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Tang JJ, Zhao MY, Lin YJ, Yang LH, Xie LY. Persulfate-Promoted Carbamoylation/Cyclization of Alkenes: Synthesis of Amide-Containing Quinazolinones. Molecules 2024; 29:997. [PMID: 38474508 DOI: 10.3390/molecules29050997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The incorporation of amide groups into biologically active molecules has been proven to be an efficient strategy for drug design and discovery. In this study, we present a simple and practical method for the synthesis of amide-containing quinazolin-4(3H)-ones under transition-metal-free conditions. This is achieved through a carbamoyl-radical-triggered cascade cyclization of N3-alkenyl-tethered quinazolinones. Notably, the carbamoyl radical is generated in situ from the oxidative decarboxylative process of oxamic acids in the presence of (NH4)2S2O8.
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Affiliation(s)
- Jia-Jun Tang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Meng-Yang Zhao
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ying-Jun Lin
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Li-Hua Yang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Long-Yong Xie
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
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2
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Zheng F, Hou S, Xue L, Yang W, Zhan CG. Human Butyrylcholinesterase Mutants for (-)-Cocaine Hydrolysis: A Correlation Relationship between Catalytic Efficiency and Total Hydrogen Bonding Energy with an Oxyanion Hole. J Phys Chem B 2023; 127:10723-10729. [PMID: 38063500 DOI: 10.1021/acs.jpcb.3c06392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
A combined computational and experimental study has been carried out to explore and test a quantitative correlation relationship between the relative catalytic efficiency (RCE) of human butyrylcholinesrase (BChE) mutant-catalyzed hydrolysis of substrate (-)-cocaine and the total hydrogen bonding energy (tHBE) of the carbonyl oxygen of the substrate with the oxyanion hole of the enzyme in the modeled transition-state structure (TS1), demonstrating a satisfactory linear correlation relationship between ln(RCE) and tHBE. The satisfactory correlation relationship has led us to computationally predict and experimentally confirm new human BChE mutants that have a further improved catalytic activity against (-)-cocaine, including the most active one (the A199S/F227S/S287G/A328W/Y332G mutant) with a 2790-fold improved catalytic efficiency (kcat/KM = 2.5 × 109 min-1 M-1) compared to the wild-type human BChE. Compared to the reference mutant (the A199S/S287G/A328W/Y332G mutant) tested in the reported clinical development of an enzyme therapy for cocaine dependence treatment, this new mutant (with a newly predicted additional F227S mutation) has an improved catalytic efficiency against (-)-cocaine by ∼2.6-fold. The good agreement between the computational and experimental ln(RCE) values suggests that the obtained correlation relationship is robust for computational prediction. A similar correlation relationship could also be explored in studying BChE or other serine hydrolases/esterases with an oxyanion hole stabilizing the carbonyl oxygen in the rate-determining reaction step of the enzymatic hydrolysis of other substrates.
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Affiliation(s)
- Fang Zheng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Shurong Hou
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Liu Xue
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Wenchao Yang
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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3
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Ren YZ, Fang CZ, Zhang BB, He L, Tu YL, Chen XY. Photocatalytic Charge-Transfer Complex Enables Hydroarylation of Alkenes for Heterocycle Synthesis. Org Lett 2023; 25:3585-3589. [PMID: 37154474 DOI: 10.1021/acs.orglett.3c01329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Here, we report a photocatalytic charge-transfer complex (CTC) strategy for one electron reduction of alkenes using thiolate as a catalytic electron donor. This catalytic CTC system could engage hydroarylation of both activated and unactivated alkenes for the synthesis of various heterocycles. The reactions do not require any photocatalysts or acids and are easy to perform. Mechanistic studies revealed the formation of a CTC between catalytic thiolate and alkene.
