzhou, 510070, China
| | - Linzhou Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jinjian Zhong
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yuyang Lin
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yihan Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Chen Lin
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China national Analytical Center), Guangzhou, 510070, China.
| | - Huajun Fan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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2
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Xiao Y, Zhou H, Shi P, Zhao X, Liu H, Li X. Clickable tryptophan modification for late-stage diversification of native peptides. SCIENCE ADVANCES 2024; 10:eadp9958. [PMID: 38985871 PMCID: PMC11235173 DOI: 10.1126/sciadv.adp9958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
As the least abundant residue in proteins, tryptophan widely exists in peptide drugs and bioactive natural products and contributes to drug-target interactions in multiple ways. We report here a clickable tryptophan modification for late-stage diversification of native peptides, via catalyst-free C2-sulfenylation with 8-quinoline thiosulfonate reagents in trifluoroacetic acid (TFA). A wide range of groups including trifluoromethylthio (SCF3), difluoromethylthio (SCF2H), (ethoxycarbonyl)difluoromethylthio (SCF2CO2Et), alkylthio, and arylthio were readily incorporated. The rapid reaction kinetics of Trp modification and full tolerance with other 19 proteinogenic amino acids, as well as the super dissolving capability of TFA, render this method suitable for all kinds of Trp-containing peptides without limitations from sequences, hydrophobicity, and aggregation propensity. The late-stage modification of 15 therapeutic peptides (1.0 to 7.6 kilodaltons) and the improved bioactivity and serum stability of SCF3- and SCF2H-modified melittin analogs illustrated the effectiveness of this method and its potential in pharmacokinetic property improvement.
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Affiliation(s)
- Yisa Xiao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, Guangdong Province 515063, P. R. China
| | - Pengfei Shi
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xueqian Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
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3
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Valencia E, Ballester P. Enhanced binding of methyl alkylammonium cations through preorganization of a water-soluble calix[4]pyrrole. Org Biomol Chem 2024. [PMID: 38957010 DOI: 10.1039/d4ob00843j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
We describe the synthesis of two tetra-α aryl-extended calix[4]pyrroles (C[4]Ps) 4a-b bearing four terminal carboxylic groups in their meso-propyl chains defining the lower rims. The synthesized C[4]Ps became soluble (1-3 mM) in water at pD = 10. We probed the interaction of 4a towards tetra-methylammonium (G1) chloride in water using 1H NMR spectroscopy. The C[4]P 4a includes G1 in the shallow aromatic cavity defined by the pyrrole rings in cone conformation forming a 1 : 1 complex G1⊂4a. Pyridine-N-oxide (PNO) binding in the larger polar aromatic cavity of 4a results in the quantitative self-assembly of the supramolecular receptor PNO@4a featuring the pyrrole rings preorganized in cone conformation. The PNO@4a receptor displays improved binding properties towards G1 than the parent C[4]P 4a. We thermodynamically characterized (1H NMR titrations and ITC experiments) the 1 : 1 complexes of PNO@4a with a series of tetra-alkylammonium salts, including biologically relevant examples. The PNO@4a supramolecular receptor displays significant affinity (log K = 3-4) but lacks selectivity in water binding of methyl trialkyl ammonium cations. Cation-π and coulombic interactions are the main intermolecular forces stabilizing the complexes. We also performed DFT calculations to gain some insights into the complexes' structures.
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Affiliation(s)
- Esteban Valencia
- Institute of Chemical Research of Catalonia (ICIQ)-CERCA, The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans 16, 43007 Tarragona, Spain.
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili (URV), c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ)-CERCA, The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans 16, 43007 Tarragona, Spain.
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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4
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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5
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Gao B, Zhu S. The evolutionary novelty of insect defensins: from bacterial killing to toxin neutralization. Cell Mol Life Sci 2024; 81:230. [PMID: 38780625 PMCID: PMC11116330 DOI: 10.1007/s00018-024-05273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Insect host defense comprises two complementary dimensions, microbial killing-mediated resistance and microbial toxin neutralization-mediated resilience, both jointly providing protection against pathogen infections. Insect defensins are a class of effectors of innate immunity primarily responsible for resistance to Gram-positive bacteria. Here, we report a newly originated gene from an ancestral defensin via genetic deletion following gene duplication in Drosophila virilis, which confers an enhanced resilience to Gram-positive bacterial infection. This gene encodes an 18-mer arginine-rich peptide (termed DvirARP) with differences from its parent gene in its pattern of expression, structure and function. DvirARP specifically expresses in D. virilis female adults with a constitutive manner. It adopts a novel fold with a 310 helix and a two CXC motif-containing loop stabilized by two disulfide bridges. DvirARP exhibits no activity on the majority of microorganisms tested and only a weak activity against two Gram-positive bacteria. DvirARP knockout flies are viable and have no obvious defect in reproductivity but they are more susceptible to the DvirARP-resistant Staphylococcus aureus infection than the wild type files, which can be attributable to its ability in neutralization of the S. aureus secreted toxins. Phylogenetic distribution analysis reveals that DvirARP is restrictedly present in the Drosophila subgenus, but independent deletion variations also occur in defensins from the Sophophora subgenus, in support of the evolvability of this class of immune effectors. Our work illustrates for the first time how a duplicate resistance-mediated gene evolves an ability to increase the resilience of a subset of Drosophila species against bacterial infection.
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Affiliation(s)
- Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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6
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He J, Bai M, Xiao X, Qiu S, Chen W, Li J, Yu Y, Tian W. Intramolecular Cation-π Interactions Organize Bowl-Shaped, Luminescent Molecular Containers. Angew Chem Int Ed Engl 2024; 63:e202402697. [PMID: 38433608 DOI: 10.1002/anie.202402697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Molecules with nonplanar architectures are highly desirable due to their unique topological structures and functions. We report here the synthesis of two molecular containers (1 ⋅ 3Br- and 1 ⋅ 3Cl-), which utilize intramolecular cation-π interactions to enforce macrocylic arrangements and exhibit high binding affinity and luminescent properties. Remarkably, the geometry of the cation-π interaction can be flexibly tailored to achieve a precise ring arrangement, irrespective of the angle of the noncovalent bonds. Additionally, the C-H⋅⋅⋅Br- hydrogen bonds within the container are also conducive to stabilizing the bowl-shaped conformation. These bowl-shaped conformations were confirmed both in solution through NMR spectroscopy and in the solid state by X-ray studies. 1 ⋅ 3Br- shows high binding affinity and selectivity: F->Cl-, through C-H⋅⋅⋅X- (X=F, Cl) hydrogen bonds. Additionally, these containers exhibited blue fluorescence in solution and yellow room-temperature phosphorescence (RTP) in the solid state. Our findings illustrate the utility of cation-π interactions in designing functional molecules.
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Affiliation(s)
- Jia He
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Minggui Bai
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Xuedong Xiao
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Shuai Qiu
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Wenzhuo Chen
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Jiaqi Li
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai, 200444, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University., Xi'an, 710072, Shaanxi, P. R. China
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7
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Zhang JA, Chao Y, Xiao X, Luo S, Chen W, Tian W. Self-Adaptive Aromatic Cation-π Driven Dimensional Polymorphism in Supramolecular Polymers for the Photocatalytic Oxidation and Separation of Aromatic/Cyclic Aliphatic Compounds. Angew Chem Int Ed Engl 2024; 63:e202402760. [PMID: 38483296 DOI: 10.1002/anie.202402760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Indexed: 04/06/2024]
Abstract
The phenomenon of polymorphism is ubiquitous in nature, the controlled manipulation of which not only increases our ontological understanding of nature but also facilitates the conceptualization and realization of novel functional materials. However, achieving targeted polymorphism in supramolecular assemblies (SAs) remains a formidable challenge, largely because of the constraints inherent in controlling the specific binding motifs of noncovalent interactions. Herein, we propose self-adaptive aromatic cation-π binding motifs to construct polymorphic SAs in both the solid and solution states. Using distinct discrete cation-π-cation and long-range cation-π binding motifs enables control of the self-assembly directionality of a C2h-symmetric bifunctional monomer, resulting in the successful formation of both two-dimensional and three-dimensional crystalline SAs (2D-CSA and 3D-CSA). The differences in the molecular packing of 3D-CSA compared with that of 2D-CSA significantly improve the charge separation and carrier mobility, leading to enhanced photocatalytic activity for the aerobic oxidation of thioanisole to methyl phenyl sulfoxide (yield of 99 % vs 57 %). 2D-CSA, which has a vertical extended structure with favorable stronger interaction with toluene though face-to-face cation-π interactions than methylcyclohexane, shows higher toluene/methylcyclohexane separation efficiency than 3D-CSA (96.9 % for 2D-CSA vs 56.3 % for 3D-CSA).
