101
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Zhai C, Isaacs L. New Synthetic Route to Water‐Soluble Prism[5]arene Hosts and Their Molecular Recognition Properties**. Chemistry 2022; 28:e202201743. [DOI: 10.1002/chem.202201743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Canjia Zhai
- Department of Chemistry and Biochemistry University of Maryland College Park 20742 Maryland USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry University of Maryland College Park 20742 Maryland USA
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102
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Uncovering Streptomyces-Derived Compounds as Cosmeceuticals for the Development of Improved Skin Photoprotection Products: An In Silico Approach to Explore Multi-Targeted Agents. Sci Pharm 2022. [DOI: 10.3390/scipharm90030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The search for novel photoprotective substances has become a challenge in cosmeceutical research. Streptomyces-derived compounds can serve as a promising source of photoprotective agents to formulate skin photoprotection products, such as sunscreens. This study aimed to identify specialized metabolites with the potential to modulate UV-induced cellular damage in the skin by identifying potential multi-target-directed ligands. Using a combination of ligand- and target-based virtual screening approaches, a public compound library comprising 6524 Streptomyces-derived specialized metabolites was studied for their photoprotective capability. The compounds were initially filtered by safety features and then examined for their ability to interact with key targets in the photodamage pathway by molecular docking. A set of 50 commercially available UV filters was used as the benchmark. The protein–ligand stability of selected Streptomyces-derived compounds was also studied by molecular dynamics (MD) simulations. From the compound library, 1981 compounds were found to meet the safety criteria for topically applied products, such as low skin permeability and low or non-toxicity-alerting substructures. A total of 34 compounds had promising binding scores against crucial targets involved in UV-induced photodamage, such as serotonin-receptor subtype 5-HT2A, platelet-activating factor receptor, IL-1 receptor type 1, epidermal growth factor receptor, and cyclooxygenase-2. Among these compounds, aspergilazine A and phaeochromycin F showed the highest ranked interactions with four of the five targets and triggered complex stabilization over time. Additionally, the predicted UV-absorbing profiles also suggest a UV-filtering effect. Streptomyces is an encouraging biological source of compounds for developing topical products. After in silico protein–ligand interactions, binding mode and stabilization of aspergilazine A and phaeochromycin F led to the discovery of potential candidates as photodamage multi-target inhibitors. Therefore, they can be further explored for the formulation of skin photoprotection products.
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103
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Cui P, Gao H, Wang Y, Tung CH, Kong L. The Cation‐π Interactions in a Potassium Alkylideneborane Complex. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ping Cui
- Shandong University School of Chemistry and Chemical Engineering CHINA
| | - Hao Gao
- Shandong University School of Chemistry and Chemical Engineering CHINA
| | - Yu Wang
- Shandong University School of Chemistry and Chemical Engineering CHINA
| | - Chen-Ho Tung
- Shandong University School of Chemistry and Chemical Engineering CHINA
| | - Lingbing Kong
- Shandong University School of Chemistry and Chemical Engineering 27 Shanda Nanlu 250100 Jinan CHINA
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104
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Wang X, Guo Y, Li J, You M, Yu Y, Yang J, Qin G, Chen Q. Tough Wet Adhesion of Hydrogen-Bond-Based Hydrogel with On-Demand Debonding and Efficient Hemostasis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:36166-36177. [PMID: 35899775 DOI: 10.1021/acsami.2c10202] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hydrogels have been widely used in wet tissues. However, the insufficient adhesion of hydrogels for wound hemostasis remains a grand challenge. Herein, a facile yet effective strategy is developed to fabricate tough wet adhesion of hydrogen-bond-based hydrogel (PAAcVI hydrogel) using copolymerization of acrylic acid and 1-vinylimidazole in dimethyl sulfoxide followed by solvent exchange with water. The PAAcVI hydrogel shows equally robust adhesion (>400 J m-2) to both wet and dry tissues. Moreover, the PAAcVI hydrogel also exhibits strong long-term stable adhesion underwater and in various wet environments. Meanwhile, the adhesion of PAAcVI hydrogel can be adjusted through Zn2+-ion-mediated on-demand debonding, which makes it easy to peel off from the tissue reducing pain during dressing removal and avoiding secondary injury. The PAAcVI hydrogel displays efficient hemostasis in the mice-tail docking model and mice-liver bleeding model. This hydrogen-bond-based hydrogel shows tough wet adhesion, and its adhesion is controllable, demonstrating its promising application in moisture-resistant adhesives, medical adhesives, and hemostatic materials.