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Affiliation(s)
- Ying-Zheng Ren
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang 832000, People's Republic of China
| | - Chang-Zhen Fang
- School of Chemical Sciences, University of Chinese Academy of Sciences Beijing 100049, People's Republic of China
| | - Bei-Bei Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences Beijing 100049, People's Republic of China
| | - Lin He
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang 832000, People's Republic of China
| | - Yong-Liang Tu
- School of Chemical Sciences, University of Chinese Academy of Sciences Beijing 100049, People's Republic of China
| | - Xiang-Yu Chen
- School of Chemical Sciences, University of Chinese Academy of Sciences Beijing 100049, People's Republic of China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou, Shandong 256606, People's Republic of China
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4
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Yang Z, Wu X, Zhang J, Yu JT, Pan C. Metal-Free Photoinduced Hydrocyclization of Unactivated Alkenes toward Ring-Fused Quinazolin-4(3 H)-ones via Intermolecular Hydrogen Atom Transfer. Org Lett 2023; 25:1683-1688. [PMID: 36883803 DOI: 10.1021/acs.orglett.3c00329] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A visible-light-induced hydrocyclization of unactivated alkenes was developed using 3CzClIPN as the photocatalyst to generate substituted α-methyldeoxyvasicinones and α-methylmackinazolinones in moderate to good yields. An intermolecular hydrogen atom transfer with THF as the hydrogen source was involved. Mechanism studies indicated that the intramolecular addition of the in situ formed aminal radical to the unactivated alkene generated the polycyclic quinazolinone.
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Affiliation(s)
- Zixian Yang
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, P. R. China
| | - Xian Wu
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, P. R. China
| | - Jie Zhang
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, P. R. China
| | - Jin-Tao Yu
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, P. R. China
| | - Changduo Pan
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, P. R. China.,School of Chemistry and Chemical Engineering, Jiangsu University of Technology, Changzhou 213001, P. R. China
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5
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Wang M, Ye W, Sun N, Yu W, Chang J. Synthesis of Quinazolinone-Fused Tetrahydroisoquinolines and Related Polycyclic Scaffolds by Iodine-Mediated sp 3 C-H Amination. J Org Chem 2023; 88:1061-1074. [PMID: 36630199 DOI: 10.1021/acs.joc.2c02509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An iodine-mediated intramolecular sp3 C-H amination reaction producing quinazolinone-fused polycyclic skeletons from 2-aminobenzamide precursors is reported. This reaction does not use transition metals, has a broad substrate scope, and can be used on a gram scale. Under the optimal reaction conditions, a variety of quinazolinone-fused tetrahydroisoquinolines and derivatives of Rutaecarpine were synthesized from readily accessible compounds. The reaction proceeds well with crude 2-aminobenzamide derivatives, allowing for the synthesis of the products from simple 2-aminobenzoic acids and tetrahydroisoquinolines without purification of the 2-aminobenzamide intermediates. Preliminary biological experiments have identified Cereblon (CRBN) inhibitory activity and relevant anti-myeloma medicinal properties in some of these polycyclic products.
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Affiliation(s)
- Manman Wang
- Green Catalysis Center and College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenjun Ye
- Green Catalysis Center and College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Nannan Sun
- Green Catalysis Center and College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenquan Yu
- Green Catalysis Center and College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Junbiao Chang
- Green Catalysis Center and College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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6
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Gui QW, Teng F, Yang H, Xun C, Huang WJ, Lu ZQ, Zhu MX, Ouyang WT, He WM. Visible-Light Photosynthesis of CHF 2 /CClF 2 /CBrF 2 -Substituted Ring-fused Quinazolinones in Dimethyl Carbonate. Chem Asian J 2022; 17:e202101139. [PMID: 34837338 DOI: 10.1002/asia.202101139] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Indexed: 12/13/2022]
Abstract
With eco-friendly and sustainable CO2 -derived dimethyl carbonate as the sole solvent, the visible-light-induced cascade radical reactions have been established as a green and efficient tool for constructing various CHF2 /CClF2 /CBrF2 -substituted ring-fused quinazolinones.