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Affiliation(s)
- Ju-An Zhang
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yi Chao
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xuedong Xiao
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Shuai Luo
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenzhuo Chen
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, College of Pharmacy, Shaanxi University of Chinese Medicine, Xian-yang, 712046, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
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8
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Rahangdale R, Ghormode P, Tender T, Balireddy S, Birangal S, Kishore R, Mohammad FS, Pasupuleti M, Chandrashekar H R. Anti-HSV activity of nectin-1-derived peptides targeting HSV gD: an in-silico and in-vitro approach. J Biomol Struct Dyn 2024:1-14. [PMID: 38720617 DOI: 10.1080/07391102.2024.2349525] [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: 11/29/2023] [Accepted: 03/24/2024] [Indexed: 05/22/2024]
Abstract
Herpes simplex virus (HSV) infections affect a wide range of the global population. The emergence of resistance to the existing anti-HSV therapy highlights the necessity for an innovative strategy. The interaction of HSV gD with its main host receptor nectin-1 is a potential target for new antiviral drugs. The aim of this study was to develop a peptide derived from nectin-1 targeting HSV gD using the in-silico method and evaluate them for anti-HSV activity. Residues 59-133 of the Nectin-1 V-domain constitute the interaction interface with HSV gD. Bioinformatic tools viz., PEP-FOLD3, ClusPro 2.0, HawkDock and Desmond were used to model the peptide and confirm its binding specificity with HSV gD protein. The peptides with potential interactions were custom synthesized and anti-HSV activity was evaluated in vitro against HSV-1 and HSV-2 by CPE inhibition assay. Five peptide sequences were identified as exhibiting good interaction with HSV-gD proteins. Among them, peptide N1 (residues 76-90) offered maximum protection against HSV-1 (66.57%) and HSV-2 (71.12%) infections. Modification of the identified peptide through peptidomimetic approaches may further enhance the activity and stability of the identified peptide.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Rahangdale
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Parnavi Ghormode
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Tenzin Tender
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sridevi Balireddy
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sumit Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Raj Kishore
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Fayaz Shaik Mohammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Mukesh Pasupuleti
- Microbiology Division, Council of Scientific and Industrial Research, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghu Chandrashekar H
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
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9
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Pagán OR. The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling. Bioessays 2024; 46:e2300195. [PMID: 38459808 DOI: 10.1002/bies.202300195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.
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Affiliation(s)
- Oné R Pagán
- Department of Biology, West Chester University, West Chester, Pennsylvania, USA
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10
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Kamayirese S, Maity S, Hansen LA, Lovas S. The Development of CDC25A-Derived Phosphoseryl Peptides That Bind 14-3-3ε with High Affinities. Int J Mol Sci 2024; 25:4918. [PMID: 38732131 PMCID: PMC11084659 DOI: 10.3390/ijms25094918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Overexpression of the 14-3-3ε protein is associated with suppression of apoptosis in cutaneous squamous cell carcinoma (cSCC). This antiapoptotic activity of 14-3-3ε is dependent on its binding to CDC25A; thus, inhibiting 14-3-3ε - CDC25A interaction is an attractive therapeutic approach to promote apoptosis in cSCC. In this regard, designing peptide inhibitors of 14-3-3ε - CDC25A interactions is of great interest. This work reports the rational design of peptide analogs of pS, a CDC25A-derived peptide that has been shown to inhibit 14-3-3ε-CDC25A interaction and promote apoptosis in cSCC with micromolar IC50. We designed new peptide analogs in silico by shortening the parent pS peptide from 14 to 9 amino acid residues; then, based on binding motifs of 14-3-3 proteins, we introduced modifications in the pS(174-182) peptide. We studied the binding of the peptides using conventional molecular dynamics (MD) and steered MD simulations, as well as biophysical methods. Our results showed that shortening the pS peptide from 14 to 9 amino acids reduced the affinity of the peptide. However, substituting Gln176 with either Phe or Tyr amino acids rescued the binding of the peptide. The optimized peptides obtained in this work can be candidates for inhibition of 14-3-3ε - CDC25A interactions in cSCC.
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Affiliation(s)
| | | | | | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
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11
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Hall A, Chatzopoulou M, Frost J. Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements. Bioorg Med Chem 2024; 104:117653. [PMID: 38579492 DOI: 10.1016/j.bmc.2024.117653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 04/07/2024]
Abstract
Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.
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Affiliation(s)
- Adrian Hall
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK.
| | - Maria Chatzopoulou
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
| | - James Frost
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
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12
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Ganguly T, Das S, Maity D, Baitalik S. Luminescent Ruthenium-Terpyridine Complexes Coupled with Stilbene-Appended Naphthalene, Anthracene, and Pyrene Motifs Demonstrate Fluoride Ion Sensing and Reversible Trans-Cis Photoisomerization. Inorg Chem 2024; 63:6883-6897. [PMID: 38567656 DOI: 10.1021/acs.inorgchem.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A new family of luminescent heteroleptic Ru(II)-terpyridine complexes coupled with stilbene-appended naphthalene, anthracene, and pyrene motifs is reported. Each of the complexes features moderately intense emission at room temperature having a lifetime of 16.7 ns for naphthalene and 11.4 ns for anthracene, while a substantially elevated lifetime of 8.3 μs was observed for the pyrene derivative. All the three complexes display a reversible couple in the positive potential window due to Ru2+/Ru3+ oxidation but multiple reversible and/or quasi-reversible peaks in the negative potential domain because of the reduction of the terpyridine moieties. All the complexes selectively sense F- among the studied anions via the intermediary of different noncovalent interactions. The interaction event is monitored through absorption, emission, and 1H and 19F NMR spectroscopy. Additionally, upon utilizing the stilbene motif, reversible trans-cis isomerization of the complexes has been undertaken upon alternate treatment of visible and UV light so that the complexes can act as potential photomolecular switches. We also carried out the anion sensing characterization of the cis form of the complexes. Theoretical calculation employing density functional theory is also executed for a selective complex (naphthalene derivative) to elucidate different noncovalent interactions that are operative during the complex-fluoride interplay.
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Affiliation(s)
- Tanusree Ganguly
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Soumi Das
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Dinesh Maity
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
- Department of Chemistry, Katwa College, Purba Bardhaman, West Bengal 713130, India
| | - Sujoy Baitalik
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
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13
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Zhang Z, Hu X, Qiu S, Su J, Bai R, Zhang J, Tian W. Boron-Nitrogen-Embedded Polycyclic Aromatic Hydrocarbon-Based Controllable Hierarchical Self-Assemblies through Synergistic Cation-π and C-H···π Interactions for Bifunctional Photo- and Electro-Catalysis. J Am Chem Soc 2024. [PMID: 38602776 DOI: 10.1021/jacs.4c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Boron-Nitrogen-embedded polycyclic aromatic hydrocarbons (BN-PAHs) as novel π-conjugated systems have attracted immense attention owing to their superior optoelectronic properties. However, constructing long-range ordered supramolecular assemblies based on BN-PAHs remains conspicuously scarce, primarily attributed to the constraints arising from coordinating multiple noncovalent interactions and the intrinsic characteristics of BN-PAHs, which hinder precise control over delicate self-assembly processes. Herein, we achieve the successful formation of BN-PAH-based controllable hierarchical assemblies through synergistically leveraged cation-π and C-H···π interactions. By carefully adjusting the solvent conditions in two progressive assembly hierarchies, the one-dimensional (1D) supramolecular assemblies with "rigid yet flexible" assembled units are first formed by cation-π interactions, and then they can be gradually fused into two-dimensional (2D) structures under specific C-H···π interactions, thus realizing the precise control of the transformation process from BN-PAH-based 1D primary structures to 2D higher-order assemblies. The resulting 2D-BNSA, characterized by enhanced electrical conductivity and ordered 2D layered structure, provides anchoring and dispersion sites for loading two appropriate nanocatalysts, thus facilitating the efficient photocatalytic CO2 reduction (with a remarkable CH4 evolution rate of 938.7 μmol g-1 h-1) and electrocatalytic acetylene semihydrogenation (reaching a Faradaic efficiency for ethylene up to 98.5%).
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Affiliation(s)
- Zhelin Zhang
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiao Hu
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Shuai Qiu
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Junlong Su
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Rui Bai
- State Key Laboratory of Solidification Processing and School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Jian Zhang
- State Key Laboratory of Solidification Processing and School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
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14
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Lin Y, Wang C, Wu J, Tang J, Ye G, Zhao X, Li H, He Y. Imaging the Iodine Sorption-Induced Synchronous Skeleton-Pore Interactions of Single Covalent Organic Framework Particles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401167. [PMID: 38528426 DOI: 10.1002/smll.202401167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Covalent organic frameworks (COFs) are promising iodine adsorbents. For improved performances, it is critical and essential to fundamentally understand the underlying mechanism. Here, using the operando dark-field optical microscopy (DFM) imaging technique, the observation of an extraordinary structure shrinkage of 2D triphenylbenzene (TPB)-dimethoxyterephthaldehyde (DMTP)-COF upon the adsorption of I2 vapor at the single-particle resolution is reported. Combining single-particle DFM imaging with other experimental and theoretical methods, it is revealed that the shrinkage mechanism of the TPB-DMTP-COF is attributed to the I2 sorption-induced synchronous skeleton-pore interactions. The redox reaction of I2 and TPB-DMTP-COF yields some cationic skeletons and I3 - species, which triggers the multi-directional halogen-bonding interactions of I2 and I3 - as well as strong cation-π interactions between neutral and cationic skeletons, accompanying the synchronous in-plane skeleton shrinking in the xy plane and compact out-of-plane layer packing in the z-direction. This understanding of the synchronous action between the skeleton and pore breaks the perspective on the structure robustness of 2D COFs with excellent stability during the I2 uptake, which offers pivotal guidance for the rational design and creation of advanced microporous adsorbents.
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Affiliation(s)
- Ying Lin
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Changjiang Wang
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Jinxiang Wu
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Jian Tang
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Guangmao Ye
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Xiaobing Zhao
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Hua Li
- SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, P. R. China
| | - Yi He
- School of Nuclear Science & Technology, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
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15
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Straus SK. Tryptophan- and arginine-rich antimicrobial peptides: Anti-infectives with great potential. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184260. [PMID: 38113954 DOI: 10.1016/j.bbamem.2023.184260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
With the increasing prevalence of multidrug resistant (MDR) bacteria, there is a need to design synthetic antimicrobial peptides (AMPs) that are effective and selective for bacteria, i.e. non-toxic to mammalian cells. One design strategy, namely the use of tryptophan- and arginine-rich AMPs, is rooted in the study of natural AMPs that are composed mainly of these amino acids, such as lactoferricin, tritrpticin, and puroindoline. A number of important studies on these AMPs by the Vogel group are reviewed here. More recent work on W-/R-rich peptides is also presented. The examples show that these peptides represent anti-infectives with great potential.