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Affiliation(s)
- Xiaodong Wang
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, P. R. China
| | - Yaxin Guo
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, P. R. China
| | - Jiangfeng Li
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 40038, P. R. China
| | - Min You
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, Zhejiang, P. R. China
| | - Yunlong Yu
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 40038, P. R. China
| | - Jia Yang
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, P. R. China
| | - Gang Qin
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, P. R. China
| | - Qiang Chen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, Zhejiang, P. R. China
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105
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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106
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Giraldo DAM, Vásquez LAR, Toscano RA, Ocampo-Cardona R, Gomez-Peña JJ, Macías MA. Synthesis and crystallographic study of six quaternary salts of N-halomethylated and non-N-halomethylated ammonium: Importance of C-H‧‧‧X (X=F, I) and I‧‧‧I− halogen interactions in the supramolecular structures. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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107
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DFT rationalization of metal-catalyst-controlled coupling of carbazole with diazo-naphthalen-2(1H)-one. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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108
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Synthesis, physico-chemical characterization, and environmental applications of meso porous crosslinked poly (azomethine-sulfone)s. Sci Rep 2022; 12:12878. [PMID: 35896584 PMCID: PMC9329479 DOI: 10.1038/s41598-022-17042-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
To develop innovative mesoporous crosslinked poly(azomethine- sulfone)s with environmental applications, a simple Schiff base condensation technique based on barbituric acid BA or condensed terephthaldehyde barbituric acid TBA in their structures as monomeric units are applied. Different analysis methodologies and viscosity measurements identify them as having stronger heat stability and an amorphous structure. The photophysical features of the multi stimuli response MSR phenomenon are observable, with white light emission at higher concentrations and blue light emission at lower concentrations. Their emission characteristics make them an excellent metal ions sensor through diverse charge transfer methods. They can have a better inhibition efficiency and be employed as both mixed-type and active corrosion inhibitors according to their fluorescence emission with metals, demonstrating their capacity to bind with diverse metals. The adsorption of two distinct dye molecules, Methylene blue MB cationic and sunset yellow SY anionic, on the mesoporous structures of the polymers is investigated, revealing their selectivity for MB dye adsorption. Quantum studies support these amazing discoveries, demonstrating a crab-like monomeric unit structure for the one that is heavily crosslinked.
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109
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Schöneich C. Advanced Oxidation Processes in Pharmaceutical Formulations: Photo-Fenton Degradation of Peptides and Proteins. Int J Mol Sci 2022; 23:ijms23158262. [PMID: 35897838 PMCID: PMC9332834 DOI: 10.3390/ijms23158262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
Formulations of therapeutic proteins are sensitive to photo-degradation by near UV and visible light. Mechanistically, especially the processes leading to protein modification under visible light exposure are not understood. Potentially, these processes may be triggered by a ligand to metal charge transfer in excipient-metal complexes. This article summarizes recent analytical and mechanistic work on such reactions under experimental conditions relevant to pharmaceutical formulations.
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Affiliation(s)
- Christian Schöneich
- Simons Research Laboratories, Department of Pharmaceutical Chemistry, The University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047, USA
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110
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Shao J, Kuiper BP, Thunnissen AMWH, Cool RH, Zhou L, Huang C, Dijkstra BW, Broos J. The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach. J Am Chem Soc 2022; 144:13815-13822. [PMID: 35868012 PMCID: PMC9354243 DOI: 10.1021/jacs.2c04986] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
In proteins, the amino acids Phe, Tyr, and especially
Trp are frequently
involved in π interactions such as π–π, cation−π,
and CH−π bonds. These interactions are often crucial
for protein structure and protein–ligand binding. A powerful
means to study these interactions is progressive fluorination of these
aromatic residues to modulate the electrostatic component of the interaction.
However, to date no protein expression platform is available to produce
milligram amounts of proteins labeled with such fluorinated amino
acids. Here, we present a Lactococcus lactis Trp
auxotroph-based expression system for efficient incorporation (≥95%)
of mono-, di-, tri-, and tetrafluorinated, as well as a methylated
Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug
transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between
Trp96 and Trp96′ in the dimer interface. Progressive fluorination
of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly
establishing the importance of electrostatic π–π
interactions for drug binding. Presteady state kinetic data of the
LmrR–drug interaction support the enthalpic nature of the interaction,
while high resolution crystal structures of the labeled protein–drug
complexes provide for the first time a structural view of the progressive
fluorination approach. The L. lactis expression system
was also used to study the role of Trp68 in the binding of riboflavin
by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a
strong electrostatic component that contributed 15–20% to the
total riboflavin-RibU binding energy.
