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Li H, Zhao X, Ren X, Wei D, Zhang S, Wang H, Zuo ZW, Li L, Yu X. Energetic and Kinetic Competition on the Stability of Pd 13 Clusters: Ab Initio Molecular Dynamics Simulations. J Phys Chem A 2024. [PMID: 39159008 DOI: 10.1021/acs.jpca.4c03230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Material stability is the focus on both experiments and calculations, which includes the energetic stability at the static state and the thermodynamic stability at the kinetic state. To show whether energetics or kinetics dominates on material stability, this study focuses on the Pd13 clusters, because of their observable magnetic moment in experiment. Energetically, the CALYPSO searching method and first-principles calculations find that Pd13(C2) is the ground state at 0 K while the static frequency calculations demonstrate that the icosahedron Pd13(Ih) becomes more favorable on free energy as temperature increases. However, their magnetic moments (8 μB) are not in agreement with the experimental value (<5.2 μB). Kinetically, ab initio molecular dynamics simulations reveal that Pd13(C3v) (6 μB) has supreme isomerization temperature and the other 11 low-lying isomers transform to Pd13(C3v) directly or indirectly, demonstrating that Pd13(C3v) has the maximum probability to be observed in experiment. The magnetic moment difference between experiment (<5.2 μB) and this calculation (6 μB) may be due to the spin multiplicities. Our result suggests that the magnetic moment disparity between theory and experiment (in Pd13 clusters) originates from the kinetic stability.
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Affiliation(s)
- Haisheng Li
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
- Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology, Luoyang 471023, China
| | - Xingju Zhao
- International Laboratory for Quantum Functional Materials of Henan, School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaoyan Ren
- International Laboratory for Quantum Functional Materials of Henan, School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Donghui Wei
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Shuai Zhang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
- Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology, Luoyang 471023, China
| | - Hui Wang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
- Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology, Luoyang 471023, China
| | - Zheng-Wei Zuo
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
- Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology, Luoyang 471023, China
| | - Liben Li
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
- Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology, Luoyang 471023, China
| | - Xiaohu Yu
- Institute of Theoretical and Computational Chemistry, Shaanxi, Key Laboratory of Catalysis, School of Chemical & Environment Sciences, Shaanxi University of Technology, Hanzhong 723000, China
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2
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Wang QQ, Song J, Wei D. Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions. J Chem Inf Model 2024; 64:4530-4541. [PMID: 38808649 DOI: 10.1021/acs.jcim.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
By performing molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and QM cluster calculations, the origin of chemoselectivity of halohydrin dehalogenase (HHDH)-catalyzed ring-opening reactions of epoxide with the nucleophilic reagent NO2- has been explored. Four possible chemoselective pathways were considered, and the computed results indicate that the pathway associated with the nucleophilic attack on the Cα position of epoxide by NO2- is most energetically favorable and has an energy barrier of 12.9 kcal/mol, which is close to 14.1 kcal/mol derived from experimental kinetic data. A hydrogen bonding network formed by residues Ser140, Tyr153, and Arg157 can strengthen the electrophilicity of the active site of the epoxide substrate to affect chemoselectivity. To predict the energy barrier trends of the chemoselective transition states, multiple analyses including distortion analysis and electrophilic Parr function (Pk+) analysis were carried out with or without an enzyme environment. The obtained insights should be valuable for the rational design of enzyme-catalyzed and biomimetic organocatalytic epoxide ring-opening reactions with special chemoselectivity.
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Affiliation(s)
- Qian-Qian Wang
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Jinshuai Song
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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3
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Chen S, Li Y, Chen X, Li L, Lu Q, Guo E, Si C, Wei M, Han X. Isomerization of surface functionalized SWCNTs and the critical influence on photoluminescence: static calculations and excited-state dynamics simulations. Phys Chem Chem Phys 2024; 26:12003-12008. [PMID: 38576321 DOI: 10.1039/d3cp05115c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Single-walled carbon nanotubes (SWCNTs) functionalized with sparse surface chemical groups are promising for a variety of optical applications such as quantum information and bio-imaging. However, the luminescence efficiencies and stability, two key aspects, undoubtedly govern their practical usage. Herein, we assess the surface migration of oxygen and triazine groups on as-modified SWCNT fragments by adopting transition state theory and explore the de-excitation of oxygen-functionalized SWCNT fragments by performing non-adiabatic excited-state dynamics simulations. According to the predicted moderate or even small reaction barriers, the migration of both oxygen and triazine groups is feasible from an sp3 defect configuration forming an energetically more stable sp2 configuration at moderate or even room temperatures. Such isomerization leads to drastically different light emission capabilities as indicated by the large or zero oscillator strengths. During the dynamics simulations, the lowest excited singlet (S1) state rapidly decays in energy within 20 fs and then fluctuates until the end, providing insights into the emission mechanism of SWCNTs. This study highlights the potential intrinsic limitations of surface-functionalized SWCNTs for luminescence applications.