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Affiliation(s)
- Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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16
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Kilgore HR, Mikhael PG, Overholt KJ, Boija A, Hannett NM, Van Dongen C, Lee TI, Chang YT, Barzilay R, Young RA. Distinct chemical environments in biomolecular condensates. Nat Chem Biol 2024; 20:291-301. [PMID: 37770698 DOI: 10.1038/s41589-023-01432-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
Diverse mechanisms have been described for selective enrichment of biomolecules in membrane-bound organelles, but less is known about mechanisms by which molecules are selectively incorporated into biomolecular assemblies such as condensates that lack surrounding membranes. The chemical environments within condensates may differ from those outside these bodies, and if these differed among various types of condensate, then the different solvation environments would provide a mechanism for selective distribution among these intracellular bodies. Here we use small molecule probes to show that different condensates have distinct chemical solvating properties and that selective partitioning of probes in condensates can be predicted with deep learning approaches. Our results demonstrate that different condensates harbor distinct chemical environments that influence the distribution of molecules, show that clues to condensate chemical grammar can be ascertained by machine learning and suggest approaches to facilitate development of small molecule therapeutics with optimal subcellular distribution and therapeutic benefit.
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Affiliation(s)
- Henry R Kilgore
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
| | - Peter G Mikhael
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kalon J Overholt
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Regina Barzilay
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Xie X, Moon PJ, Crossley SWM, Bischoff AJ, He D, Li G, Dao N, Gonzalez-Valero A, Reeves AG, McKenna JM, Elledge SK, Wells JA, Toste FD, Chang CJ. Oxidative cyclization reagents reveal tryptophan cation-π interactions. Nature 2024; 627:680-687. [PMID: 38448587 PMCID: PMC11198740 DOI: 10.1038/s41586-024-07140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.
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Affiliation(s)
- Xiao Xie
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick J Moon
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Steven W M Crossley
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda J Bischoff
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dan He
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gen Li
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Nam Dao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Audrey G Reeves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | | | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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18
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Yang K, Alkhamis O, Canoura J, Bryant A, Gong EM, Barbu M, Taylor S, Nikic D, Banerjee S, Xiao Y, Stojanovic MN, Landry DW. Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine. JACS AU 2024; 4:760-770. [PMID: 38425914 PMCID: PMC10900216 DOI: 10.1021/jacsau.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
We reported over 20 years ago MNS-4.1, the first DNA aptamer with a micromolar affinity for cocaine. MNS-4.1 is based on a structural motif that is very common in any random pool of oligonucleotides, and it is actually a nonspecific hydrophobic receptor with wide cross-reactivity with alkaloids and steroids. Despite such weaknesses preventing broad applications, this aptamer became widely used in proof-of-concept demonstrations of new formats of biosensors. We now report a series of progressively improved DNA aptamers recognizing cocaine, with the final optimized receptors having low nanomolar affinity and over a thousand-fold selectivity over the initial cross-reactants. In the process of optimization, we tested different methods to eliminate cross-reactivities and improve affinity, eventually achieving properties that are comparable to those of the reported monoclonal antibody candidates for the therapy of overdose. Multiple aptamers that we now report share structural motifs with the previously reported receptor for serotonin. Further mutagenesis studies revealed a palindromic, highly adaptable, broadly cross-reactive hydrophobic motif that could be rebuilt through mutagenesis, expansion of linker regions, and selections into receptors with exceptional affinities and varying specificities.
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Affiliation(s)
- Kyungae Yang
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Obtin Alkhamis
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alexandra Bryant
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Edward M. Gong
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Mihaela Barbu
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Steven Taylor
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Dragan Nikic
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Saswata Banerjee
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Yi Xiao
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Milan N. Stojanovic
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
- Departments
of Biomedical Engineering and Systems Biology, Columbia University, New York, New York 10032, United States
| | - Donald W. Landry
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
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19
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Nalivaiko EY, Vasseur CM, Seebeck FP. Enzyme-Catalyzed Oxidative Degradation of Ergothioneine. Angew Chem Int Ed Engl 2024; 63:e202318445. [PMID: 38095354 DOI: 10.1002/anie.202318445] [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: 12/01/2023] [Indexed: 01/13/2024]
Abstract
Ergothioneine is a sulfur-containing metabolite that is produced by bacteria and fungi, and is absorbed by plants and animals as a micronutrient. Ergothioneine reacts with harmful oxidants, including singlet oxygen and hydrogen peroxide, and may therefore protect cells against oxidative stress. Herein we describe two enzymes from actinobacteria that cooperate in the specific oxidative degradation of ergothioneine. The first enzyme is an iron-dependent thiol dioxygenase that produces ergothioneine sulfinic acid. A crystal structure of ergothioneine dioxygenase from Thermocatellispora tengchongensis reveals many similarities with cysteine dioxygenases, suggesting that the two enzymes share a common mechanism. The second enzyme is a metal-dependent ergothioneine sulfinic acid desulfinase that produces Nα-trimethylhistidine and SO2 . The discovery that certain actinobacteria contain the enzymatic machinery for O2 -dependent biosynthesis and O2 -dependent degradation of ergothioneine indicates that these organisms may actively manage their ergothioneine content.
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Affiliation(s)
- Egor Y Nalivaiko
- Department of Chemistry, University of Basel, Mattenstrasse 22, 4002, Basel, Switzerland
| | - Camille M Vasseur
- Department of Chemistry, University of Basel, Mattenstrasse 22, 4002, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 22, 4002, Basel, Switzerland
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20
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Sathyavageeswaran A, Bonesso Sabadini J, Perry SL. Self-Assembling Polypeptides in Complex Coacervation. Acc Chem Res 2024; 57:386-398. [PMID: 38252962 DOI: 10.1021/acs.accounts.3c00689] [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: 01/24/2024]
Abstract
Intracellular compartmentalization plays a pivotal role in cellular function, with membrane-bound organelles and membrane-less biomolecular "condensates" playing key roles. These condensates, formed through liquid-liquid phase separation (LLPS), enable selective compartmentalization without the barrier of a lipid bilayer, thereby facilitating rapid formation and dissolution in response to stimuli. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs), which are often rich in charged and polar amino acid sequences, scaffold many condensates, often in conjunction with RNA.Comprehending the impact of IDP/IDR sequences on phase separation poses a challenge due to the extensive chemical diversity resulting from the myriad amino acids and post-translational modifications. To tackle this hurdle, one approach has been to investigate LLPS in simplified polypeptide systems, which offer a narrower scope within the chemical space for exploration. This strategy is supported by studies that have demonstrated how IDP function can largely be understood based on general chemical features, such as clusters or patterns of charged amino acids, rather than residue-level effects, and the ways in which these kinds of motifs give rise to an ensemble of conformations.Our laboratory has utilized complex coacervates assembled from oppositely charged polypeptides as a simplified material analogue to the complexity of liquid-liquid phase separated biological condensates. Complex coacervation is an associative LLPS that occurs due to the electrostatic complexation of oppositely charged macro-ions. This process is believed to be driven by the entropic gains resulting from the release of bound counterions and the reorganization of water upon complex formation. Apart from their direct applicability to IDPs, polypeptides also serve as excellent model polymers for investigating molecular interactions due to the wide range of available side-chain functionalities and the capacity to finely regulate their sequence, thus enabling precise control over interactions with guest molecules.Here, we discuss fundamental studies examining how charge patterning, hydrophobicity, chirality, and architecture affect the phase separation of polypeptide-based complex coacervates. These efforts have leveraged a combination of experimental and computational approaches that provide insight into molecular level interactions. We also examine how these parameters affect the ability of complex coacervates to incorporate globular proteins and viruses. These efforts couple directly with our fundamental studies into coacervate formation, as such "guest" molecules should not be considered as experiencing simple encapsulation and are instead active participants in the electrostatic assembly of coacervate materials. Interestingly, we observed trends in the incorporation of proteins and viruses into coacervates formed using different chain length polypeptides that are not well explained by simple electrostatic arguments and may be the result of more complex interactions between globular and polymeric species. Additionally, we describe experimental evidence supporting the potential for complex coacervates to improve the thermal stability of embedded biomolecules, such as viral vaccines.Ultimately, peptide-based coacervates have the potential to help unravel the physics behind biological condensates, while paving the way for innovative methods in compartmentalization, purification, and biomolecule stabilization. These advancements could have implications spanning medicine to biocatalysis.
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Affiliation(s)
- Arvind Sathyavageeswaran
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
| | - Júlia Bonesso Sabadini
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 10003, United States
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21
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Huang Z, Li P, Lei Y, Deng XY, Chen YN, Tian S, Pan X, Lei X, Song C, Zheng Y, Wang JY, Zhang Z, Lei T. Azonia-Naphthalene: A Cationic Hydrophilic Building Block for Stable N-Type Organic Mixed Ionic-Electronic Conductors. Angew Chem Int Ed Engl 2024; 63:e202313260. [PMID: 37938169 DOI: 10.1002/anie.202313260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/09/2023]
Abstract
Conjugated polymers that can efficiently transport both ionic and electronic charges have broad applications in next-generation optoelectronic, bioelectronic, and energy storage devices. To date, almost all the conjugated polymers have hydrophobic backbones, which impedes efficient ion diffusion/transport in aqueous media. Here, we design and synthesize a novel hydrophilic polymer building block, 4a-azonia-naphthalene (AN), drawing inspiration from biological systems. Because of the strong electron-withdrawing ability of AN, the AN-based polymers show typical n-type charge transport behaviors. We find that cationic aromatics exhibit strong cation-π interactions, leading to smaller π-π stacking distance, interesting ion diffusion behavior, and good morphology stability. Additionally, AN enhances the hydrophilicity and ionic-electronic coupling of the polymer, which can help to improve ion diffusion/injection speed, and operational stability of organic electrochemical transistors (OECTs). The integration of cationic building blocks will undoubtedly enrich the material library for high-performance n-type conjugated polymers.