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Affiliation(s)
- Jinfeng Shao
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bastiaan P Kuiper
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Liang Zhou
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Chenxi Huang
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bauke W Dijkstra
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jaap Broos
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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111
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Song KH, Wang JJ, Feng LZ, He F, Yin YC, Yang JN, Song YH, Zhang Q, Ru XC, Lan YF, Zhang G, Yao HB. Thermochromic Phosphors Based on One‐Dimensional Ionic Copper‐Iodine Chains Showing Solid‐State Photoluminescence Efficiency Exceeding 99%. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kuang-Hui Song
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Jing-Jing Wang
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Li-Zhe Feng
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Fuxiang He
- University of Science and Technology of China CAS Key Laboratory of Quantum Information CHINA
| | - Yi-Chen Yin
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Jun-Nan Yang
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Yong-Hui Song
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Qian Zhang
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Xue-Chen Ru
- University of Science and Technology of China Hefei National Research Center for Physical Sciences at the Microscale CHINA
| | - Yi-Feng Lan
- University of Science and Technology of China Appiled Chemistry CHINA
| | - Guozhen Zhang
- University of Science and Technology of China Chemical Physics CHINA
| | - Hong-Bin Yao
- University of Science and Technology of China Chemistry 96 Jinzhai Road 230026 Hefei CHINA
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112
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Belli RG, Tafuri VC, Roberts CC. Improving Alkyl–Alkyl Cross-Coupling Catalysis with Early Transition Metals through Mechanistic Understanding and Metal Tuning. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Roman G. Belli
- University of Minnesota, Minneapolis, Minnesota 55455, United States
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113
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Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
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114
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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115
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Yu X, Zhang X, Hu X, Zhao X, Ren D, Li X, Ma P, Wang C, Wu Y, Luo S, Ding D. Femtosecond Time-Resolved Neighbor Roles in the Fragmentation Dynamics of Molecules in a Dimer. PHYSICAL REVIEW LETTERS 2022; 129:023001. [PMID: 35867441 DOI: 10.1103/physrevlett.129.023001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
How the neighbor effect plays its role in the fragmentation of molecular clusters attracts great attention for physicists and chemists. Here, we study this effect in the fragmentation of N_{2}O dimer by performing three-body coincidence measurements on the femtosecond timescale. Rotations of bound N_{2}O^{+} triggered by neutral or ionic neighbors are tracked. The forbidden dissociation path between B^{2}Π and ^{4}Π is opened by the spin-exchange effect due to the existence of neighbor ions, leading to a new channel of N_{2}O^{+}→NO+N^{+} originating from B^{2}Π. The formation and dissociation of the metastable product N_{3}O_{2}^{+} from two ion-molecule reaction channels are tracked in real time, and the corresponding trajectories are captured. Our results demonstrate a significant and promising step towards the understanding of neighbor roles in the reactions within clusters.
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Affiliation(s)
- Xitao Yu
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Xinyu Zhang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Xiaoqing Hu
- Institute of Applied Physics and Computational Mathematics, Beijing 100088, China
| | - Xinning Zhao
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Dianxiang Ren
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Xiaokai Li
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Pan Ma
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Chuncheng Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Yong Wu
- Institute of Applied Physics and Computational Mathematics, Beijing 100088, China
| | - Sizuo Luo
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
| | - Dajun Ding
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University, Changchun 130012, China
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116
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Chinnaraj M, Flaumenhaft R, Pozzi N. Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles. J Biol Chem 2022; 298:102217. [PMID: 35780832 PMCID: PMC9352907 DOI: 10.1016/j.jbc.2022.102217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O1 and O2) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O1, O2, and C more evenly and in a slower fashion, reduced PDI predominantly populates O1 and O2 and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.
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Affiliation(s)
- Mathivanan Chinnaraj
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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117
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Long S, Xie C, Lu X. Natural polymer‐based adhesive hydrogel for biomedical applications. BIOSURFACE AND BIOTRIBOLOGY 2022. [DOI: 10.1049/bsb2.12036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Siyu Long
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Southwest Jiaotong University Chengdu China
- Yibin Research Institute Southwest Jiaotong University Yibin China
| | - Chaoming Xie
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Southwest Jiaotong University Chengdu China
- Yibin Research Institute Southwest Jiaotong University Yibin China
| | - Xiong Lu
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Southwest Jiaotong University Chengdu China
- Yibin Research Institute Southwest Jiaotong University Yibin China
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118
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Jin MY, Zhen Q, Xiao D, Tao G, Xing X, Yu P, Xu C. Engineered non-covalent π interactions as key elements for chiral recognition. Nat Commun 2022; 13:3276. [PMID: 35672365 PMCID: PMC9174283 DOI: 10.1038/s41467-022-31026-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/25/2022] [Indexed: 12/31/2022] Open
Abstract
Molecular recognition and self-assembly are often mediated by intermolecular forces involving aromatic π-systems. Despite the ubiquity of such interactions in biological systems and in the design of functional materials, the elusive nature of aromatic π interaction results in that they have been seldom used as a design element for promoting challenging chemical reactions. Described here is a well-engineered catalytic system into which non-covalent π interactions are directly incorporated. Enabled by a lone pair-π interaction and a π-π stacking interaction operating collectively, efficient chiral recognition is successfully achieved in the long-pursued dihydroxylation-based kinetic resolution. Density functional theory calculations shed light on the crucial role played by the lone pair-π interaction between the carbonyl oxygen of the cinchona alkaloid ligand and the electron-deficient phthalazine π moiety of the substrate in the stereoselectivity-determining transition states. This discovery serves as a proof-of-principle example showing how the weak non-covalent π interactions, if ingeniously designed, could be a powerful guide in attaining highly enantioselective catalysis. Non-covalent π interactions have been rarely used as a design element for promoting chemical reactions. Here the authors report a Sharpless asymmetric dihydroxylation (SAD)-based kinetic resolution in which a-priori-designed non-covalent forces play a central role in differentiating the enantiomeric substrates.