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Affiliation(s)
- Shunwei Chen
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Yi Li
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Xinxin Chen
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Lingyun Li
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Qifang Lu
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Enyan Guo
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Conghui Si
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Mingzhi Wei
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Xiujun Han
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
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4
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Zhou J, Sang X, Wang J, Xu Y, An J, Chu ZT, Saha A, Warshel A, Huang Z. Elucidation of the α-Ketoamide Inhibition Mechanism: Revealing the Critical Role of the Electrostatic Reorganization Effect of Asp17 in the Active Site of the 20S Proteasome. ACS Catal 2023; 13:14368-14376. [PMID: 39188993 PMCID: PMC11346796 DOI: 10.1021/acscatal.3c03538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
The 20S proteasome is an attractive drug target for the development of anticancer agents because it plays an important role in cellular protein degradation. It has a threonine residue that can act as a nucleophile to attack inhibitors with an electrophilic warhead, forming a covalent adduct. Fundamental understanding of the reaction mechanism between covalent inhibitors and the proteasome may assist the design and refinement of compounds with the desired activity. In this study, we investigated the covalent inhibition mechanism of an α-keto phenylamide inhibitor of the proteasome. We calculated the noncovalent binding free energy using the PDLD/S-LRA/β method and the reaction free energy through the empirical valence bond method (EVB). Several possible reaction pathways were explored. Subsequently, we validated the calculated activation and reaction free energies of the most plausible pathways by performing kinetic experiments. Furthermore, the effects of different ionization states of Asp17 on the activation energy at each step were also discussed. The results revealed that the ionization states of Asp17 remarkably affect the activation energies and there is an electrostatic reorganization of Asp17 during the course of the reaction. Our results demonstrate the critical electrostatic effect of Asp17 in the active site of the 20S proteasome.
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Affiliation(s)
- Jiao Zhou
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xiaohong Sang
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Juan Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Xu
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California at San Diego, La Jolla, California 92037, United States
| | - Jing An
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California at San Diego, La Jolla, California 92037, United States
| | - Zhen Tao Chu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Arjun Saha
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53213, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Ziwei Huang
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong Shenzhen 518172, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California at San Diego, La Jolla, California 92037, United States
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5
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Zhang QY, Li X, Luo J, Li X, Song J, Wei D. Cofactor-Free Dioxygenases-Catalyzed Reaction Pathway via Proton-Coupled Electron Transfer. J Phys Chem B 2023; 127:95-103. [PMID: 36525303 DOI: 10.1021/acs.jpcb.2c03161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the general mechanism of the metal-free and cofactor-free oxidases and oxygenases catalyzed activation of triplet O2 is one of the most challenging questions in the field of enzymatic catalysis. Herein, we have performed Quantum Mechanics/Molecular Mechanics (QM/MM) multiscale simulations to reveal the detailed mechanism of the HOD catalyzed (i.e., 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from Arthrobacter nitroguajacolicus Rü61a) decomposition of N-heteroaromatic compounds. The complete catalytic mechanism includes four steps: (1) proton transfer from 1-H-3-hydroxy-4-oxoquinaldine (QND) substrate to His251 residue coupled with an electron transfer from QND to triplet O2 (i.e., PCET), (2) formation of C-O bond via an open-shell singlet diradical recombination pathway, (3) ring-closure to form a bicyclic ring, and (4) dissociation of CO. The dissociation of CO is determined as the rate-limiting step, and its calculated energy barrier of 14.9 kcal/mol is consistent with the 15.5 kcal/mol barrier derived from experimental kinetic data. The mechanistic profile is not only valuable for understanding the fundamental pathway of cofactor-free oxidases and oxygenases-catalyzed reactions involving the triplet O2 activation but also discloses a new pathway that undergoes the processes of PCET and open-shell singlet transition state.
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Affiliation(s)
- Qiao-Yu Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xing Li
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong510280, China
| | - Jing Luo
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xue Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials and Engineering, Henan University, Kaifeng475001, China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
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6
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Han LL, Zhang QY, Li X, Qiao Y, Lan Y, Wei D. The chiral pyridoxal-catalyzed biomimetic Mannich reaction: the mechanism and origin of stereoselectivity. Org Chem Front 2022. [DOI: 10.1039/d2qo00705c] [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
A biomimetic organocatalyst with a pyridoxal-like structure is one of the most successful examples of catalyzing organic reactions under mild conditions in an asymmetric synthesis field.
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Affiliation(s)
- Li-Li Han
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Qiao-Yu Zhang
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Xue Li
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
| | - Yu Lan
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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7
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Zhang QY, Wang Y, Li SJ, Wang Y, Wei D. Organocatalytic insertion into C–B bonds by in situ generated carbene: mechanism, role of the catalyst, and origin of stereoselectivity. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01232k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The calculated results showed that C–H⋯X (X = I, Br) hydrogen bond interactions should be the determining factors of stereoselectivity, and FMO overlap mode and ELF analyses along IRC results were performed to explore the nature of carbene insertion.