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Affiliation(s)
- Zhen Huang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peiyun Li
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Yuqiu Lei
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xin-Yu Deng
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Yu-Nan Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Shuangyan Tian
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Xiran Pan
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Xun Lei
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Cheng Song
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yuting Zheng
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Jie-Yu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhi Zhang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Ting Lei
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
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22
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Hőgye F, Farkas LB, Balogh ÁK, Szilágyi L, Alnukari S, Bajza I, Borbás A, Fehér K, Illyés TZ, Timári I. Saturation Transfer Difference NMR and Molecular Docking Interaction Study of Aralkyl-Thiodigalactosides as Potential Inhibitors of the Human-Galectin-3 Protein. Int J Mol Sci 2024; 25:1742. [PMID: 38339036 PMCID: PMC10855533 DOI: 10.3390/ijms25031742] [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: 12/31/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3'-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3'-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation-π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3.
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Affiliation(s)
- Fanni Hőgye
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - László Bence Farkas
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Álex Kálmán Balogh
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - László Szilágyi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - Samar Alnukari
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - István Bajza
- GlycOptim Kft., Egyetem tér 1, H-4032 Debrecen, Hungary;
| | - Anikó Borbás
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Krisztina Fehér
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Tünde Zita Illyés
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
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23
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de Souza Neto LR, Montoya BO, Brandão-Neto J, Verma A, Bowyer S, Moreira-Filho JT, Dantas RF, Neves BJ, Andrade CH, von Delft F, Owens RJ, Furnham N, Silva-Jr FP. Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Sci Rep 2024; 14:1582. [PMID: 38238498 PMCID: PMC10796382 DOI: 10.1038/s41598-024-52018-2] [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: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. Praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, but despite that it is ineffective against juvenile worms and size and taste issues with its pharmaceutical forms impose challenges for treating school-aged children. It is also important to note that PZQ resistant strains can be generated in laboratory conditions and observed in the field, hence its extensive use in mass drug administration programs raises concerns about resistance, highlighting the need to search for new schistosomicidal drugs. Schistosomes survival relies on the redox enzyme thioredoxin glutathione reductase (TGR), a validated target for the development of new anti-schistosomal drugs. Here we report a high-throughput fragment screening campaign of 768 compounds against S. mansoni TGR (SmTGR) using X-ray crystallography. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the "doorstop pocket" near the NADPH binding site. We have compared results from hotspots and pocket druggability analysis of SmTGR with the experimental binding sites found in this work, with our results indicating only limited coincidence between experimental and computational results. Finally, we discuss that binding sites at the doorstop/NADPH binding site and in the SmTGR dimer interface, should be prioritized for developing SmTGR inhibitors as new antischistosomal drugs.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bogar Omar Montoya
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
| | - Anil Verma
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sebastian Bowyer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rafael Ferreira Dantas
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
- CRAFT - Center for Research and Advancement of Fragments and Molecular Targets, University of São Paulo, São Paulo, Brazil
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Structural Biology, Rosalind Franklin Institute, Harwell, UK.
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Floriano Paes Silva-Jr
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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24
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Stefania R, Palagi L, Di Gregorio E, Ferrauto G, Dinatale V, Aime S, Gianolio E. Seeking for Innovation with Magnetic Resonance Imaging Paramagnetic Contrast Agents: Relaxation Enhancement via Weak and Dynamic Electrostatic Interactions with Positively Charged Groups on Endogenous Macromolecules. J Am Chem Soc 2024; 146:134-144. [PMID: 38152996 PMCID: PMC10785807 DOI: 10.1021/jacs.3c06275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Gd-L1 is a macrocyclic Gd-HPDO3A derivative functionalized with a short spacer to a trisulfonated pyrene. When compared to Gd-HPDO3A, the increased relaxivity appears to be determined by both the higher molecular weight and the occurrence of an intramolecularly catalyzed prototropic exchange of the coordinated OH moiety. In water, Gd-L1 displayed a relaxivity of 7.1 mM-1 s-1 (at 298 K and 0.5 T), slightly increasing with the concentration likely due to the onset of intermolecular aggregation. A remarkably high and concentration-dependent relaxivity was measured in human serum (up to 26.5 mM-1 s-1 at the lowest tested concentration of 0.005 mM). The acquisition of 1H-nuclear magnetic relaxation dispersion (NMRD) and 17O-R2 vs T profiles allowed to get an in-depth characterization of the system. In vitro experiments in the presence of human serum albumin, γ-globulins, and polylysine, as well as using media mimicking the extracellular matrix, provided strong support to the view that the trisulfonated pyrene fosters binding interactions with the exposed positive groups on the surface of proteins, responsible for a remarkable in vivo hyperintensity in T1w MR images. The in vivo MR images of the liver, kidneys, and spleen showed a marked contrast enhancement in the first 10 min after the i.v. injection of Gd-L1, which was 2-6-fold higher than that for Gd-HPDO3A, while maintaining a very similar excretion behavior. These findings may pave the way to an improved design of MRI GBCAs, for the first time, based on the setup of weak and dynamic interactions with abundant positive groups on serum and ECM proteins.
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Affiliation(s)
- Rachele Stefania
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
- Department
of Science and Technological Innovation, University of Eastern Piedmont, Alessandria 15120, Italy
| | - Lorenzo Palagi
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Enza Di Gregorio
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Giuseppe Ferrauto
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Valentina Dinatale
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | | | - Eliana Gianolio
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
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25
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Zheng R, Cheng M, Ma R, Schipper D, Pichugin K, Sciaini G. Solvent effects on the intramolecular charge transfer excited state of 3CzClIPN: a broadband transient absorption study. Phys Chem Chem Phys 2024; 26:1039-1045. [PMID: 38093689 DOI: 10.1039/d3cp04975b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The prediction of solvent properties using molecular probes often relies on correlating steady-state absorption and fluorescence measurements, as well as determining absorption maxima and/or Stokes shifts. In this study, we employ femtosecond broadband transient absorption (fs-bb-TA) spectroscopy to investigate the spectroscopic behaviour of the intramolecular charge transfer (ICT) excited state of 3CzClIPN (2,4,6-tri(9H-carbazol-9-yl)-5-chloroisophthalonitrile), a representative ICT organic molecule, in both aromatic and non-aromatic solvents. Unlike observations in non-aromatic media, fs-bb-TA spectra of 3CzClIPN in aromatic solvents exhibit enhanced spectral broadening that strongly correlates with the solvent's polarity. We hypothesise that this spectral broadening originates from a wider configurational energy landscape experienced by the positively charged carbazole Cz+ group, owing to the larger size and, consequently, reduced solvation effectiveness of aromatic solvent molecules.
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Affiliation(s)
- Ruofei Zheng
- The Ultrafast Electron Imaging Laboratory, University of Waterloo, Waterloo, Canada.
- Department of Chemistry, University of Waterloo, Waterloo, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada
| | - Meixin Cheng
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Ruishu Ma
- The Ultrafast Electron Imaging Laboratory, University of Waterloo, Waterloo, Canada.
- Department of Chemistry, University of Waterloo, Waterloo, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada
| | - Derek Schipper
- Department of Chemistry, University of Waterloo, Waterloo, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada
| | - Kostyantyn Pichugin
- The Ultrafast Electron Imaging Laboratory, University of Waterloo, Waterloo, Canada.
- Department of Chemistry, University of Waterloo, Waterloo, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada
| | - Germán Sciaini
- The Ultrafast Electron Imaging Laboratory, University of Waterloo, Waterloo, Canada.
- Department of Chemistry, University of Waterloo, Waterloo, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada
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26
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Park MY, Kim S, Kwon NH, Moon G, Cha J, Kwon I. Enhanced anti-tumor activity of arginine decarboxylase through the incorporation of aromatic amino acids at the multimer-forming interface. Biotechnol J 2024; 19:e2300453. [PMID: 37899497 DOI: 10.1002/biot.202300453] [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: 09/01/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 10/31/2023]
Abstract
The pressing challenge of cancer's high mortality and invasiveness demands improved therapeutic approaches. Targeting the nutrient dependencies within cancer cells has emerged as a promising approach. This study is dedicated to demonstrating the potential of arginine depletion for cancer treatment. Notably, the focus centers on arginine decarboxylase (RDC), a pH-dependent enzyme expecting enhanced activity within the slightly acidic microenvironments of tumors. To investigate the effect of a single-site mutation on the catalytic efficacy of RDC, diverse amino acids, including glycine, alanine, phenylalanine, tyrosine, tryptophan, p-azido-phenylalanine, and a phenylalanine analog with a hydrogen-substituted tetrazine, were introduced at the crucial threonine site (position 39) in the multimer-forming interface. Remarkably, the introduction of either a natural or a non-natural aromatic amino acid at position 39 substantially boosted enzymatic activity, while amino acids with smaller side chains did not show the same effect. This enhanced enzymatic activity is likely attributed to the reinforced formation of multimer structures through favorable interactions between the introduced aromatic amino acid and the neighboring subunit. Noteworthy, at slightly acidic pH, the RDC variant featuring tryptophan at position 39 demonstrated augmented cytotoxicity against tumor cells compared to the wild-type RDC. This attribute aligns with the tumor microenvironment and positions these variants as potential candidates for targeted cancer therapy.