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119
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“Stacked-arene”-type organocatalysts: utilization of π-π interaction as an electron tuning tool. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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120
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Hu Y, Gao H, Yang Q, Zhou W, Sun C. Adsorption of Pb2+ and Cd2+ on reduced graphene oxide hydrogel prepared from natural cryptocrystalline graphite. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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121
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Zhu YJ, Zhao MK, Rebek J, Yu Y. Recent Advances in the Applications of Water-soluble Resorcinarene-based Deep Cavitands. Chemistry 2022; 11:e202200026. [PMID: 35701378 PMCID: PMC9197774 DOI: 10.1002/open.202200026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/04/2022] [Indexed: 11/08/2022]
Abstract
We review here the use of container molecules known as cavitands for performing organic reactions in water. Central to these endeavors are binding forces found in water, and among the strongest of these is the hydrophobic effect. We describe how the hydrophobic effect can be used to drive organic molecule guests into the confined space of cavitand hosts. Other forces participating in guest binding include cation-π interactions, chalcogen bonding and even hydrogen bonding to water involved in the host structure. The reactions of guests take advantage of their contortions in the limited space of the cavitands which enhance macrocyclic and site-selective processes. The cavitands are applied to the removal of organic pollutants from water and to the separation of isomeric guests. Progress is described on maneuvering the containers from stoichiometric participation to roles as catalysts.
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Affiliation(s)
- Yu-Jie Zhu
- Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
| | - Ming-Kai Zhao
- Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
| | - Julius Rebek
- Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
| | - Yang Yu
- Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
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122
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Han X, Li. P, Han Y, Chen C. Enantiomeric Water‐Soluble Octopus[3]arenes for Highly Enantioselective Recognition of Chiral Ammonium Salts in Water. Angew Chem Int Ed Engl 2022; 61:e202202527. [DOI: 10.1002/anie.202202527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Xiao‐Ni Han
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100084 China
| | - Peng‐Fei Li.
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Advanced Research Institute of Multidisciplinary Science School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Ying Han
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Chuan‐Feng Chen
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100084 China
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123
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Geng H, Zhong QZ, Li J, Lin Z, Cui J, Caruso F, Hao J. Metal Ion-Directed Functional Metal-Phenolic Materials. Chem Rev 2022; 122:11432-11473. [PMID: 35537069 DOI: 10.1021/acs.chemrev.1c01042] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal ions are ubiquitous in nature and play significant roles in assembling functional materials in fields spanning chemistry, biology, and materials science. Metal-phenolic materials are assembled from phenolic components in the presence of metal ions through the formation of metal-organic complexes. Alkali, alkali-earth, transition, and noble metal ions as well as metalloids interacting with phenolic building blocks have been widely exploited to generate diverse hybrid materials. Despite extensive studies on the synthesis of metal-phenolic materials, a comprehensive summary of how metal ions guide the assembly of phenolic compounds is lacking. A fundamental understanding of the roles of metal ions in metal-phenolic materials engineering will facilitate the assembly of materials with specific and functional properties. In this review, we focus on the diversity and function of metal ions in metal-phenolic material engineering and emerging applications. Specifically, we discuss the range of underlying interactions, including (i) cation-π, (ii) coordination, (iii) redox, and (iv) dynamic covalent interactions, and highlight the wide range of material properties resulting from these interactions. Applications (e.g., biological, catalytic, and environmental) and perspectives of metal-phenolic materials are also highlighted.
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Affiliation(s)
- Huimin Geng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Qi-Zhi Zhong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China.,Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jianhua Li
- Department of Biomaterials, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhixing Lin
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jiwei Cui
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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124
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Enhanced removal of multiple metal ions on S-doped graphene-like carbon-supported layered double oxide: Mechanism and DFT study. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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125
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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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126
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Kubik S. Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092821. [PMID: 35566168 PMCID: PMC9103335 DOI: 10.3390/molecules27092821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.
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Affiliation(s)
- Stefan Kubik
- Fachbereich Chemie-Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
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127
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Jian J, Hammink R, Tinnemans P, Bickelhaupt FM, McKenzie CJ, Poater J, Mecinović J. Probing Noncovalent Interactions in [3,3]Metaparacyclophanes. J Org Chem 2022; 87:6087-6096. [PMID: 35471006 DOI: 10.1021/acs.joc.2c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arene-arene interactions are fundamentally important in molecular recognition. To precisely probe arene-arene interactions in cyclophanes, we designed and synthesized (2,6-phenol)paracyclophanes and (2,6-aniline)paracyclophanes that possess two aromatic rings in close proximity. Fine-tuning the aromatic character of one aromatic ring by fluorine substituents enables investigations on the intramolecular interactions between the electron-rich phenol and aniline with tetra-H- and tetra-F-substituted benzene. pKa measurements revealed that the tetra-F-template increases the acidity of the phenol (ΔpKa = 0.55). X-ray crystallography and computational analyses demonstrated that all [3,3]metaparacyclophanes adopt cofacial parallel conformations, implying the presence of π-π stacking interactions. Advanced quantum chemical analyses furthermore revealed that both electrostatic interactions and orbital interactions provide the key contribution to the structure and stability of [3,3]metaparacyclophanes.