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Affiliation(s)
- Qing-Wen Gui
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Fan Teng
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Hao Yang
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Changping Xun
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Wen-Jie Huang
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Zi-Qin Lu
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Meng-Xue Zhu
- College of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, P. R. China
| | - Wen-Tao Ouyang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, P. R. China
| | - Wei-Min He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, P. R. China
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7
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Deng J, Kim K, Zheng X, Shang L, Zhan CG, Zheng F. Cocaine hydrolase blocks cocaine-induced dopamine transporter trafficking to the plasma membrane. Addict Biol 2022; 27:e13089. [PMID: 34363291 PMCID: PMC8720053 DOI: 10.1111/adb.13089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Cocaine blocks dopamine uptake via dopamine transporter (DAT) on plasma membrane of neuron cells and, as a result, produces the high and induces DAT trafficking to plasma membrane which contributes to the drug seeking or craving. In this study, we first examined the dose dependence of cocaine-induced DAT trafficking and hyperactivity in rats, demonstrating that cocaine at an intraperitoneal dose of 10 mg/kg or higher led to redistribution of most DAT to the plasma membrane while inducing significant hyperactivity in rats. However, administration of 5-mg/kg cocaine (ip) did not significantly induce DAT trafficking or hyperactivity in rats. So the threshold (intraperitoneal) dose of cocaine that can significantly induce DAT trafficking or hyperactivity should be between 5 and 10 mg/kg. These data suggest that when a cocaine dose is high enough to induce significant hyperactivity, it can also significantly induce DAT trafficking to the plasma membrane. Further, the threshold brain cocaine concentration required to induce significant hyperactivity and DAT trafficking was estimated to be ~2.0 ± 0.8 μg/g. Particularly, for treatment of cocaine abuse, previous studies demonstrated that an exogenous cocaine-metabolizing enzyme, for example, CocH3-Fc(M3), can effectively block cocaine-induced hyperactivity. However, it was unknown whether an enzyme could also effectively block cocaine-induced DAT trafficking to the plasma membrane. This study demonstrates, for the first time, that the enzyme is also capable of effectively blocking cocaine from reaching the brain even with a lethal dose of 60-mg/kg cocaine (ip) and, thus, powerfully preventing cocaine-induced physiological effects such as the hyperactivity and DAT trafficking.
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Affiliation(s)
- Jing Deng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Kyungbo Kim
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Xirong Zheng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Linyue Shang
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
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8
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Kashyap K, Siddiqi MI. Recent trends in artificial intelligence-driven identification and development of anti-neurodegenerative therapeutic agents. Mol Divers 2021; 25:1517-1539. [PMID: 34282519 DOI: 10.1007/s11030-021-10274-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022]
Abstract
Neurological disorders affect various aspects of life. Finding drugs for the central nervous system is a very challenging and complex task due to the involvement of the blood-brain barrier, P-glycoprotein, and the drug's high attrition rates. The availability of big data present in online databases and resources has enabled the emergence of artificial intelligence techniques including machine learning to analyze, process the data, and predict the unknown data with high efficiency. The use of these modern techniques has revolutionized the whole drug development paradigm, with an unprecedented acceleration in the central nervous system drug discovery programs. Also, the new deep learning architectures proposed in many recent works have given a better understanding of how artificial intelligence can tackle big complex problems that arose due to central nervous system disorders. Therefore, the present review provides comprehensive and up-to-date information on machine learning/artificial intelligence-triggered effort in the brain care domain. In addition, a brief overview is presented on machine learning algorithms and their uses in structure-based drug design, ligand-based drug design, ADMET prediction, de novo drug design, and drug repurposing. Lastly, we conclude by discussing the major challenges and limitations posed and how they can be tackled in the future by using these modern machine learning/artificial intelligence approaches.
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Affiliation(s)
- Kushagra Kashyap
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Mohammad Imran Siddiqi
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India. .,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.
