1
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Hasan MN, Ray M, Saha A. Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery. J Phys Chem B 2023; 127:9663-9684. [PMID: 37921534 DOI: 10.1021/acs.jpcb.3c04710] [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: 11/04/2023]
Abstract
Covalent drug discovery has been a challenging research area given the struggle of finding a sweet balance between selectivity and reactivity for these drugs, the lack of which often leads to off-target activities and hence undesirable side effects. However, there has been a resurgence in covalent drug design following the success of several covalent drugs such as boceprevir (2011), ibrutinib (2013), neratinib (2017), dacomitinib (2018), zanubrutinib (2019), and many others. Design of covalent drugs includes many crucial factors, where "evaluation of the binding affinity" and "a detailed mechanistic understanding on covalent inhibition" are at the top of the list. Well-defined experimental techniques are available to elucidate these factors; however, often they are expensive and/or time-consuming and hence not suitable for high throughput screens. Recent developments in in silico methods provide promise in this direction. In this report, we review a set of recent publications that focused on developing and/or implementing novel in silico techniques in "Computational Covalent Drug Discovery (CCDD)". We also discuss the advantages and disadvantages of these approaches along with what improvements are required to make it a great tool in medicinal chemistry in the near future.
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Affiliation(s)
- Md Nazmul Hasan
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
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2
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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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3
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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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4
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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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5
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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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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17
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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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18
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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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19
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Yuan B, He R, Shen W, Li M. Influence of Base Strength on the Proton-Transfer Reaction by Density Functional Theory. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Binfang Yuan
- School of Chemistry and Chemical Engineering; Southwest University; No. 2 Tiansheng Road 400715 Chongqing BeiBei District P. R.China
| | - Rongxing He
- School of Chemistry and Chemical Engineering; Southwest University; No. 2 Tiansheng Road 400715 Chongqing BeiBei District P. R.China
| | - Wei Shen
- School of Chemistry and Chemical Engineering; Southwest University; No. 2 Tiansheng Road 400715 Chongqing BeiBei District P. R.China
| | - Ming Li
- School of Chemistry and Chemical Engineering; Southwest University; No. 2 Tiansheng Road 400715 Chongqing BeiBei District P. R.China
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20
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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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21
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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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22
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Wei D, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA). Org Biomol Chem 2016; 13:6857-65. [PMID: 26018983 DOI: 10.1039/c5ob00737b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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23
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Qiao Y, Yang W, Wei D, Chang J. Theoretical investigations toward TMEDA-catalyzed [2 + 4] annulation of allenoate with 1-aza-1,3-diene: mechanism, regioselectivity, and role of the catalyst. RSC Adv 2016. [DOI: 10.1039/c6ra09507k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A computational study on the reaction between allenoate and 1-aza-1,3-diene catalyzed by TMEDA has been performed using the DFT method.
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Affiliation(s)
- Yan Qiao
- Department of Pathophysiology
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- China
| | - Wanjing Yang
- Department of Pathophysiology
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Junbiao Chang
- Department of Pathophysiology
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- China
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24
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Yao Y, Liu J, Zheng F, Zhan CG. Reaction Pathway for Cocaine Hydrolase-Catalyzed Hydrolysis of (+)-Cocaine. Theor Chem Acc 2016; 135. [PMID: 28250715 DOI: 10.1007/s00214-015-1788-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently designed and discovered cocaine hydrolase (CocH), engineered from human butyrylcholinesterase (BChE), has been proven promising as a novel enzyme therapy for treatment of cocaine overdose and addiction because it is highly efficient in catalyzing hydrolysis of naturally occurring (-)-cocaine. It has been known that the CocH also has a high catalytic efficiency against (+)-cocaine, a synthetic enantiomer of cocaine. Reaction pathway and the corresponding free energy profile for the CocH-catalyzed hydrolysis of (+)-cocaine have been determined, in the present study, by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Acordingt to the QM/MM-FE results, the catalytic hydrolysis process is initiated by the nucleophilic attack on carbonyl carbon of (-)-cocaine benzoyl ester via hydroxyl oxygen of S198 side chain, and the second reaction step (i.e. dissociation of benzoyl ester) is rate-determining. This finding for CocH-catalyzed hydrolysis of (+)-cocaine is remarkably different from that for the (+)-cocaine hydrolysis catalyzed by bacterial cocaine esterase in which the first reaction step of the deacylation is associated with the highest free energy barrier (~17.9 kcal/mol). The overall free energy barrier (~16.0 kcal/mol) calculated for the acylation stage of CocH-catalyzed hydrolysis of (+)-cocaine is in good agreement with the experimental free energy barrier of ~14.5 kcal/mol derivated from the experimental kinetic data.