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Affiliation(s)
- Qiao-Yu Zhang
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering, Zhengzhou University of Light Industry, 136 Science Avenue, Zhengzhou 450002, Henan Province, P.R. China
| | - Shi-Jun Li
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Yanyan Wang
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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8
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Yang TT, Zhang M, Zhang QY, Wang C, Chen LH, Wei D. Transformation of 1,1′-biphosphirane-M(CO)5 (M = Mo, Cr, W) complexes: Possible mechanisms and reactivity of active intermediates. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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9
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Mihalovits LM, Ferenczy GG, Keserű GM. Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors. Comput Struct Biotechnol J 2021; 19:4486-4496. [PMID: 34471494 PMCID: PMC8379283 DOI: 10.1016/j.csbj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The kinact value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant Ki of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated Ki and kinact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect Ki, the noncovalent affinity, and importantly alter kinact, the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
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Deng Q, Mu F, Qiao Y, Wei D. N-Heterocyclic Carbene-Catalyzed Asymmetric C-O Bond Construction Between Benzoic Acid and o-Phthalaldehyde: Mechanism and Origin of Stereoselectivity. Chem Asian J 2021; 16:2346-2350. [PMID: 34224204 DOI: 10.1002/asia.202100351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/21/2021] [Indexed: 12/27/2022]
Abstract
A computational study was contributed to explore the origin of stereoselectivity of NHC-mediated cyclization reaction between benzoic acid and o-phthalaldehyde for asymmetric construction of phthalidyl ester. The most energetically favorable pathway mainly includes the following steps: (1) nucleophilic attack on carbonyl carbon of o-phthalaldehyde by catalyst NHC, (2) formation of Breslow intermediate, (3) oxidation by DQ, (4) asymmetric formation of dual C-O bonds, and (5) dissociation of catalyst with the product. The C-O bond formation was testified as the stereoselectivity-determining step, the R-configurational pathway is more energetically favorable than the S-configurational one. The non-covalent interaction (NCI) and atom-in-molecule (AIM) analyses were performed to reveal that the O-H ⋅⋅⋅ O and C-H ⋅⋅⋅ O hydrogen-bond interactions are the key factors for controlling the stereoselectivity. The detailed mechanism and origin of stereoselectivity give useful insights for understanding organocatalytic reactions for asymmetric construction of C-O bond.
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Affiliation(s)
- Qianqian Deng
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Fangjing Mu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University of Light Industry, 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China
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11
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Aliabadi F, Sohrabi B, Mostafavi E, Pazoki-Toroudi H, Webster TJ. Ubiquitin-proteasome system and the role of its inhibitors in cancer therapy. Open Biol 2021; 11:200390. [PMID: 33906413 PMCID: PMC8080017 DOI: 10.1098/rsob.200390] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite all the other cells that have the potential to prevent cancer development and metastasis through tumour suppressor proteins, cancer cells can upregulate the ubiquitin–proteasome system (UPS) by which they can degrade tumour suppressor proteins and avoid apoptosis. This system plays an extensive role in cell regulation organized in two steps. Each step has an important role in controlling cancer. This demonstrates the importance of understanding UPS inhibitors and improving these inhibitors to foster a new hope in cancer therapy. UPS inhibitors, as less invasive chemotherapy drugs, are increasingly used to alleviate symptoms of various cancers in malignant states. Despite their success in reducing the development of cancer with the lowest side effects, thus far, an appropriate inhibitor that can effectively inactivate this system with the least drug resistance has not yet been fully investigated. A fundamental understanding of the system is necessary to fully elucidate its role in causing/controlling cancer. In this review, we first comprehensively investigate this system, and then each step containing ubiquitination and protein degradation as well as their inhibitors are discussed. Ultimately, its advantages and disadvantages and some perspectives for improving the efficiency of these inhibitors are discussed.
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Affiliation(s)
- Fatemeh Aliabadi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Beheshteh Sohrabi
- Department of Chemistry, Surface Chemistry Research Laboratory, Iran University of Science and Technology, PO Box 16846-13114, Tehran, Iran
| | - Ebrahim Mostafavi
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Thomas J Webster
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
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12
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Elsässer B, Goettig P. Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. Int J Mol Sci 2021; 22:3232. [PMID: 33810118 PMCID: PMC8004986 DOI: 10.3390/ijms22063232] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
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Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
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13
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Uranga J, Hasecke L, Proppe J, Fingerhut J, Mata RA. Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome. J Chem Inf Model 2021; 61:1942-1953. [PMID: 33719420 DOI: 10.1021/acs.jcim.0c01459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The 20S proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells and in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome (caspase-like), an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy- and boronic acid-containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics, and Bayesian optimization of nonbonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach for the reevaluation of nonbonded potentials making use of the hybrid quantum mechanics molecular mechanics dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the studied inhibitors.
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Affiliation(s)
- Jon Uranga
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Lukas Hasecke
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jonny Proppe
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jan Fingerhut
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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14
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Yang T, Wang C, Li S, Zhang M, Wei D, Lan Y. Possible Mechanisms and Origin of Selectivities for Phosphine‐Catalyzed [2+n] (n=3, 4) Annulations of Saturated Amines and δ‐Acetoxy Allenoates. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ting‐Ting Yang
- Green Catalysis Center, and College of Chemistry Zhengzhou University 100 Science Avenue Zhengzhou 450001, Henan P. R. China
| | - Congcong Wang
- School of Pharmaceutical Sciences Zhengzhou University Zhengzhou 450001 P. R. China
| | - Shi‐Jun Li
- Green Catalysis Center, and College of Chemistry Zhengzhou University 100 Science Avenue Zhengzhou 450001, Henan P. R. China
| | - Min Zhang
- Green Catalysis Center, and College of Chemistry Zhengzhou University 100 Science Avenue Zhengzhou 450001, Henan P. R. China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry Zhengzhou University 100 Science Avenue Zhengzhou 450001, Henan P. R. China
| | - Yu Lan
- Green Catalysis Center, and College of Chemistry Zhengzhou University 100 Science Avenue Zhengzhou 450001, Henan P. R. China
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15
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Saha A, Oanca G, Mondal D, Warshel A. Exploring the Proteolysis Mechanism of the Proteasomes. J Phys Chem B 2020; 124:5626-5635. [PMID: 32498514 DOI: 10.1021/acs.jpcb.0c04435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.