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Affiliation(s)
- Jie Jian
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Roel Hammink
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.,Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - F Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Christine J McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi Poater
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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128
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Geng H, Zhang P, Peng Q, Cui J, Hao J, Zeng H. Principles of Cation-π Interactions for Engineering Mussel-Inspired Functional Materials. Acc Chem Res 2022; 55:1171-1182. [PMID: 35344662 DOI: 10.1021/acs.accounts.2c00068] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Supramolecular assembly is commonly driven by noncovalent interactions (e.g., hydrogen bonding, electrostatic, hydrophobic, and aromatic interactions) and plays a predominant role in multidisciplinary research areas ranging from materials design to molecular biology. Understanding these noncovalent interactions at the molecular level is important for studying and designing supramolecular assemblies in chemical and biological systems. Cation-π interactions, initially found through their influence on protein structure, are generally formed between electron-rich π systems and cations (mainly alkali, alkaline-earth metals, and ammonium). Cation-π interactions play an essential role in many biological systems and processes, such as potassium channels, nicotinic acetylcholine receptors, biomolecular recognition and assembly, and the stabilization and function of biomacromolecular structures. Early fundamental studies on cation-π interactions primarily focused on computational calculations, protein crystal structures, and gas- and solid-phase experiments. With the more recent development of spectroscopic and nanomechanical techniques, cation-π interactions can be characterized directly in aqueous media, offering opportunities for the rational manipulation and incorporation of cation-π interactions into the design of supramolecular assemblies. In 2012, we reported the essential role of cation-π interactions in the strong underwater adhesion of Asian green mussel foot proteins deficient in l-3,4-dihydroxyphenylalanine (DOPA) via direct molecular force measurements. In another study in 2013, we reported the experimental quantification and nanomechanics of cation-π interactions of various cations and π electron systems in aqueous solutions using a surface forces apparatus (SFA).Over the past decade, much progress has been achieved in probing cation-π interactions in aqueous solutions, their impact on the underwater adhesion and cohesion of different soft materials, and the fabrication of functional materials driven by cation-π interactions, including surface coatings, complex coacervates, and hydrogels. These studies have demonstrated cation-π interactions as an important driving force for engineering functional materials. Nevertheless, compared to other noncovalent interactions, cation-π interactions are relatively less investigated and underappreciated in governing the structure and function of supramolecular assemblies. Therefore, it is imperative to provide a detailed overview of recent advances in understanding of cation-π interactions for supramolecular assembly, and how these interactions can be used to direct supramolecular assembly for various applications (e.g., underwater adhesion). In this Account, we present very recent advances in probing and applying cation-π interactions for mussel-inspired supramolecular assemblies as well as their structural and functional characteristics. Particular attention is paid to experimental characterization techniques for quantifying cation-π interactions in aqueous solutions. Moreover, the parameters responsible for modulating the strengths of cation-π interactions are discussed. This Account provides useful insights into the design and engineering of smart materials based on cation-π interactions.
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Affiliation(s)
- Huimin Geng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Peiyu Zhang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Jiwei Cui
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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129
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Coronado JN, Ngo P, Anslyn EV, Ellington AD. Chemical insights into flexizyme-mediated tRNA acylation. Cell Chem Biol 2022; 29:1071-1112. [PMID: 35413283 DOI: 10.1016/j.chembiol.2022.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
A critical step in repurposing the cellular translation machinery for the synthesis of polymeric products is the acylation of transfer RNA (tRNA) with unnatural monomers. Toward this goal, flexizymes, ribozymes capable of aminoacylation, have emerged as a uniquely adept tool for charging tRNA with ever increasingly diverse substrates. In this review, we present a library of monomer substrates that have been tested for tRNA acylation with the flexizyme system. From this mile-high view, we provide insights for understanding the chemical factors that influence flexizyme-mediated tRNA acylation. We conclude that flexizymes are primitive esterification catalysts that display a modest binding affinity to the monomer's aromatic recognition element. Together, these robust, yet flexible, flexizyme systems provide researchers with unprecedented access for preparing unnatural acyl-tRNA and the opportunity to repurpose the translation machinery for the synthesis of novel biologically derived structures beyond native proteins and peptides.