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9
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Yuan X, Cui Y, Zhang X, Qin L, Sun Q, Duan X, Chen L, Li G, Qiu J, Guo K. Electrochemical Tri‐ and Difluoromethylation‐Triggered Cyclization Accompanied by the Oxidative Cleavage of Indole Derivatives. Chemistry 2021; 27:6522-6528. [DOI: 10.1002/chem.202005368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/25/2021] [Indexed: 01/02/2023]
Affiliation(s)
- Xin Yuan
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Yu‐Sheng Cui
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Xin‐Peng Zhang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Long‐Zhou Qin
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Qi Sun
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Xiu Duan
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Lin Chen
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Guigen Li
- Institute of Chemistry & Biomedical Science Nanjing University No.163, Xianlin Avenue, Qixia District Nanjing 210093 P. R. China
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409-1061 USA
| | - Jiang‐Kai Qiu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
| | - Kai Guo
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 30 Puzhu Rd S Nanjing 211816 P. R. China
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10
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Kumar V, De P, Ojha PK, Saha A, Roy K. A Multi-layered Variable Selection Strategy for QSAR Modeling of Butyrylcholinesterase Inhibitors. Curr Top Med Chem 2020; 20:1601-1627. [DOI: 10.2174/1568026620666200616142753] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/23/2019] [Accepted: 10/28/2019] [Indexed: 02/08/2023]
Abstract
Background:
Alzheimer’s disease (AD), a neurological disorder, is the most common cause
of senile dementia. Butyrylcholinesterase (BuChE) enzyme plays a vital role in regulating the brain acetylcholine
(ACh) neurotransmitter, but in the case of Alzheimer’s disease (AD), BuChE activity gradually
increases in patients with a decrease in the acetylcholine (ACh) concentration via hydrolysis. ACh
plays an essential role in regulating learning and memory as the cortex originates from the basal forebrain,
and thus, is involved in memory consolidation in these sites.
Methods:
In this work, we have developed a partial least squares (PLS)-regression based two dimensional
quantitative structure-activity relationship (2D-QSAR) model using 1130 diverse chemical classes
of compounds with defined activity against the BuChE enzyme. Keeping in mind the strict Organization
for Economic Co-operation and Development (OECD) guidelines, we have tried to select significant
descriptors from the large initial pool of descriptors using multi-layered variable selection strategy using
stepwise regression followed by genetic algorithm (GA) followed by again stepwise regression technique
and at the end best subset selection prior to development of final model thus reducing noise in the
input. Partial least squares (PLS) regression technique was employed for the development of the final
model while model validation was performed using various stringent validation criteria.
Results:
The results obtained from the QSAR model suggested that the quality of the model is acceptable
in terms of both internal (R2= 0.664, Q2= 0.650) and external (R2
Pred= 0.657) validation parameters.
The QSAR studies were analyzed, and the structural features (hydrophobic, ring aromatic and hydrogen
bond acceptor/donor) responsible for enhancement of the activity were identified. The developed model
further suggests that the presence of hydrophobic features like long carbon chain would increase the
BuChE inhibitory activity and presence of amino group and hydrazine fragment promoting the hydrogen
bond interactions would be important for increasing the inhibitory activity against BuChE enzyme.
Conclusion:
Furthermore, molecular docking studies have been carried out to understand the molecular
interactions between the ligand and receptor, and the results are then correlated with the structural features
obtained from the QSAR models. The information obtained from the QSAR models are well corroborated
with the results of the docking study.
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Affiliation(s)
- Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Priyanka De
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Probir Kumar Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92 APC Road, Kolkata 700 032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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11
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Beglari M, Goudarzi N, Shahsavani D, Arab Chamjangali M, Mozafari Z. Combination of radial distribution functions as structural descriptors with ligand-receptor interaction information in the QSAR study of some 4-anilinoquinazoline derivatives as potent EGFR inhibitors. Struct Chem 2020. [DOI: 10.1007/s11224-020-01505-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Makhouri FR, Ghasemi JB. In Silico Studies in Drug Research Against Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:664-725. [PMID: 28831921 PMCID: PMC6080098 DOI: 10.2174/1570159x15666170823095628] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023] Open
Abstract
Background Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computer-aided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
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Affiliation(s)
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran, Iran
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13
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Minovski N, Novič M. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although almost fully automated, the discovery of novel, effective, and safe drugs is still a long-term and highly expensive process. Consequently, the need for fleet, rational, and cost-efficient development of novel drugs is crucial, and nowadays the advanced in silico drug design methodologies seem to effectively meet these issues. The aim of this chapter is to provide a comprehensive overview of some of the current trends and advances in the in silico design of novel drug candidates with a special emphasis on 6-fluoroquinolone (6-FQ) antibacterials as potential novel Mycobacterium tuberculosis DNA gyrase inhibitors. In particular, the chapter covers some of the recent aspects of a wide range of in silico drug discovery approaches including multidimensional machine-learning methods, ligand-based and structure-based methodologies, as well as their proficient combination and integration into an intelligent virtual screening protocol for design and optimization of novel 6-FQ analogs.