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Affiliation(s)
- Arjun Saha
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Dibyendu Mondal
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
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16
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Cui H, Li K, Wang Y, Song M, Wang C, Wei D, Li EQ, Duan Z, Mathey F. Copper(i)/Ganphos catalysis: enantioselective synthesis of diverse spirooxindoles using iminoesters and alkyl substituted methyleneindolinones. Org Biomol Chem 2020; 18:3740-3746. [PMID: 32367104 DOI: 10.1039/d0ob00546k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A copper-catalyzed asymmetric 1,3-dipolar cycloaddition of glycine iminoesters with alkyl substituted 3-methylene-2-oxindoles is described. By using de novo design of P-stereogenic phosphines as ligands, spiro[pyrrolidin-3,3'-oxindole]s are generated in good to excellent yields with high asymmetric induction. A further reduced catalyst loading of 0.1 mol% is sufficient to achieve a satisfactory enantioselectivity of 90% ee. The DFT calculations suggest the second Michael addition of the 1,3-dipole to be the rate- and enantio-determining step. A key feature of this 1,3-dipolar cycloaddition is the wide substrate applicability, even with alkyl aldehyde-derived azomethine ylide; thus it has streamlined a highly enantioselective access to a new class of antiproliferative agents, MDM2-p53.
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Affiliation(s)
- Hao Cui
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Ke Li
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Yue Wang
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Manman Song
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Congcong Wang
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Donghui Wei
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Er-Qing Li
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Zheng Duan
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - François Mathey
- College of Chemistry, Green Catalysis Center, International Phosphorus Laboratory, International Joint Research Laboratory for Functional Organophosphorus Materials of Henan Province, Zhengzhou University, Zhengzhou 450001, P. R. China.
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17
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He N, Zhu Z, Li F, Zhu Y, Qu L, Chen H. Theoretical understanding mechanisms and stereoselectivities of [2+2] cycloaddition of ketenes with ketimines catalyzed by bifunctional N-heterocyclic carbene. Struct Chem 2020. [DOI: 10.1007/s11224-019-01389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Wang C, Li SJ, Zhang M, Wei D, Ding L. Origin of stereoselectivity in an isothiourea catalyzed Michael addition reaction of aryl ester with vinyl disulfone. NEW J CHEM 2020. [DOI: 10.1039/d0nj03540h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of stereoselectivity in an isothiourea-catalyzed addition reaction of aryl ester with vinyl disulfone was explored for the first time.
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Affiliation(s)
- Congcong Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province
- Key Laboratory of Technology of Drug Preparation (Zhengzhou University)
- Ministry of Education of China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences
- Zhengzhou University
| | - Shi-Jun Li
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Min Zhang
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province
- Key Laboratory of Technology of Drug Preparation (Zhengzhou University)
- Ministry of Education of China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences
- Zhengzhou University
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19
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Deng Q, Li SJ, Wei D, Lan Y. Insights into Lewis base-catalyzed chemoselective [3 + 2] and [3 + 4] annulation reactions of MBH carbonates. Org Chem Front 2020. [DOI: 10.1039/d0qo00457j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemoselectivity of Lewis base-catalyzed [3 + 2] and [3 + 4] annulation reactions of MBH carbonates can be predicted using FMO overlap analysis.
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Affiliation(s)
- Qianqian Deng
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Shi-Jun Li
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yu Lan
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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20
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Deng Q, Wang Y, Li SJ, Qu LB, Lan Y, Wei D. Origin and stabilization of axial chirality in the construction of naphthyl-C2-indoles: a DFT study. Org Chem Front 2020. [DOI: 10.1039/d0qo00936a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A novel method for predicting the stabilization of axial chirality in the construction of naphthyl-C2-indoles has been suggested for the first time.
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Affiliation(s)
- Qianqian Deng
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Shi-Jun Li
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Ling-Bo Qu
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yu Lan
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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21
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Wang C, Li SJ, Zhang QC, Wei D, Ding L. Insights into isothiourea-catalyzed asymmetric [3 + 3] annulation of α,β-unsaturated aryl esters with 2-acylbenzazoles: mechanism, origin of stereoselectivity and switchable chemoselectivity. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00295j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The switchable chemoselectivity of isothiourea-catalyzed asymmetric [3 + 3] annulation of α,β-unsaturated aryl esters with 2-acylbenzazoles has been predicted successfully.
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Affiliation(s)
- Congcong Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province
- Key Laboratory of Technology of Drug Preparation (Zhengzhou University)
- Ministry of Education of China
- Key Laboratory of Henan Province for Drug Quality and Evaluation
- School of Pharmaceutical Sciences
| | - Shi-Jun Li
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Qiao-Chu Zhang
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry, and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province
- Key Laboratory of Technology of Drug Preparation (Zhengzhou University)
- Ministry of Education of China
- Key Laboratory of Henan Province for Drug Quality and Evaluation
- School of Pharmaceutical Sciences
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22
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Wang X, Wang Y, Song J, Wei D. Insights into N-heterocyclic carbene and Lewis acid cooperatively catalyzed oxidative [3 + 3] annulation reactions of α,β-unsaturated aldehyde with 1,3-dicarbonyl compounds. Org Chem Front 2020. [DOI: 10.1039/d0qo00091d] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
N-Heterocyclic carbene and Lewis acid cooperatively catalyzed oxidative [3 + 3] annulation reactions of 1,3-dicarbonyl compounds have been systematically studied in theory.