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Affiliation(s)
- Yuan Yao
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; The Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P.R. China
| | - Junjun Liu
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; Tongji School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, P.R. China
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
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25
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Azad CS, Khan IA, Narula AK. Organocatalyzed asymmetric Michael addition by an efficient bifunctional carbohydrate–thiourea hybrid with mechanistic DFT analysis. Org Biomol Chem 2016; 14:11454-11461. [DOI: 10.1039/c6ob02158a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of thiourea based bifunctional organocatalysts having d-glucose as a core scaffold were synthesized and examined as catalysts for the asymmetric Michael addition reaction of aryl/alkyl trans-β-nitrostyrenes over cyclohexanone and other Michael donors having active methylene.
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Affiliation(s)
- Chandra S. Azad
- “Hygeia” Centre of Excellence in Pharmaceutical Sciences (CEPS)
- GGS Indraprastha University
- New Delhi
- India
| | - Imran A. Khan
- Department of Chemistry
- Guru Nanak Dev University
- Amritsar
- India
| | - Anudeep K. Narula
- “Hygeia” Centre of Excellence in Pharmaceutical Sciences (CEPS)
- GGS Indraprastha University
- New Delhi
- India
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26
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Zhang M, Wei D, Wang Y, Li S, Liu J, Zhu Y, Tang M. DFT study on the reaction mechanisms and stereoselectivities of NHC-catalyzed [2 + 2] cycloaddition between arylalkylketenes and electron-deficient benzaldehydes. Org Biomol Chem 2015; 12:6374-83. [PMID: 24940721 DOI: 10.1039/c4ob00606b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, two possible mechanisms (mechanisms A and B) on the stereoselective [2 + 2] cycloaddition of aryl(alkyl)ketenes and electron-deficient benzaldehydes catalyzed by N-heterocyclic carbenes (NHCs) have been investigated using density functional theory (DFT). Our calculated results indicate that the favorable mechanism (mechanism A) includes three processes: the first step is the nucleophilic attack on the arylalkylketene by the NHC catalyst to form an intermediate, the second step is the [2 + 2] cycloaddition of the intermediate and benzaldehyde for the formation of a β-lactone, and the last step is the dissociation of the NHC catalyst and the β-lactone. Notably, the [2 + 2] cycloaddition, in which two chiral centers associated with four configurations (SS, RR, SR and RS) are formed, is demonstrated to be both the rate- and stereoselectivity-determining step. Moreover, the reaction pathway associated with the SR configuration is the most favorable pathway and leads to the main product, which is in good agreement with the experimental results. Furthermore, the analysis of global and local reactivity indexes has been performed to explain the role of the NHC catalyst in the [2 + 2] cycloaddition reaction. Therefore, this study will be of great use for the rational design of more efficient catalysts for this kind of cycloaddition.
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Affiliation(s)
- Mengmeng Zhang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, Zhengzhou, Henan Province 450001, P.R. China.
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27
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Wang Y, Guo X, Wu B, Wei D, Tang M. Mechanistic and stereoselectivity study for the reaction of trifluoropyruvates with arylpropenes catalyzed by a cationic Lewis acid rhodium complex. RSC Adv 2015. [DOI: 10.1039/c5ra21074g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanism and stereoselectivity of a Lewis acid catalyzed carbonyl–ene reaction of trifluoropyruvates with arylpropenes have been investigated using a DFT method.