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Affiliation(s)
- Min Yeong Park
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Seoungkyun Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Na Hyun Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Giseok Moon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jaehyun Cha
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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27
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Chen SY, Koch M, Chávez-Gutiérrez L, Zacharias M. How Modulator Binding at the Amyloidβ-γ-Secretase Interface Enhances Substrate Binding and Attenuates Membrane Distortion. J Med Chem 2023; 66:16772-16782. [PMID: 38059872 DOI: 10.1021/acs.jmedchem.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Inhibition of γ-secretase, an intramembrane protease, to reduce secretion of Amyloid-β (Aβ) peptides has been considered for treating Alzheimer's disease. However, γ-secretase inhibitors suffer from severe side effects. As an alternative, γ-secretase modulators (GSM) reduce the generation of toxic peptides by enhancing the cleavage processivity without diminishing the enzyme activity. Starting from a known γ-secretase structure without substrate but in complex with an E2012 GSM, we generated a structural model that included a bound Aβ43 peptide and studied interactions among enzyme, substrate, GSM, and lipids. Our result suggests that E2012 binding at the enzyme-substrate-membrane interface attenuates the membrane distortion by shielding the substrate-membrane interaction. The model predicts that the E2012 modulation is charge-dependent and explains the preserved hydrogen acceptor and the aromatic ring observed in many imidazole-based GSM. Predicted effects of γ-secretase mutations on E2012 modulation were confirmed experimentally. We anticipate that the study will facilitate the future development of effective GSMs.
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Affiliation(s)
- Shu-Yu Chen
- Center for Functional Protein Assemblies, Garching 85748, Germany
| | - Matthias Koch
- VIB/KU Leuven, VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
| | | | - Martin Zacharias
- Center for Functional Protein Assemblies, Garching 85748, Germany
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28
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Yadav K, Kuldeep J, Shabeer Ali H, Siddiqi MI, Tripathi R. Metacaspase (Pf MCA-1) as antimalarial drug target: An in silico approach and their biological validation. Life Sci 2023; 335:122271. [PMID: 37977356 DOI: 10.1016/j.lfs.2023.122271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
AIMS Acquired drug resistance of Plasmodium is a global issue for the treatment of malaria. There are various proteases in the genome of Plasmodium falciparum (P. falciparum) including metacaspase-1 (PfMCA-1) that are essential and are being considered as an attractive drug target. It is aimed to identify novel therapeutics against malaria and their action on PfMCA-1 along with other apoptotic pathway events. MAIN METHODS High throughput virtual screening of 55,000 compounds derived from Maybridge library was performed against PfMCA-1. Based on the docking score, sixteen compounds were selected for in vitro antimalarial screening against drug sensitive and resistant strains of P. falciparum using SYBR green-based assay. Subsequently, three lead molecules were selected and subjected to the evaluation of cytotoxicity, caspase like protease activity, mitochondrial membrane potential, ROS generation and DNA fragmentation via TUNEL assay. KEY FINDINGS The in silico and in vitro approaches have brought forward some Maybridge library compounds with antiplasmodial activity most likely by enhancing the metacaspase activity. The compound CD11095 has shown better antimalarial efficacy, and KM06591 depicted higher caspase mediated killing, elevated TUNEL positive cells and moderate ROS generation. Mitochondrial membrane depolarization was augmented by RJC0069. Exposure of P. falciparum to CD11095, KM06591 and RJC0069 has ended up in parasite growth arrest via multiple mechanisms. SIGNIFICANCE It is proposed that the Maybridge molecules CD11095, KM06591 and RJC0069 have antimalarial activity. Their mechanism of action was found to be by enhancing the metacaspases-like protease activity, mitochondrial depolarization and DNA fragmentation which stipulates significant insights towards promising candidates for drug development.
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Affiliation(s)
- Kanchan Yadav
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jitendra Kuldeep
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - H Shabeer Ali
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Mohammad Imran Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Renu Tripathi
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
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29
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Assaf KI, Nau WM. Dispersion Interactions in Condensed Phases and inside Molecular Containers. Acc Chem Res 2023; 56:3451-3461. [PMID: 37956240 DOI: 10.1021/acs.accounts.3c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
ConspectusThe past decade has seen significant progress in the understanding and appreciation of the importance of London dispersion interactions (LDIs) in supramolecular systems and solutions. The Slater-Kirkwood formula relates LDIs to the molecular polarizabilities of the two interacting molecular species (α) and their interaction distance (a dependence of R-6). When advancing arguments related to intermolecular interactions, it is frequently assumed that molecules with larger molecular polarizabilities are more amenable to larger LDIs. However, arguments related to molecular polarizabilities are not always transferable to the condensed phase. In fact, the underlying bulk and molecular polarizabilities of common solvents show opposing trends. The intuitive concept that aromatic molecules are more polarizable than saturated hydrocarbons and that perfluorinated molecules are less polarizable than saturated hydrocarbons applies to the condensed phase only. When treating association phenomena in solution, where LDIs are generally very attenuated, the use of bulk polarizabilities is recommended, which are experimentally accessible through either refractive index measurements or suitable solvatochromic probes. Such probes can also be used to assess polarizabilities inside molecular container compounds, such as cucurbit[n]urils (CBn), cyclodextrins, calixarenes, and hemicarcerands. These macrocyclic cavities can have extreme microenvironments. For example, the inner concave phase of CB7 has been shown to be weakly polarizable, falling in between the gas phase and perfluorohexane; those of β-cyclodextrin and p-sulfonatocalix[4]arene have been found to be similarly polarizable as water and alkanes, respectively, and the inside of hemicarcerands displays a very large bulk polarizability, exceeding that of diiodomethane. CBn compounds are privileged molecular container compounds, which we exemplify in this Account through case studies. (1) CBn macrocycles are prime water-soluble receptors for hydrocarbons, allowing for the reduction of the binding free energies to two components: the hydrophobic effect and dispersion interactions. To understand hydrocarbon binding, we initiated the HYDROPHOBE challenge, which revealed the shortcomings of both quantum-chemical and molecular dynamics approaches. (2) The smallest CBn receptor, CB5, is uniquely suited to bind the entire noble gas series, where hydrophobic effects and dispersion interactions operate in opposite directions. CB5 was revaled to be a unique synthetic receptor for noble gases, with the dominant driving force being the recovery of the cavitation energies for the hydration of noble gases in aqueous solution. Computational methods that encounter challenges in predicting hydrocarbon affinities and trends for CB6 and CB7 perform well for noble gases binding to CB5. (3) The larger homologue, CB8, allows one to set up intermolecular interaction chambers by the encapsulation of a (first) aromatic guest, thereby tuning LDIs inside the receptor cavity. In this manner, CB8 can be modulated to preferentially bind unsaturated and aromatic rather than saturated hydrocarbons, while the unmodified cavities of the smaller macrocycles CB6 and CB7 show selective binding of saturated hydrocarbons. (4) The (charged) host-guest complexes of CBn hosts are sufficiently stable in the gas phase, allowing for the study of the influence of LDIs on inner-phase chemical reactions. These studies are particularly interesting for the theoretical analysis of isolated host-guest LDIs, as experimental and computational data are directly comparable in the gas phase due to the absence of the solvation effect.
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Affiliation(s)
- Khaleel I Assaf
- Al-Balqa Applied University, Faculty of Science, Department of Chemistry, 19117 Al-Salt, Jordan
| | - Werner M Nau
- Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
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30
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Li W, Wang M, Wang S, Wang X, Avila A, Kuang X, Mu X, Garciamendez CE, Jiang Z, Manríquez J, Tang G, Guo J, Mille LS, Robledo JA, Wang D, Cheng F, Li H, Flores RS, Zhao Z, Delavaux C, Wang Z, López A, Yi S, Zhou C, Gómez A, Schuurmans C, Yang GY, Wang Y, Zhang X, Zhang X, Zhang YS. An Adhesive Bioink toward Biofabrication under Wet Conditions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205078. [PMID: 36587991 PMCID: PMC10960222 DOI: 10.1002/smll.202205078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Three-dimensional (3D) bioprinting is driving significant innovations in biomedicine over recent years. Under certain scenarios such as in intraoperative bioprinting, the bioinks used should exhibit not only cyto/biocompatibility but also adhesiveness in wet conditions. Herein, an adhesive bioink composed of gelatin methacryloyl, gelatin, methacrylated hyaluronic acid, and skin secretion of Andrias davidianus is designed. The bioink exhibits favorable cohesion to allow faithful extrusion bioprinting in wet conditions, while simultaneously showing good adhesion to a variety of surfaces of different chemical properties, possibly achieved through the diverse bonds presented in the bioink formulation. As such, this bioink is able to fabricate sophisticated planar and volumetric constructs using extrusion bioprinting, where the dexterity is further enhanced using ergonomic handheld bioprinters to realize in situ bioprinting. In vitro experiments reveal that cells maintain high viability; further in vivo studies demonstrate good integration and immediate injury sealing. The characteristics of the bioink indicate its potential widespread utility in extrusion bioprinting and will likely broaden the applications of bioprinting toward situations such as in situ dressing and minimally invasive tissue regeneration.