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Affiliation(s)
- Xinghua Wang
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Jinshuai Song
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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23
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Unravelling the Mechanism and Selectivity of the NHC‐catalyzed Three‐Membered Ring‐Opening/Fluorination of Epoxy Enals: A DFT Study. ChemCatChem 2019. [DOI: 10.1002/cctc.201900424] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Liu Q, Sun L, Li S, Li X, Qu L, Lan Y, Wei D. Insights into N‐Heterocyclic Carbene (NHC)‐Catalyzed Asymmetric Addition of 2H‐Azirine with Aldehyde. Chem Asian J 2019; 14:2000-2007. [DOI: 10.1002/asia.201900076] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Qiuli Liu
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Ling Sun
- Basic Teaching DepartmentHuanghe Jiaotong University No. 333 Yingbin Road Wuzhi Henan 454950 P. R. China
| | - Shi‐Jun Li
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Xue Li
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Ling‐Bo Qu
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Yu Lan
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
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25
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Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin. Eur J Med Chem 2019; 164:399-407. [DOI: 10.1016/j.ejmech.2018.12.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/12/2018] [Accepted: 12/24/2018] [Indexed: 01/10/2023]
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26
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Deng Z, Wang Y, Mou D, Sun Y, Da H, Gao J. Theoretical investigation on acetylene cyclotrimerization catalysed by TiO2and Ti. J PHYS ORG CHEM 2019. [DOI: 10.1002/poc.3934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Zhe‐Peng Deng
- College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou China
- Running Maintenance DepartmentGansu Computing Center Lanzhou China
| | - Yong‐Cheng Wang
- College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou China
| | - Dan Mou
- Huining, No. 1 Middle School Huining County China
| | - Yu Sun
- Experiment Center of Northwest University for Nationalities Lanzhou China
| | - Hu Da
- Running Maintenance DepartmentGansu Computing Center Lanzhou China
| | - Jian‐De Gao
- Gansu University of Chinese Medicine Lanzhou China
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27
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Zhang QC, Li X, Wang X, Li SJ, Qu LB, Lan Y, Wei D. Insights into highly selective ring expansion of oxaziridines under Lewis base catalysis: a DFT study. Org Chem Front 2019. [DOI: 10.1039/c8qo01370e] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The possible mechanism and stereoselectivity of the NHC-catalyzed ring expansion reaction of oxaziridines have been theoretically studied for the first time.
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Affiliation(s)
- Qiao-Chu Zhang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xue Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xinghua Wang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yu Lan
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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28
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Gao J, Wang Y. Mechanistic studies on the N-heterocyclic carbene-catalyzed reaction of isatin-derived enals with hydrazones. Org Biomol Chem 2019; 17:7442-7447. [DOI: 10.1039/c9ob01317b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The detailed mechanism and origin of stereoselectivity of the NHC-catalyzed annulation reaction were investigated.
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Affiliation(s)
- Jinxin Gao
- Department of Cooking Food
- Henan Polytechnic
- Zhengzhou
- P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P. R. China
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29
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Shi Q, Wang W, Wang Y, Lan Y, Yao C, Wei D. Prediction on the origin of chemoselectivity in Lewis base-mediated competition cyclizations between allenoates and chalcones: a computational study. Org Chem Front 2019. [DOI: 10.1039/c9qo00606k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The HOMOTSs and p-orbital contributions of the center atoms were used to predict the origin of chemoselectivity in this work.
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Affiliation(s)
- Qianqian Shi
- College of Chemistry and Molecular Engineering
- and School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Wei Wang
- College of Chemistry and Molecular Engineering
- and School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P. R. China
| | - Yu Lan
- College of Chemistry and Molecular Engineering
- and School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Changsheng Yao
- Jiangsu Key Lab of Green Synthetic Chemistry for Functional Materials
- School of Chemistry & Materials Science
- Jiangsu Normal University
- Xuzhou
- P. R. China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering
- and School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
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30
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Li X, Li SJ, Wang Y, Wang Y, Qu LB, Li Z, Wei D. Insights into NHC-catalyzed oxidative α-C(sp3)–H activation of aliphatic aldehydes and cascade [2 + 3] cycloaddition with azomethine imines. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00526a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The NHC catalyst is identified to promote [2 + 3] cycloaddition by avoiding the poor FMO overlap mode in theory.
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Affiliation(s)
- Xue Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yanyan Wang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Zhongjun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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31
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Wang Y, Qu L, Wei D. Prediction on the Origin of Selectivities in Base‐controlled Switchable NHC‐catalyzed Transformations. Chem Asian J 2018; 14:293-300. [DOI: 10.1002/asia.201801583] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/28/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Yang Wang
- Department of Material and Chemical EngineeringZhengzhou University of Light Industry 136 Science Avenue Zhengzhou Henan Province 450002 P. R. China
| | - Ling‐Bo Qu
- College of Chemistry and Molecular EngineeringZhengzhou University 100 Science Avenue Zhengzhou Henan Province 450002 P. R. China
| | - Donghui Wei
- College of Chemistry and Molecular EngineeringZhengzhou University 100 Science Avenue Zhengzhou Henan Province 450002 P. R. China
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32
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Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP. Int J Mol Sci 2018; 19:ijms19123858. [PMID: 30514002 PMCID: PMC6321098 DOI: 10.3390/ijms19123858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 11/16/2022] Open
Abstract
A combination of molecular dynamics (MD) simulations and computational analyses uncovers structural features that may influence substrate passage and exposure to the active sites within the proteolytic chamber of the 20S proteasome core particle (CP). MD simulations of the CP reveal relaxation dynamics in which the CP slowly contracts over the 54 ns sampling period. MD simulations of the SyringolinA (SylA) inhibitor within the proteolytic B 1 ring chamber of the CP indicate that favorable van der Waals and electrostatic interactions account for the predominant association of the inhibitor with the walls of the proteolytic chamber. The time scale required for the inhibitor to travel from the center of the proteolytic chamber to the chamber wall is on the order of 4 ns, accompanied by an average energetic stabilization of approximately -20 kcal/mol.