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Affiliation(s)
- Jaime N Coronado
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Phuoc Ngo
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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130
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Xue Z, Hu M, Miao X, Zang L, Guo J. Synthesis of a hydrophobic associating polymer and its application in plugging spacer fluid. RSC Adv 2022; 12:11402-11412. [PMID: 35425085 PMCID: PMC9006056 DOI: 10.1039/d2ra01477g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/01/2022] [Indexed: 12/03/2022] Open
Abstract
The high temperature of formation and multiple stages of leakage zone seriously affect the efficiency and safety of drilling and cementing operations. To improve leakage plugging quality before the cementing process, the hydrophobic associating polymer PHAAO was synthesized from acrylamide (AM), 2-acrylamide-2-methyl propane sulfonic acid (AMPS), and the long side-chain hydrophobic monomer octadecyl dimethyl allyl ammonium chloride (ODAAC) in this study. The structure and molecular weight of the polymer were characterized, and it was proved that the polymer has strong association properties and excellent heat resistance. Utilizing the bridge plugging principle, the polymer PHAAO was used with 36-mesh walnut shells and lignin fiber to form a compound plugging agent. This agent was added to spacer fluid to become a plugging spacer. API water loss tests and loading capacity tests under high temperatures show that the filter cake formed by the spacer fluid is dense. The sealing pressure of the spacer fluid on a 1 mm crack can reach 6.5 MPa at 160 °C, and it has good compatibility with cement slurry. A scanning electron microscopy (SEM) test was conducted to explore the membrane formation mechanism of the polymer. An ultra-low permeability membrane is formed on the surface of the filter cake from the spacer fluid due to the hydrophobic association and hydrogen bonding between the polymer and lignin fiber, thereby greatly reducing the loss of spacer fluid. The polymer PHAAO not only has a strong hydrophobic association feature but also forms hydrogen bonds and cationic–π bonds with lignin fibers, combining with walnut shells enables the spacer fluid to show a strong plugging performance.![]()
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Affiliation(s)
- Zhaofeng Xue
- School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China .,Institute of Shaoxing, Tianjin University Zhejiang 312300 China
| | - Miaomiao Hu
- School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China .,Institute of Shaoxing, Tianjin University Zhejiang 312300 China
| | - Xia Miao
- Sinopec Research Institute of Petroleum Engineering Beijing 102206 China
| | - Long Zang
- School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China .,Institute of Shaoxing, Tianjin University Zhejiang 312300 China
| | - Jintang Guo
- School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China .,Institute of Shaoxing, Tianjin University Zhejiang 312300 China
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131
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Zhao H, Liu C, Ding W, Tang L, Fang Y, Chen Y, Hu L, Yuan Y, Fang D, Lin S. Manipulating Cation-π Interactions with Genetically Encoded Tryptophan Derivatives. J Am Chem Soc 2022; 144:6742-6748. [PMID: 35380832 DOI: 10.1021/jacs.1c12944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cation-π interactions are the major noncovalent interactions for molecular recognition and play a central role in a broad area of chemistry and biology. Despite tremendous success in understanding the origin and biological importance of cation-π interactions, the design and synthesis of stronger cation-π interactions remain elusive. Here, we report an approach that greatly increases the binding energy of cation-π interactions by replacing Trp in the aromatic box with an electron-rich Trp derivative using the genetic code expansion strategy. The binding affinity between histone H3K4me3 and its reader is increased more than eightfold using genetically encoded 6-methoxy-Trp. Furthermore, through a systematic engineering process, we construct an H3K4me3 Super-Reader with single-digit nM affinity for H3K4me3 detection and imaging. More broadly, this approach paves the way for manipulating cation-π interactions for a variety of applications.
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Affiliation(s)
- Hongxia Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chao Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Wenlong Ding
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ling Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yu Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Linzhen Hu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Dong Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Cancer Center, Zhejiang University, Hangzhou 310058, China
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. Chemistry 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022]
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water‐mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor‐substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität Kaiserslautern, Fachbereich Chemie - Organische Chemie, Erwin-Schrödinger-Straße 54, 67663, Kaiserslautern, Germany
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133
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Pramanik M, Mathuri A, Mal P. t BuOLi-promoted terminal alkyne functionalizations by aliphatic thiols and alcohols. Org Biomol Chem 2022; 20:2671-2680. [PMID: 35293412 DOI: 10.1039/d2ob00079b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective radical addition to terminal alkynes is always a difficult task to achieve because it gives a mixture of stereo- and regioisomers. Herein we describe the selective addition of aliphatic thiols or alcohols to N-phenylpropiolamides (terminal alkynes) using lithium tert-butoxide (tBuOLi) in ethanol as a promoter. Mechanistically, it has been shown that the reaction proceeded through the generation of a thiyl radical intermediate, and the amide group in N-phenylpropiolamide could help in the activation of the alkyne, which led to thioacetalization via the formation of a (Z)-selective anti-Markovnikov vinyl sulfide. The (Z)-selectivity during the formation of vinyl sulfides was controlled by an intramolecular sulfur⋯oxygen interaction.
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Affiliation(s)
- Milan Pramanik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Ashis Mathuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
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134
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Gibbs CA, Fedoretz-Maxwell BP, Warren JJ. On the roles of methionine and the importance of its microenvironments in redox metalloproteins. Dalton Trans 2022; 51:4976-4985. [PMID: 35253809 DOI: 10.1039/d1dt04387k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.