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Affiliation(s)
- Wanlu Li
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 20030, P. R. China
| | - Mian Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Shiwei Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- National Center for International Joint Research of Micro-Nano Molding Technology, School of Mechanics & Safety Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Xiaoping Wang
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences & Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education & Stomatological Hospital of Chongqing Medical University, Chongqing, 401174, P. R. China
| | - Alan Avila
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Biotechnology Program, Tecnológico de Monterrey, Monterrey, NL, 64849, México
| | - Xiao Kuang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Xuan Mu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Carlos Ezio Garciamendez
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Zewei Jiang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Jennifer Manríquez
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Biotechnology Program, Tecnológico de Monterrey, Monterrey, NL, 64849, México
| | - Guosheng Tang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Jie Guo
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Luis Santiago Mille
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Juan Antonio Robledo
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Di Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Feng Cheng
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Hongbin Li
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Regina Sanchez Flores
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Zhibo Zhao
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Clément Delavaux
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Zixuan Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Arturo López
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Biotechnology Program, Tecnológico de Monterrey, Monterrey, NL, 64849, México
| | - Sili Yi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Cuiping Zhou
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Ameyalli Gómez
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Biotechnology Program, Tecnológico de Monterrey, Monterrey, NL, 64849, México
| | - Carl Schuurmans
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Science for Life, Utrecht University, Universiteitsweg 99, 3508, TB, Utrecht, The Netherlands
| | - Guo-Yuan Yang
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 20030, P. R. China
| | - Yongting Wang
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 20030, P. R. China
| | - Xingcai Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ximu Zhang
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences & Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education & Stomatological Hospital of Chongqing Medical University, Chongqing, 401174, P. R. China
| | - Yu Shrike Zhang
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences & Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education & Stomatological Hospital of Chongqing Medical University, Chongqing, 401174, P. R. China
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31
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Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Commun Biol 2023; 6:1214. [PMID: 38030679 PMCID: PMC10687169 DOI: 10.1038/s42003-023-05602-7] [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: 05/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
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Affiliation(s)
- Da Eun Jeong
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Jun Kim
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Ho-Chul Shin
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
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32
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Tobajas-Curiel G, Sun Q, Sanders JKM, Ballester P, Hunter CA. Solvation rules: aromatic interactions outcompete cation-π interactions in synthetic host-guest complexes in water. Chem Commun (Camb) 2023; 59:14146-14148. [PMID: 37955118 DOI: 10.1039/d3cc04399a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Chemical double mutant cycles were used to measure the interaction of a N-methyl pyridinium cation with a π-box in a calix[4]pyrrole receptor. Although the cation-π interaction is attractive (-11 kJ mol-1), it is 7 kJ mol-1 less favourable than the corresponding aromatic interaction with the isosteric but uncharged tolyl group.
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Affiliation(s)
- Gloria Tobajas-Curiel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Qingqing Sun
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007, Tarragona, Spain.
- Yangzhou University, School of Chemistry and Chemical Engineering, Yangzhou, Jiangsu 225002, China.
| | - Jeremy K M Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007, Tarragona, Spain.
- ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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33
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Weber L, Gilat A, Maillot N, Byrne D, Arnoux P, Giudici-Orticoni MT, Méjean V, Ilbert M, Genest O, Rosenzweig R, Dementin S. Bacterial adaptation to cold: Conservation of a short J-domain co-chaperone and its protein partners in environmental proteobacteria. Environ Microbiol 2023; 25:2447-2464. [PMID: 37549929 DOI: 10.1111/1462-2920.16478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Bacterial genomes are a huge reservoir of genes encoding J-domain protein co-chaperones that recruit the molecular chaperone DnaK to assist protein substrates involved in survival, adaptation, or fitness. The atc operon of the aquatic mesophilic bacterium Shewanella oneidensis encodes the proteins AtcJ, AtcA, AtcB, and AtcC, and all of them, except AtcA, are required for growth at low temperatures. AtcJ is a short J-domain protein that interacts with DnaK, but also with AtcC through its 21 amino acid C-terminal domain. This interaction network is critical for cold growth. Here, we show that AtcJ represents a subfamily of short J-domain proteins that (i) are found in several environmental, mostly aquatic, β- or ɣ-proteobacteria and (ii) contain a conserved PX7 W motif in their C-terminal extension. Using a combination of NMR, biochemical and genetic approaches, we show that the hydrophobic nature of the tryptophan of the S. oneidensis AtcJ PX7 W motif determines the strong AtcJ-AtcC interaction essential for cold growth. The AtcJ homologues are encoded by operons containing at least the S. oneidensis atcA, atcB, and atcC homologues. These findings suggest a conserved network of DnaK and Atc proteins necessary for low-temperature growth and, given the variation in the atc operons, possibly for other biological functions.
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Affiliation(s)
- Lana Weber
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Atar Gilat
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathanael Maillot
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix-Marseille University, French National Center for Scientific Research (CNRS), IMM FR3479, Marseille, France
| | - Pascal Arnoux
- Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM UMR7265), Aix-Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), French National Center for Scientific Research (CNRS), Saint Paul-Lez-Durance, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Vincent Méjean
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Marianne Ilbert
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Olivier Genest
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Dementin
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
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Ravikumar Y, Koonyosying P, Srichairatanakool S, Ponpandian LN, Kumaravelu J, Srichairatanakool S. In Silico Molecular Docking and Dynamics Simulation Analysis of Potential Histone Lysine Methyl Transferase Inhibitors for Managing β-Thalassemia. Molecules 2023; 28:7266. [PMID: 37959685 PMCID: PMC10650625 DOI: 10.3390/molecules28217266] [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: 09/17/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
A decreased hemoglobin synthesis is contemplated as a pathological indication of β-thalassemia. Recent studies show that EPZ035544 from Epizyme could induce fetal hemoglobin (HbF) levels due to its proven capability to inhibit euchromatin histone lysine methyl transferase (EHMT2). Therefore, the development of EHMT2 inhibitors is considered promising in managing β-thalassemia. Our strategy to find novel compounds that are EHMT2 inhibitors relies on the virtual screening of ligands that have a structural similarity to N2-[4-methoxy-3-(2,3,4,7-tetrahydro-1H-azepin-5-yl) phenyl]-N4,6-dimethyl-pyrimidine-2,4-diamine (F80) using the PubChem database. In silico docking studies using Autodock Vina were employed to screen a library of 985 compounds and evaluate their binding ability with EHMT2. The selection of hit compounds was based on the docking score and mode of interaction with the protein. The top two ranked compounds were selected for further investigations, including pharmacokinetic properties analysis and molecular dynamics simulations (MDS). Based on the obtained docking score and interaction analysis, N-(4-methoxy-3-methylphenyl)-4,6-diphenylpyrimidin-2-amine (TP1) and 2-N-[4-methoxy-3-(5-methoxy-3H-indol-2-yl)phenyl]-4-N,6-dimethylpyrimidine-2,4-diamine (TP2) were found to be promising candidates, and TP1 exhibited better stability in the MDS study compared to TP2. In summary, our approach helps identify potential EHMT2 inhibitors, and further validation using in vitro and in vivo experiments could certainly enable this molecule to be used as a therapeutic drug in managing β-thalassemia disease.
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Affiliation(s)
- Yuvaraj Ravikumar
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (Y.R.); (P.K.)
| | - Pimpisid Koonyosying
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (Y.R.); (P.K.)
| | - Sirichai Srichairatanakool
- Division of Hematology, Department of Internal Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | | | - Jayanthi Kumaravelu
- Department of Microbiology and Biotechnology, Bharath Institute of Higher Education and Research, Agharam Road Selaiyur, Chennai 600073, India
| | - Somdet Srichairatanakool
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (Y.R.); (P.K.)
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35
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Fressigné C, Jean A, Sanselme M, Blanchet J, Rouden J, Maddaluno J, De Paolis M. Intra- and Intermolecular Cation-π Interactions between Onium Salts and Alkynes/Acetylene: Experimental and Theoretical Insights. J Org Chem 2023; 88:14494-14503. [PMID: 37819740 DOI: 10.1021/acs.joc.3c01514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Cation-π interactions between various onium salts, alkynes, and acetylene were studied, taking into account the substituents of the triple bond, the nature of the anions, and the polarity of the solvent, through a combination of MP2 calculations and experiments. In an intramolecular setting, these data (including single-crystal X-ray crystallography) concurred with the stability of folded conformers of alkynyl onium salts, even substituted with electron-withdrawing groups. To examine the contribution of these interactions on the alkyne electronic population, a thorough in silico study was carried out using natural bonding orbital analysis of the conformers. Intramolecular interactions from sulfonium salt tethered to phenylalkyne were highlighted, as illustrated above by the computed folded conformation (MP2) along with noncovalent interaction (NCI) analysis. Furthermore, investigations of intermolecular interactions, involving acetylene or phenylacetylene with various onium ions, revealed the high energy interactions of their complexes with phenyldimethylsulfonium chloride, as illustrated above with the complex PhC≡CH/PhMe2SCl (MP2 calculations and NCI analysis).
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Affiliation(s)
- Catherine Fressigné
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Alexandre Jean
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
- LCMT, ENSICAEN et Université de Caen Basse-Normandie, CNRS, 6 bd du Maréchal Juin, 14050 Caen, France
| | - Morgane Sanselme
- Univ Rouen Normandie, Normandie Univ, SMS, UR 3233, F-76000 Rouen, France
| | - Jérôme Blanchet
- LCMT, ENSICAEN et Université de Caen Basse-Normandie, CNRS, 6 bd du Maréchal Juin, 14050 Caen, France
| | - Jacques Rouden
- LCMT, ENSICAEN et Université de Caen Basse-Normandie, CNRS, 6 bd du Maréchal Juin, 14050 Caen, France
| | - Jacques Maddaluno
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Michaël De Paolis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
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36
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Lin XC, Cui YS, Xie SJ, Chen DP, Zhai DD, Shi ZJ. Jellyfish-type Dinuclear Hafnium Azido Complexes: Synthesis and Reactivity. Chem Asian J 2023; 18:e202300659. [PMID: 37700430 DOI: 10.1002/asia.202300659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Di- and multinuclear hafnium complexes bridged by ligands have been rarely reported. In this article, a novel 3,5-disubstituted pyrazolate-bridged ligand LH5 with two [N2 N]2- -type chelating side arms was designed and synthesized, which supported a series of dinuclear hafnium complexes. Dinuclear hafnium azides [LHf2 (μ-1,1-N3 )2 (N3 )2 ][Na(THF)4 ] 3 and [LHf2 (μ-1,1-N3 )2 (N3 )2 ][Na(2,2,2-Kryptofix)] 4 were further synthesized and structurally characterized, featuring two sets of terminal and bridging azido ligands like jellyfishes. The reactivity of 3 under reduction conditions was conducted, leading to a formation of a tetranuclear hafnium imido complex [L1 Hf2 (μ1 -NH)(N3 ){μ2 -K}]2 5. DFT calculations revealed that the mixed imido azide 5 was generated via an intramolecular C-H insertion from a putative dinuclear HfIV -nitridyl intermediate.