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14
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Zhang C, Li S, Bureš F, Lee R, Ye X, Jiang Z. Visible Light Photocatalytic Aerobic Oxygenation of Indoles and pH as a Chemoselective Switch. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01969] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chenhao Zhang
- Key
Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, Henan, China
| | - Sanliang Li
- Key
Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, Henan, China
| | - Filip Bureš
- Institute
of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, Pardubice 53210, Czech Republic
| | - Richmond Lee
- ARC
Centre of Excellence for Electromaterials Science and Research School
of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Xinyi Ye
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Zhiyong Jiang
- Key
Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, Henan, China
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15
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Fang J, Pang X, Wu P, Yan R, Gao L, Li C, Lian W, Wang Q, Liu AL, Du GH. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations. Chem Biol Drug Des 2016; 87:649-63. [PMID: 26648584 DOI: 10.1111/cbdd.12700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/21/2015] [Accepted: 11/20/2015] [Indexed: 12/31/2022]
Abstract
A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.
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Affiliation(s)
- Jiansong Fang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Institute of Clinical Pharmacology, Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510006, China
| | - Xiaocong Pang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ping Wu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rong Yan
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Li Gao
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chao Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenwen Lian
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510006, China
| | - Ai-lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Beijing Key Laboratory of Drug Target and Screening Research, Beijing, 100050, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, 100050, China
| | - Guan-hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Beijing Key Laboratory of Drug Target and Screening Research, Beijing, 100050, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, 100050, China
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16
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Dolles D, Nimczick M, Scheiner M, Ramler J, Stadtmüller P, Sawatzky E, Drakopoulos A, Sotriffer C, Wittmann HJ, Strasser A, Decker M. Aminobenzimidazoles and Structural Isomers as Templates for Dual-Acting Butyrylcholinesterase Inhibitors andhCB2R Ligands To Combat Neurodegenerative Disorders. ChemMedChem 2015; 11:1270-83. [DOI: 10.1002/cmdc.201500418] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Dominik Dolles
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Martin Nimczick
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Matthias Scheiner
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Jacqueline Ramler
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Patricia Stadtmüller
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Edgar Sawatzky
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Antonios Drakopoulos
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Christoph Sotriffer
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Hans-Joachim Wittmann
- Pharmaceutical and Medicinal Chemistry II; Institute of Pharmacy; University of Regensburg; 95053 Regensburg Germany
| | - Andrea Strasser
- Pharmaceutical and Medicinal Chemistry II; Institute of Pharmacy; University of Regensburg; 95053 Regensburg Germany
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry; Institute of Pharmacy and Food Chemistry; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
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17
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Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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18
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Oh BK, Ko EB, Han JW, Oh CH. Synthesis of N-Heteropolycyclic Compounds Including Quinazolinone Skeleton Using Friedel–Crafts Alkylation. SYNTHETIC COMMUN 2015. [DOI: 10.1080/00397911.2014.987353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bu Keun Oh
- Department of Chemistry, Hanyang University, Seoul, Korea
| | - Eun Bi Ko
- Department of Chemistry, Hanyang University, Seoul, Korea
| | - Jin Wook Han
- Department of Chemistry, Hanyang University, Seoul, Korea
| | - Chang Ho Oh
- Department of Chemistry, Hanyang University, Seoul, Korea
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19
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Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC, Nandan SR, Pissurlenkar RR. Quantifying ligand–receptor interactions for gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. J Biomol Struct Dyn 2014; 33:1107-25. [DOI: 10.1080/07391102.2014.931824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Li P, Jia J, Fang M, Zhang L, Guo M, Xie J, Xia Y, Zhou L, Wei D. In vitro and in vivo ACE inhibitory of pistachio hydrolysates and in silico mechanism of identified peptide binding with ACE. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.02.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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