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33
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Liu Q, Li SJ, Li. X, Qu LB, Wei D. A Computational Study on the 4-Dimethylaminopyridine (DMAP)-Catalyzed Regioselective [2+4] Cyclization of Allenic Ester with Cyclic Ketimine. ChemistrySelect 2018. [DOI: 10.1002/slct.201802267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qiuli Liu
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Xue Li.
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
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Liu N, Xie YF, Wang C, Li SJ, Wei D, Li M, Dai B. Cooperative Multifunctional Organocatalysts for Ambient Conversion of Carbon Dioxide into Cyclic Carbonates. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01925] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ning Liu
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, North Fourth Road, Shihezi, Xinjiang 832003, People’s Republic of China
| | - Ya-Fei Xie
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, North Fourth Road, Shihezi, Xinjiang 832003, People’s Republic of China
| | - Chuan Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
| | - Shi-Jun Li
- College of Chemistry and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, People’s Republic of China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, People’s Republic of China
| | - Min Li
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, North Fourth Road, Shihezi, Xinjiang 832003, People’s Republic of China
| | - Bin Dai
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, North Fourth Road, Shihezi, Xinjiang 832003, People’s Republic of China
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35
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Li X, Wang Y, Wang Y, Tang M, Qu LB, Li Z, Wei D. Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Oxidative γ-C(sp 3)-H Deprotonation of Alkylenals and Cascade [4 + 2] Cycloaddition with Alkenylisoxazoles. J Org Chem 2018; 83:8543-8555. [PMID: 29927597 DOI: 10.1021/acs.joc.8b01112] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The N-heterocyclic carbene (NHC)-catalyzed oxidative C-H deprotonations have attracted increasing attention; however, the general mechanism regarding this kind of oxidative organocatalysis remains unclear. In this paper, the competing mechanisms and origin of the stereoselectivity of the NHC-catalyzed oxidative γ-C(sp3)-H deprotonation of alkylenals and cascade [4 + 2] cycloaddition with alkenylisoxazoles were systematically investigated for the first time using density functional theory (DFT). The computed results indicate that the oxidation of the Breslow intermediate by 3,3',5,5'-tetra- tert-butyl diphenoquinone (DQ) via a hydride transfer to oxygen (HTO) pathway is the most favorable among the four competing pathways. In addition, the analyses demonstrate that oxidant DQ plays a double role, i.e., strengthening the acidity of the hydrogen of the γ-carbon of alkylenal and forming π···π interactions with conjugated C═C bonds to promote the γ-C(sp3)-H deprotonation. The NHC catalyst acts as a Lewis base, and the hydrogen-bond network between the NHC and the substrate formed in the key Michael addition step is responsible for the origin of the stereoselectivity. Further DFT calculations reveal that the nonpolar solvent can stabilize the nonpolar R isomer but destabilize the polar S isomer for the stereoselectivity-determining transition states, thus improving the stereoselectivity.
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36
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Li X, Tang M, Wang Y, Wang Y, Li Z, Qu LB, Wei D. Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Intramolecular Cyclization of Aldimines: General Mechanism and Role of Catalyst. Chem Asian J 2018; 13:1710-1718. [PMID: 29667337 DOI: 10.1002/asia.201800313] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/02/2018] [Indexed: 12/14/2022]
Abstract
One of the most challenging questions in the Lewis base organocatalyst field is how to predict the most electrophilic carbon for the complexation of N-heterocyclic carbene (NHC) and reactant. This study provides a valuable case for this issue. Multiple mechanisms (A, B, C, D, and E) for the intramolecular cyclization of aldimine catalyzed by NHC were investigated by using density functional theory (DFT). The computed results reveal that the NHC energetically prefers attacking the iminyl carbon (AIC mode, which is associated with mechanisms A and C) rather than attacking the olefin carbon (AOC mode, which is associated with mechanisms B and D) or attacking the carbonyl carbon (ACC mode, which is associated with mechanism E) of aldimine. The calculated results based on the different reaction models indicate that mechanism A (AIC mode), which is associated with the formation of the aza-Breslow intermediate, is the most favorable pathway. For mechanism A, there are five steps: (1) nucleophilic addition of NHC to the iminyl carbon of aldimine; (2) [1,2]-proton transfer to form an aza-Breslow intermediate; (3) intramolecular cyclization; (4) the other [1,2]-proton transfer; and (5) regeneration of NHC. The analyses of reactivity indexes have been applied to explain the chemoselectivity, and the general principles regarding the possible mechanisms would be useful for the rational design of NHC-catalyzed chemoselective reactions.
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Affiliation(s)
- Xue Li
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Mingsheng Tang
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Yanyan Wang
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 100 Kexue Street, Zhengzhou, Henan, 450002, P. R. China
| | - Zhongjun Li
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
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37
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Zhang H, Xu H, Bai H, Wei D, Zhu Y, Zhang W. Theoretical study on the mechanism and enantioselectivity of NHC-catalyzed intramolecular SN2′ nucleophilic substitution: what are the roles of NHC and DBU? Org Chem Front 2018. [DOI: 10.1039/c8qo00129d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A possible catalytic mechanism was proposed and studied in very detail by using the DFT method for a recently reported enantioselective intramolecular SN2′ substitution of aldehydes with trisubstituted allylic bromides.