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Affiliation(s)
- Xin-Cheng Lin
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Yun-Shu Cui
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Si-Jun Xie
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Dong-Ping Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Dan-Dan Zhai
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Zhang-Jie Shi
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
- State Key Laboratory of Organometallic Chemistry, SIOC, CAS, Shanghai, 200032, P. R. China
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37
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Gutiérrez López MÁ, Ali R, Tan ML, Sakai N, Wirth T, Matile S. Electric field-assisted anion-π catalysis on carbon nanotubes in electrochemical microfluidic devices. SCIENCE ADVANCES 2023; 9:eadj5502. [PMID: 37824606 PMCID: PMC10569703 DOI: 10.1126/sciadv.adj5502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/07/2023] [Indexed: 10/14/2023]
Abstract
The vision to control the charges migrating during reactions with external electric fields is attractive because of the promise of general catalysis, emergent properties, and programmable devices. Here, we explore this idea with anion-π catalysis, that is the stabilization of anionic transition states on aromatic surfaces. Catalyst activation by polarization of the aromatic system is most effective. This polarization is induced by electric fields. The use of electrochemical microfluidic reactors to polarize multiwalled carbon nanotubes as anion-π catalysts emerges as essential. These reactors provide access to high fields at low enough voltage to prevent electron transfer, afford meaningful effective catalyst/substrate ratios, and avoid interference from additional electrolytes. Under these conditions, the rate of pyrene-interfaced epoxide-opening ether cyclizations is linearly voltage-dependent at positive voltages and negligible at negative voltages. While electromicrofluidics have been conceived for redox chemistry, our results indicate that their use for supramolecular organocatalysis has the potential to noncovalently electrify organic synthesis in the broadest sense.
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Affiliation(s)
- M. Ángeles Gutiérrez López
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Rojan Ali
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK
| | - Mei-Ling Tan
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Thomas Wirth
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
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38
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Arakawa T, Akuta T. Mechanistic Insight into Poly-Reactivity of Immune Antibodies upon Acid Denaturation or Arginine Mutation in Antigen-Binding Regions. Antibodies (Basel) 2023; 12:64. [PMID: 37873861 PMCID: PMC10594486 DOI: 10.3390/antib12040064] [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: 08/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
The poly-reactivity of antibodies is defined as their binding to specific antigens as well as to related proteins and also to unrelated targets. Poly-reactivity can occur in individual molecules of natural serum antibodies, likely due to their conformation flexibility, and, for therapeutic antibodies, it plays a critical role in their clinical development. On the one hand, it can enhance their binding to target antigens and cognate receptors, but, on the other hand, it may lead to a loss of antibody function by binding to off-target proteins. Notably, poly-reactivity has been observed in antibodies subjected to treatments with dissociating, destabilizing or denaturing agents, in particular acidic pH, a common step in the therapeutic antibody production process involving the elution of Protein-A bound antibodies and viral clearance using low pH buffers. Additionally, poly-reactivity can emerge during the affinity maturation in the immune system, such as the germinal center. This review delves into the underlying potential causes of poly-reactivity, highlighting the importance of conformational flexibility, which can be further augmented by the acid denaturation of antibodies and the introduction of arginine mutations into the complementary regions of antibody-variable domains. The focus is placed on a particular antibody's acid conformation, meticulously characterized through circular dichroism, differential scanning calorimetry, and sedimentation velocity analyses. By gaining a deeper understanding of these mechanisms, we aim to shed light on the complexities of antibody poly-reactivity and its implications for therapeutic applications.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130, USA
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26 Aza-Asayama, Kamitezuna, Takahagi-shi 318-0004, Ibaraki, Japan;
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39
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Li X, Li J, Li X, Dang R, Li Z, Li Y, Wang B. A straightforward synthesis and physicochemical properties of chiral phosphorus-doped coronenes. Chem Commun (Camb) 2023; 59:11831-11834. [PMID: 37711078 DOI: 10.1039/d3cc03768a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Novel N,P-fused coronene derivatives have been successfully designed and achieved in one step using a three-fold Bischler-Napieralski cyclization as the key step. The unique structure, and tunable photophysical and electronic properties make them promising candidates for emissive and electron-transport materials.
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Affiliation(s)
- Xuexiang Li
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Jia Li
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Xingchen Li
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Rui Dang
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Zhihao Li
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Ying Li
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Biyao Wang
- School of Chemistry and Chemical Engineering Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
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40
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Tan ML, Ángeles Gutiérrez López M, Sakai N, Matile S. Anion-(π) n -π Catalytic Micelles. Angew Chem Int Ed Engl 2023; 62:e202310393. [PMID: 37574867 DOI: 10.1002/anie.202310393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023]
Abstract
Anion-π catalysis operates by stabilizing anionic transition states on π-acidic aromatic surfaces. In anion-(π)n -π catalysis, π stacks add polarizability to strengthen interactions. In search of synthetic methods to extend π stacks beyond the limits of foldamers, the self-assembly of micelles from amphiphilic naphthalenediimides (NDIs) is introduced. To interface substrates and catalysts, charge-transfer complexes with dialkoxynaphthalenes (DANs), a classic in supramolecular chemistry, are installed. In π-stacked micelles, the rates of bioinspired ether cyclizations exceed rates on monomers in organic solvents by far. This is particularly impressive considering that anion-π catalysis in water has been elusive so far. Increasing rates with increasing π acidity of the micelles evince operational anion-(π)n -π catalysis. At maximal π acidity, autocatalytic behavior emerges. Dependence on position and order in confined micellar space promises access to emergent properties. Anion-(π)n -π catalytic micelles in water thus expand supramolecular systems catalysis accessible with anion-π interactions with an inspiring topic of general interest and great perspectives.
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Affiliation(s)
- Mei-Ling Tan
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | | | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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Kazim M, Feng Z, Vemulapalli S, Siegler MA, Chopra A, Minh Nguyen P, Gargiulo Holl M, Guan L, Dudding T, Tantillo DJ, Lectka T. Through-Space, Lone-Pair Promoted Aromatic Substitution: A Relay Mechanism Can Beat Out Direct Activation. Chemistry 2023; 29:e202301550. [PMID: 37219499 DOI: 10.1002/chem.202301550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
We report a detailed experimental and theoretical analysis of through-space arene activation with halogens, tetrazoles and achiral esters and amides. Contrary to previously assumed direct activation through σ-complex stabilization, our results suggest that these reactions proceed by a relay mechanism wherein the lone pair-containing activators form exothermic π-complexes with electrophilic nitronium ion before transferring it to the probe ring through low barrier transition states. Noncovalent interactions (NCI) plots and Quantum Theory of Atoms in Molecules (QTAIM) analyses depict favorable interactions between the Lewis base (LB) and the nitronium ion in the precomplexes and the transition states, suggesting directing group participation throughout the mechanism. The regioselectivity of substitution also comports with a relay mechanism. In all, these data pave the way for an alternate platform of electrophilic aromatic substitution (EAS) reactions.
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Affiliation(s)
- Muhammad Kazim
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
- Current address: Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhitao Feng
- Department of Chemistry, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Srini Vemulapalli
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Anant Chopra
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Phuong Minh Nguyen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Maxwell Gargiulo Holl
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Liangyu Guan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Travis Dudding
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Dean J Tantillo
- Department of Chemistry, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Wong JYK, Ekanayake AI, Kharchenko S, Kirberger SE, Qiu R, Kelich P, Sarkar S, Li J, Fernandez KX, Alvizo-Paez ER, Miao J, Kalhor-Monfared S, John JD, Kang H, Choi H, Nuss JM, Vederas JC, Lin YS, Macauley MS, Vukovic L, Pomerantz WCK, Derda R. Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo. Nat Commun 2023; 14:5654. [PMID: 37704629 PMCID: PMC10499988 DOI: 10.1038/s41467-023-41427-y] [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: 08/25/2022] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
Peptide-based therapeutics have gained attention as promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. In this paper, we report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry, with decafluoro-diphenylsulfone (DFS). Testing of the binding of the selected peptides to albumin identified SICRFFC as the lead sequence. We replaced DFS with isosteric pentafluorophenyl sulfide (PFS) and the PFS-SICRFFCGG exhibited KD = 4-6 µM towards human serum albumin. When injected in mice, the concentration of the PFS-SICRFFCGG in plasma was indistinguishable from the reference peptide, SA-21. More importantly, a conjugate of PFS-SICRFFCGG and peptide apelin-17 analogue (N3-PEG6-NMe17A2) showed retention in circulation similar to SA-21; in contrast, apelin-17 analogue was cleared from the circulation after 2 min. The PFS-SICRFFC is the smallest known peptide macrocycle with a significant affinity for human albumin and substantial in vivo circulation half-life. It is a productive starting point for future development of compact macrocycles with extended half-life in vivo.
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Affiliation(s)
- Jeffrey Y K Wong
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Serhii Kharchenko
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Steven E Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ryan Qiu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiaqian Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Edgar R Alvizo-Paez
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | | | - J Dwyer John
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - Hongsuk Kang
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - Hwanho Choi
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - John M Nuss
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | | | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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Chen W, Chen Z, Chi Y, Tian W. Double Cation-π Directed Two-Dimensional Metallacycle-Based Hierarchical Self-Assemblies for Dual-Mode Catalysis. J Am Chem Soc 2023; 145:19746-19758. [PMID: 37657081 DOI: 10.1021/jacs.3c05143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Hierarchical self-assembly of Pt(II) metallacycles for the construction of functional materials has received considerable research interest, owing to their potential to meet increasing complexity and functionality demands while being based on well-defined scaffolds. However, the fabrication of long-range-ordered Pt(II) metallacycle-based two-dimensional hierarchical self-assemblies (2D HSAs) remains a challenge, primarily because of the limitations of conventional orthogonal noncovalent interaction (NCI) motifs and the intrinsic characteristics of Pt(II) metallacycles, making the delicate self-assembly processes difficult to control. Herein, we prepare well-regulated Pt(II)-metallacycle-based 2D HSAs through a directed strategy involving double cation-π interactions derived from C3-symmetric hexagonal Pt(II) metallacycles and C2-symmetric sodium phenate monomers. Spatially confined arrays of planar Pt(II) metallacycles and the selective growth of self-assemblies at desired locations are achieved by employing strong cation-π driving forces with well-defined directionality as the second orthogonal NCI, realizing the bottom-up, three-stage construction of Pt(II)-metallacycle-based 2D HSAs. The resultant 2D HSAs are applied as dual-mode catalysis platforms, which are loaded with two different nanocatalysts, one promoting catalytic oxidation and the other promoting photocatalytic reduction.