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Affiliation(s)
- Curtis A Gibbs
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
| | | | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
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135
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Lorenzetto T, Fabris F, Scarso A. A resorcin[4]arene hexameric capsule as a supramolecular catalyst in elimination and isomerization reactions. Beilstein J Org Chem 2022; 18:337-349. [PMID: 35422886 PMCID: PMC8978922 DOI: 10.3762/bjoc.18.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
The hexameric resorcin[4]arene capsule as a self-assembled organocatalyst promotes a series of reactions like the carbonyl–ene cyclization of (S)-citronellal preferentially to isopulegol, the water elimination from 1,1-diphenylethanol, the isomerization of α-pinene and β-pinene preferentially to limonene and minor amounts of camphene. The role of the supramolecular catalyst consists in promoting the protonation of the substrates leading to the formation of cationic intermediates that are stabilized within the cavity with consequent peculiar features in terms of acceleration and product selectivity. In all cases the catalytic activity displayed by the hexameric capsule is remarkable if compared to many other strong Brønsted or Lewis acids.
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Affiliation(s)
- Tommaso Lorenzetto
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di Venezia, via Torino 155, 30172, Mestre-Venezia, Italy
| | - Fabrizio Fabris
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di Venezia, via Torino 155, 30172, Mestre-Venezia, Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari di Venezia, via Torino 155, 30172, Mestre-Venezia, Italy
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136
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Han X, Li. P, Han Y, Chen C. Enantiomeric Water‐Soluble Octopus[3]arenes for Highly Enantioselective Recognition of Chiral Ammonium Salts in Water. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiao‐Ni Han
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100084 China
| | - Peng‐Fei Li.
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Advanced Research Institute of Multidisciplinary Science School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Ying Han
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Chuan‐Feng Chen
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100084 China
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137
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Sang Z, Xiang Y, Bahar I, Shi Y. Llamanade: An open-source computational pipeline for robust nanobody humanization. Structure 2022; 30:418-429.e3. [PMID: 34895471 DOI: 10.1016/j.str.2021.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Nanobodies (Nbs) have emerged as a promising class of biologics. Despite having marked physicochemical properties, Nbs are derived from camelids and may require humanization to improve translational potentials. By systematically analyzing the sequence and structural properties of Nbs, we found substantial framework diversities and revealed the key differences between Nbs and human immunoglobulin G antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen binding, providing insights into Nb humanization. Based on big data analysis, we developed "Llamanade," an open-source software to facilitate rational humanization of Nbs. Using sequence as input, Llamanade can rapidly extract sequence features, model structures, and optimize solutions to humanize Nbs. Finally, we used Llamanade to successfully humanize a cohort of structurally diverse and potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a server to support the development of therapeutic Nbs into safe and effective trials.
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Affiliation(s)
- Zhe Sang
- Department of Cell Biology, Pittsburgh, PA, USA; Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA.
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138
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Yang Y, Liang S, Wu H, Shi G, Fang H. Revisit the Hydrated Cation-π Interaction at the Interface: A New View of Dynamics and Statistics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2401-2408. [PMID: 35171618 DOI: 10.1021/acs.langmuir.1c03106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Carbon-based matter, such as biomolecules and graphitic structures, often form a liquid-solid/soft matter interface in salt solution and continuously affect the surrounding cations through hydrated cation-π interactions. In this Perspective, we revisit the effect of the hydrated cation-π interactions at the interface using statistical physics, which reveals how hydrated cation-π interactions affect every component dynamically and cause a time-dependent statistical effect at the liquid-solid/soft interface. We also highlight several pieces of experimental evidence from a statistical perspective and discuss the remarkable applications related to environmental protection, industrial manufacturing, and biological sciences.
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Affiliation(s)
- Yizhou Yang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
| | - Shanshan Liang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
| | - Guosheng Shi
- State Key Laboratory Advanced Special Steel, Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
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139
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Selective recognition of methyl viologen by an endo-functionalized naphthobox. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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140
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Warnica JM, Gleason JL. The stabilized iminium catalyzed ( E)-polyene cyclization: trapping of non-activated terminating groups enabled by cation–π interactions. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A cyclic hydrazide catalyst bearing a pendant anthracene catalyzes the polyene cyclization of 1,5-hexadiene-2-carboxaldehydes. Bicyclic closure proceeds in substrates with non-activated terminating groups that fail to react with simple hydrazide catalysts. Computational analysis shows that stabilization through cation–π interactions throughout the reaction sequence leads to the enhanced reactivity of the catalyst.
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Affiliation(s)
- Josephine M. Warnica
- Department of Chemistry, McGill University, 801 Sherbrooke W., Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke W., Montreal, QC H3A 0B8, Canada
| | - James L. Gleason
- Department of Chemistry, McGill University, 801 Sherbrooke W., Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke W., Montreal, QC H3A 0B8, Canada
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141
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Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. J Am Chem Soc 2022; 144:2535-2545. [PMID: 35108000 PMCID: PMC8923077 DOI: 10.1021/jacs.1c09902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.