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Affiliation(s)
- Yang Wang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Xiaokang Guo
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Bohua Wu
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Mingsheng Tang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
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28
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Mechanistic insights into the stereoselective C2-functionalization of 1-substituted imidazoles with cyanophenylacetylene and aldehydes. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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Qiao Y, Han K, Zhan CG. Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine. Org Biomol Chem 2014; 12:2214-27. [PMID: 24595354 DOI: 10.1039/c3ob42464b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow similar catalytic reaction mechanisms, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2(a)/TS2(b) should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal mol(-1)) is 2.5 kcal mol(-1) lower than that for the BChE-catalyzed hydrolysis (20.8 kcal mol(-1)). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal mol(-1) for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2(a) relative to TS2(b). The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, P. R. China
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30
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Wang Y, Wei D, Li Z, Zhu Y, Tang M. DFT study on the mechanisms and diastereoselectivities of Lewis acid-promoted ketene-alkene [2 + 2] cycloadditions: what is the role of Lewis acid in the ketene and C = X (X = O, CH₂, and NH) [2 + 2] cycloaddition reactions? J Phys Chem A 2014; 118:4288-300. [PMID: 24874716 DOI: 10.1021/jp500358m] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The detailed mechanisms and diastereoselectivities of Lewis acid-promoted ketene-alkene [2 + 2] cycloaddition reactions have been studied by density functional theory (DFT). Four possible reaction channels, including two noncatalyzed diastereomeric reaction channels (channels A and B) and two Lewis acid (LA) ethylaluminum dichloride (EtAlCl2) catalyzed diastereomeric reaction channels (channels C and D), have been investigated in this work. The calculated results indicate that channel A (associated with product R-configurational cycloputanone) is more energy favorable than channel B (associated with the other product S-configurational cyclobutanone) under noncatalyzed condition, but channel D leading to S-configurational cyclobutanone is more energy-favorable than channel C, leading to R-configurational cycloputanone under a LA-promoted condition, which is consistent with the experimental results. And Lewis acid can make the energy barrier of ketene-alkene [2 + 2] cycloaddition much lower. In order to explore the role of LA in ketene and C = X (X = O, CH2, and NH) [2 + 2] cycloadditions, we have tracked and compared the interaction modes of frontier molecular orbitals (FMOs) along the intrinsic reaction coordinate (IRC) under the two different conditions. Besides by reducing the energy gap between the FMOs of the reactants, our computational results demonstrate that Lewis acid lowers the energy barrier of the ketene and C = X [2 + 2] cycloadditions by changing the overlap modes of the FMOs, which is remarkably different from the traditional FMO theory. Furthermore, analysis of global reactivity indexes has also been performed to explain the role of LA catalyst in the ketene-alkene [2 + 2] cycloaddition reaction.
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Affiliation(s)
- Yang Wang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University , Zhengzhou, Henan Province 450001, P.R. China
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31
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Vorob’ev V. How to turn real substance liquid–gas coexistence curve in binodal of lattice gas. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Li Z, Wei D, Wang Y, Zhu Y, Tang M. DFT Study on the Mechanisms and Stereoselectivities of the [4 + 2] Cycloadditions of Enals and Chalcones Catalyzed by N-Heterocyclic Carbene. J Org Chem 2014; 79:3069-78. [DOI: 10.1021/jo500194d] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zhenyu Li
- 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
| | - Yang Wang
- The College of Chemistry
and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, Zhengzhou, Henan Province, 450001, P.R. China
| | - Yanyan Zhu
- The College of Chemistry
and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, Zhengzhou, Henan Province, 450001, P.R. China
| | - Mingsheng Tang
- The College of Chemistry
and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, Zhengzhou, Henan Province, 450001, P.R. China
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