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Affiliation(s)
- Wenzhuo Chen
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang 712046, China
| | - Zipei Chen
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yingnan Chi
- Key Laboratory of Cluster Science Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
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Wang D, Xiao Z, He J, Xu W, Wang J. Strong Synergistic Molecular Interaction in Catanionic Surfactant Mixtures: Unravelling the Role of the Benzene Ring. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12649-12661. [PMID: 37651421 DOI: 10.1021/acs.langmuir.3c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Noncovalent interactions play a crucial role in driving the formation of diverse self-assembled structures in surfactant systems. Surfactants containing a benzene ring structure are an important subset of surfactants. These surfactants exhibit unique colloid and interfacial properties, which give rise to fascinating transformations in the aggregate structures. These transformations are directly influenced by specific noncovalent interactions facilitated by the benzene ring structure including cation-π and π-π interactions. Investigating catanionic surfactant systems that incorporate benzene ring structures provides valuable insights into the distinct noncovalent interactions observed in mixed surfactant systems. Our approach involved studying the enthalpy change ΔH during the titration process, utilizing isothermal titration calorimetry (ITC). Simultaneously, we employed cryogenic transmission electron microscopy (cryo-TEM) to observe the corresponding self-assembly structures. To gain further insight, we delved into the noncovalent interactions of the mixed systems by analyzing the molecular environments variations through chemical shifts of the aggregates using proton magnetic resonance (1H NMR). The intermolecular interaction was also confirmed by the two-dimensional nuclear Overhauser enhancement spectroscopy (2D NOESY). We conducted a systematic study of the effects of NaCl concentrations, molar ratios, and molecular structures of surfactants on aggregate structures. The existence forms of surfactants are closely linked to the shape of the titration curve and the transition of the aggregate structures. When cationic surfactants were titrated into sodium dodecylbenzenesulfonate (SDBS) micelle solutions, the dominant cation-π interaction leads to the direct formation of vesicle structures. Conversely, when the SDBS system is titrated into benzyldimethyldodecylammonium chloride (DDBAC) micelles, a delicate balance of multiple noncovalent interactions, including cation-π, π-π, hydrophobic, and electrostatic forces, results in a range of aggregate structure transformations such as worm-like micelles and vesicular structures.
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Affiliation(s)
- Dianlin Wang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
- Oil and Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Southwest Petroleum University, Chengdu 610500, China
| | - Zili Xiao
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
| | - Jiang He
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
| | - Wei Xu
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
| | - Jingyi Wang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
- Oil and Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Southwest Petroleum University, Chengdu 610500, China
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46
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Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X. Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res 2023; 51:8447-8462. [PMID: 37439339 PMCID: PMC10484683 DOI: 10.1093/nar/gkad594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12-15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1-ZF7 and ZF3-ZF11 in complex with DNA that incorporates the CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1-ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9-ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1-ZF7 and ZF8-ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1-ZF7 and bulkier and polar/charged residues for ZF8-ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine-guanine and glutamine-adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9-ZF11. The differences between ZF1-ZF7 and ZF8-ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Zou Y, Qi B, Tan J, Guan L, Zhang Q, Sun Y, Huang F. Deciphering the Inhibitory Mechanism of Naphthoquinone-Dopamine on the Aggregation of Tau Core Fragments PHF6* and PHF6. ACS Chem Neurosci 2023; 14:3265-3277. [PMID: 37585669 DOI: 10.1021/acschemneuro.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
The formation of neurofibrillary tangles by abnormal aggregation of tau protein is considered to be an important pathological characteristic of tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. Two hexapeptides 275VQIINK280 and 306VQIVYK311 in the microtubule binding region, named PHF6* and PHF6, are known to be aggregation-prone and responsible for tau fibrillization. Previous experiments reported that naphthoquinone-dopamine (NQDA) could effectively inhibit the aggregation of PHF6* and PHF6 and disrupt the fibrillar aggregates into nontoxic species, displaying a dual effect on the amyloid aggregation. However, the underlying molecular mechanism remains mostly elusive. Herein, we performed all-atom molecular dynamics (MD) simulations for 114 μs in total to systematically investigate the impacts of NQDA on the oligomerization of PHF6* and PHF6. The conformational ensembles of PHF6* and PHF6 peptides generated by replica exchange MD simulations show that NQDA could effectively prevent the hydrogen bond formation, reduce the ability of peptides to self-assemble into long β-strand and large β-sheets, and induce peptides to form a loosely packed and coil-rich oligomer. The interaction analysis shows that the binding of NQDA to PHF6* is mainly through hydrophobic interactions with residue I277 and hydrogen bonding interactions with Q276; for the PHF6 peptides, NQDA displays a strong π-π stacking interaction with residue Y310, thus impeding the Y310-Y310 π-π stacking and I308-Y310 CH-π interactions. The DA group of NQDA displays a stronger cation-π interaction than the NQ group, while the NQ group exhibits a stronger π-π stacking interaction. MD simulations demonstrate that NQDA prevents the conformational conversion to β-sheet-rich aggregates and displays an inhibitory effect on the oligomerization dynamics of PHF6* and PHF6. Our results provide a complete picture of inhibitory mechanisms of NQDA on PHF6* and PHF6 oligomerization, which may pave the way for designing drug candidates for the treatment of tauopathies.
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Affiliation(s)
- Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, P. R. China
| | - Yunxiang Sun
- Department of Physics, Ningbo University, 818 Fenghua Road, Ningbo 315211, Zhejiang, P. R. China
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, Zhejiang, P. R. China
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Ouyang C, Yu H, Wang L, Ni Z, Liu X, Shen D, Yang J, Shi K, Wang H. Tough adhesion enhancing strategies for injectable hydrogel adhesives in biomedical applications. Adv Colloid Interface Sci 2023; 319:102982. [PMID: 37597358 DOI: 10.1016/j.cis.2023.102982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/20/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Injectable hydrogel adhesives have gained widespread attention due to their ease of use, fast application time, and suitability for minimally invasive procedures. Several biomedical applications depend on tough adhesion between hydrogel adhesives and tissues, including wound closure and healing, hemostasis, tissue regeneration, drug delivery, and wearable electronic devices. Compared with bulk hydrogel adhesives formed ex situ, injectable hydrogel adhesives are more difficult to achieve strong adhesion strength due to a further balance of cohesion and adhesion while maintaining their flowability. In this review, the critical principles in designing tough adhesion of injectable hydrogel adhesives are summarized, including simultaneously enhancing their intrinsic interfacial toughness (Γ0inter) and mechanical dissipation (ΓDinter). Thereafter, various design strategies to enhance the Γ0inter and ΓDinter are discussed and evaluated respectively, involving multiple noncovalent/covalent interactions, topological connections, and polymer network structures. Furthermore, targeted biomedical applications of injectable hydrogel adhesives for specific tissue needs are systematically highlighted. In the end, this review outlines the challenges and trends in producing next-generation multifunctional injectable hydrogels for both practical and translational applications.
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Affiliation(s)
- Chenguang Ouyang
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Haojie Yu
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China; Zhejiang-Russia Joint Laboratory of Photo-Electron-Megnetic Functional Materials, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China.
| | - Li Wang
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China; Zhejiang-Russia Joint Laboratory of Photo-Electron-Megnetic Functional Materials, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Zhipeng Ni
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Xiaowei Liu
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Di Shen
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Jian Yang
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Kehang Shi
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Huanan Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
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49
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Papamokos GV, Kaxiras E. How to evict HP1 from H3: Using a complex salt bridge. Biophys Chem 2023; 300:107062. [PMID: 37302360 DOI: 10.1016/j.bpc.2023.107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/21/2023] [Accepted: 06/03/2023] [Indexed: 06/13/2023]
Abstract
In an effort to unravel the unknown "binary switch" mechanisms underlying the "histone code" hypothesis of gene silencing and activation, we study the dynamics of Heterochromatin Protein 1 (HP1). We find in the literature that when HP1 is bound to tri-methylated Lysine9 (K9me3) of histone-H3 through an aromatic cage consisting of two tyrosines and one tryptophan, it is evicted upon phosphorylation of Serine10 (S10phos) during mitosis. In this work, the kick-off intermolecular interaction of the eviction process is proposed and described in detail on the basis of quantum mechanical calculations: specifically, an electrostatic interaction competes with the cation-π interaction and draws away K9me3 from the aromatic cage. An arginine, abundant in the histonic environment, can form an intermolecular "complex salt bridge" with S10phos and dislodge HP1. The study attempts to reveal the role of phosphorylation of Ser10 on the H3 tail in atomic detail.
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Affiliation(s)
- George V Papamokos
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA..
| | - Efthimios Kaxiras
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA..
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Yu L, Wang Y, Sun Y, Tang Y, Xiao Y, Wu G, Peng S, Zhou X. Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305171. [PMID: 37616525 DOI: 10.1002/adma.202305171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.
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Affiliation(s)
- Long Yu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuhao Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqing Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongling Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxiu Xiao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
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