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Affiliation(s)
- Huimin Zhang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Hao Xu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Huining Bai
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Yanyan Zhu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Wenjing Zhang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
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38
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Liu C, Han P, Xie Z, Xu Z, Wei D. Insights into Ag(i)-catalyzed addition reactions of amino alcohols to electron-deficient olefins: competing mechanisms, role of catalyst, and origin of chemoselectivity. RSC Adv 2018; 8:40338-40346. [PMID: 35558202 PMCID: PMC9091461 DOI: 10.1039/c8ra09065c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
The competing mechanisms of Ag(i)-catalyzed chemoselective addition reactions of amino alcohols and electron-deficient olefins leading to the O-adduct or N-adduct products were systematically studied with density functional theory methods. Calculations indicate that the AgHMDS/dppe versus AgOAc/dppe catalytic systems can play different roles and thereby generate two different products. The AgHMDS/dppe system works as a Brønsted base to deprotonate the amino alcohol OH to form the Ag–O bond, which leads to formation of the O-adduct. In contrast, the AgOAc/dppe system mainly acts as a Lewis acid to coordinate with O and N atoms of the amino alcohol, but it cannot act as the Brønsted base to further activate the OH group because of its weaker basicity. Therefore, the AgOAc/dppe catalyzed reaction has a mechanism that is similar to the non-catalyzed reaction, and generates the same N-adduct. The obtained insights will be important for rational design of the various kinds of cooperatively catalyzed chemoselective addition reactions, including the use of the less nucleophilic hydroxyl groups of unprotected amino alcohols. The origin of the chemoselectivities of Ag(i)-catalyzed addition reactions of amino alcohols to olefin has been predicted for the first time.![]()
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Affiliation(s)
- Chunhui Liu
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Peilin Han
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Zhizhong Xie
- Department of Chemistry
- School of Chemistry, Chemical Engineering and Life Sciences
- Wuhan University of Technology
- Wuhan
- P. R. China
| | - Zhihong Xu
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University of China
- Zhengzhou
- P. R. China
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39
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Wang Y, Wang Y, Wang X, Li X, Qu LB, Wei D. Competing mechanisms and origins of chemo- and stereo-selectivities of NHC-catalyzed reactions of enals with 2-aminoacrylates. Catal Sci Technol 2018. [DOI: 10.1039/c8cy01272e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A DFT study on competing mechanisms of NHC-catalyzed reactions of enals with 2-aminoacrylates has been performed for the first time.
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Affiliation(s)
- Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P.R. China
| | - Yanyan Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xinghua Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xue Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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40
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Shi Q, Zhang W, Wang Y, Qu L, Wei D. Insights into the isothiourea-catalyzed asymmetric [4 + 2] annulation of phenylacetic acid with alkylidene pyrazolone. Org Biomol Chem 2018. [DOI: 10.1039/c7ob03142d] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational study on the isothiourea-catalyzed asymmetric [4 + 2] annulation of phenylacetic acid with alkylidene pyrazolone was performed using the DFT method.
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Affiliation(s)
- Qianqian Shi
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Wei Zhang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P.R. China
| | - Lingbo Qu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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41
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Shi Q, Wang Y, Wang Y, Qu LB, Qiao Y, Wei D. Insights into N-heterocyclic carbene-catalyzed [3 + 4] annulation reactions of 2-bromoenals with N-Ts hydrazones. Org Chem Front 2018. [DOI: 10.1039/c8qo00716k] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A DFT study toward N-heterocyclic carbene-catalyzed [3 + 4] annulation reactions of 2-bromoenals has been performed for the first time.
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Affiliation(s)
- Qianqian Shi
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P.R. China
| | - Yanyan Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yan Qiao
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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42
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Wang FR, Li ZY, Wei DH, Niu YY, Hou HW, Wu BL. The conformational behavior of multivalent tris(imidazolium)cyclophanes in the hybrids with metal (pseudo)halides or polyoxometalates. CrystEngComm 2018. [DOI: 10.1039/c8ce01372a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Three 3D imidazole or benzimidazole-bearing cages as trivalent cationic templates react with metal (pseudo)halides or polyoxometalates to obtain a series of different organic–inorganic hybrids in which the cages exhibit breathing behavior of expansion and contraction.
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Affiliation(s)
- Fu-Rong Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
| | - Zi-Yan Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
| | - Dong-Hui Wei
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
| | - Yun-Yin Niu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
| | - Hong-Wei Hou
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
| | - Ben-Lai Wu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- P. R. China
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43
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Jin L, Shi S, Zhao Y, Luo L, Zhao C, Lu J, Jiang M. Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Shengnan Shi
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Yang Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Liyang Luo
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Min Jiang
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
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44
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Liu Y, Peng Y, Lu J, Wang J, Ma H, Song C, Liu B, Qiao Y, Yu W, Wu J, Chang J. Design, synthesis, and biological evaluation of new 1,2,3-triazolo-2'-deoxy-2'-fluoro- 4'-azido nucleoside derivatives as potent anti-HBV agents. Eur J Med Chem 2017; 143:137-149. [PMID: 29174810 DOI: 10.1016/j.ejmech.2017.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 01/15/2023]
Abstract
Novel drugs are urgently needed to combat hepatitis B virus (HBV) infection due to drug-resistant virus. In this paper, a series of novel 4-monosubstituted 2'-deoxy-2'-β-fluoro-4'-azido-β-d-arabinofuranosyl 1,2,3-triazole nucleoside analogues (1a-g) were designed, synthesized and screened for in vitro anti-HBV activity. At 5.0 μM in the cellular model, all the synthetic compounds display activities comparable to that of the positive control, lamivudine at 20 μM. Of the compounds tested, the amide-substituted analogue (1a) shows the most promising anti-HBV activity and low cytotoxicity in the cell model. In particular, it retains excellent activity against lamivudine-resistant HBV mutants. In duck HBV (DHBV)-infected duck models, both the serum and liver DHBV DNA levels (67.4% and 53.3%, respectively) were reduced markedly by the treatment with 1a. Analysis of the structure of HBV polymer/1a-triphosphate (1a-TP) complex shows that 1a-TP is stabilized by specific van der Waals interactions with the enzyme residues arising from 4-amino-1,2,3-triazole and the 4'-azido group.