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Affiliation(s)
- Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Rodney Park
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
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142
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Kean KM, Baril SA, Lamb KN, Dishman SN, Treacy JW, Houk KN, Brustad EM, James LI, Waters ML. Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding. J Med Chem 2022; 65:2646-2655. [PMID: 35014255 PMCID: PMC9048841 DOI: 10.1021/acs.jmedchem.1c02049] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.
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Affiliation(s)
- Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Sarah N. Dishman
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA,Corresponding Author: Marcey L. Waters – Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States;
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143
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Adhesive hydrogels with toughness, stretchability, and conductivity performances for motion monitoring. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-022-04110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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144
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Meng J, Zhang Y, Pan L, Chen J. Dynamic Control of Self-Assembly of Amphiphilic Conjugated Alkenes in Water by Reactions. ACS OMEGA 2022; 7:4677-4682. [PMID: 35155959 PMCID: PMC8829865 DOI: 10.1021/acsomega.1c07026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Nature sets a great example of how to precisely control self-assembly to obtain distinct structures upon external stimuli and perform specific functions to sustain important biological tasks. In the present study, we report the design and control of self-assembly of an amphiphilic conjugated alkene in water. The morphologies of the self-assembled structures are highly dependent on the anions. The hydrophilic tosylate group can trigger the formation of nanotubes, while the less-hydrophilic inorganic bromide generates vesicles. The interchange of the two different structures can be controlled by employing different anions combined with a couple of reactions that act as signals. The result shown here provides an important tool for manipulating self-assembled behaviors in water and paves the way toward more complex systems.
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145
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π-π Stacking Interaction of Metal Phenoxyl Radical Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031135. [PMID: 35164397 PMCID: PMC8840625 DOI: 10.3390/molecules27031135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
π-π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.
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146
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Wu B, Gu L, Chun BW, Kuhl TL. Adsorption and interaction forces of commercial Poly(naphthalene sulfonate) (PNS) and Poly(carboxylate ether) (PCE) polyelectrolytes with negatively charged surfaces in monovalent and divalent electrolytes. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.127992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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147
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Ibarra-Hernández JA, Gómez-Balderas R, Nivón-Ramírez D, García-Estrada JG, Mendoza-Jiménez DA, Martínez-Zaldívar A, Cruz-Sánchez TA, Tovar-Betancourt N, Luna-Mora RA, Penieres-Carrillo JG. Novel Compounds Based on Chalcone- and Pyrazoline-DIM Hybrids as Inhibitors of Staphylococcus aureus, Synthesis, DFT Studies, Biological Evaluation and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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148
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Mishra R, Behera LM, Rana S. Binding of raloxifene to human complement fragment 5a ( hC5a): a perspective on cytokine storm and COVID19. J Biomol Struct Dyn 2022; 40:982-994. [PMID: 32930050 PMCID: PMC7544936 DOI: 10.1080/07391102.2020.1820381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/02/2020] [Indexed: 01/08/2023]
Abstract
Human C5a (hC5a), one of the pro-inflammatory glycoproteins of the complement system is known to undergo production hyperdrive in response to stress and infection. hC5a has been associated with the pathogenesis of many chronic and acute diseases, due to its proven ability in triggering the 'cytokine storm', by binding to its cognate receptor C5aR, expressed in myriad of tissues. Given the pleiotropic downstream function of hC5a, it is logical to consider the hC5a or its precursors as potential drug targets, and thus, we have been rationally pursuing the idea of neutralizing the harmful effect of excessive hC5a, by implementing the repurposing strategies for FDA-approved drugs. Indeed, the proof of principle biophysical studies published recently is encouraging, which strongly supports the potential of this strategy. Considering BSA-carprofen as a reference model system, the current study further explores the inherent conformational plasticity of hC5a and its effect in accommodating more than one drug molecule cooperatively at multiple sites. The data generated by recruiting a battery of experimental and computational biology techniques strongly suggest that hC5a can sequentially accommodate more than one raloxifene molecule with an estimated Ki ∼ 0.5 µM and Ki ∼ 3.58 µM on its surface at non-analogous sites. The study hints at exploration of polypharmacology approach, as a new avenue for discovering synergistic drug molecule pairs, or drug molecules with 'broad-range' binding affinity for targeting the different 'hot spots' on hC5a, as an alternative combination therapy for possible management of the 'cytokine storm'-related inflammatory diseases, like COVID19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Richa Mishra
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
| | - Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
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149
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Xu Y, Song J, Wang T, Xu M, Zhang L, Jia H, Wang J, Song L, Jia H, Lian P. Novel insights into the self-assembly behaviors of cationic surfactant and bivalent acid: Effects of group positions in bivalent acid. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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150
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Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants. ENVIRONMENTS 2022. [DOI: 10.3390/environments9020023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.
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