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Affiliation(s)
- Yuan Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Youmei Peng
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, PR China
| | - Jingjing Lu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Jingwen Wang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Haoran Ma
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Chuanjun Song
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Bingjie Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Yan Qiao
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Wenquan Yu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China
| | - Jie Wu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China.
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Henan 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Zhengzhou 450001, PR China.
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45
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Li X, Wei D, Li Z. Theoretical Study on DBU-Catalyzed Insertion of Isatins into Aryl Difluoronitromethyl Ketones: A Case for Predicting Chemoselectivity Using Electrophilic Parr Function. ACS OMEGA 2017; 2:7029-7038. [PMID: 31457285 PMCID: PMC6645149 DOI: 10.1021/acsomega.7b00907] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 10/05/2017] [Indexed: 06/10/2023]
Abstract
The possible mechanisms of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)-catalyzed chemoselective insertion of N-methyl isatin into aryl difluoronitromethyl ketone to synthesize 3,3-disubstituted and 2,2-disubstituted oxindoles have been studied in this work. As revealed by calculated results, the reaction occurs via two competing paths, including α and β carbonyl paths, and each path contains five steps, that is, nucleophilic addition of DBU to ketone, C-C bond cleavage affording difluoromethylnitrate anion and phenylcarbonyl-DBU cation, nucleophilic addition of difluoromethylnitrate anion to carbonyl carbon of N-methyl isatin, acyl transfer process, and dissociation of DBU and product. The computational results suggest that nucleophilic additions on different carbonyl carbons of N-methyl isatin via α and β carbonyl paths would lead to different products in the third step, and β carbonyl path associated with the main product 3,3-disubstituted oxindole is more energetically favorable, which is consistent with the experimental observations. Noteworthy, electrophilic Parr function can be successfully applied for exactly predicting the activity of reaction site and reasonably explaining the chemoselectivity. In addition, the distortion/interaction and noncovalent interaction analyses show that much more hydrogen bond interactions should be responsible for the lower energy of the transition state associated with β carbonyl path. The obtained insights would be valuable for the rational design of efficient organocatalysts for this kind of reactions with high selectivities.
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46
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Wang W, Wei D. A DFT Study of N-Heterocyclic Carbene Catalyzed [4+2] Annulation between Saturated Carboxylate withortho-Quinone Methide: Possible Mechanisms and Origin of Enantioselectivity. ChemistrySelect 2017. [DOI: 10.1002/slct.201701679] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wei Wang
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
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47
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Insights into chemoselective fluorination reaction of alkynals via N-heterocyclic carbene and Brønsted base cooperative catalysis. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2127-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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48
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Bai J, Wang RH, Qiao Y, Wang A, Fang CJ. Schiff base derived from thiosemicarbazone and anthracene showed high potential in overcoming multidrug resistance in vitro with low drug resistance index. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:2227-2237. [PMID: 28814831 PMCID: PMC5546733 DOI: 10.2147/dddt.s138371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Multidrug resistance (MDR) is a huge obstacle in cancer chemotherapeutics. Overcoming MDR is a great challenge for anticancer drug discovery. Here, DNA binding and cytotoxicity of Schiff base L1 and L2 were explored to assess their efficiency in fighting cancer and overcoming the MDR. L1 and L2 could treat extremely chemoresistant MCF-7/ADR cell as drug-sensitive cell, with drug resistance index (DRI) <2.13, showing high potential in overcoming the MDR. The apoptotic ratio induced by L1 and L2 was low for both MCF-7 and MCF-7/ADR cells. L1 and L2 induced an impairment of cell cycle progression of MCF-7 and MCF-7/ADR cell lines and suppressed cell growth by perturbing progress through the G0/G1 phase, with L2 causing more profound effect, which might account for lower drug resistance after L2 treatment. The molecular docking revealed weak interaction between L1/L2 and P-glycoprotein (P-gp), the most important drug efflux pump and intracellular Rhodamine 123 accumulation indicated that the activity of P-gp was not inhibited by L1 and L2. Combined with the cellular uptake results, it implied that L1 and L2 could bypass P-gp efflux to exert anticancer activity.
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Affiliation(s)
- Jie Bai
- Department of Chemical Biology, School of Pharmaceutical Sciences, Capital Medical University, Beijing
| | - Rui-Hui Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Capital Medical University, Beijing
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan
| | - Aidong Wang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Huangshan University, Huangshan, Anhui, China
| | - Chen-Jie Fang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Capital Medical University, Beijing
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49
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Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
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Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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50
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Wang W, Wang Y, Zheng L, Qiao Y, Wei D. A DFT Study on Mechanisms and Origin of Selectivity of Phosphine-Catalyzed Vicinal Acylcyanation of Alkynoates. ChemistrySelect 2017. [DOI: 10.1002/slct.201700996] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Wei Wang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Yang Wang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Linjie Zheng
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
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