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Ma T, Gao S, Zhao LX, Ye F, Fu Y. 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors: From Molecular Design to Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17125-17137. [PMID: 39047218 DOI: 10.1021/acs.jafc.4c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Weed resistance is a critical issue in crop production. Among the known herbicides, 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors are crucial for addressing weed resistance. HPPD inhibitors constitute a pivotal aspect of contemporary crop protection strategies. The advantages of these herbicides are their broad weed spectrum, flexible application, and excellent compatibility with other herbicides. They also exhibit satisfactory crop selectivity and low toxicity and are environmentally friendly. An increasing number of new HPPD inhibitors have been designed by combining computer-aided drug design with conventional design approaches. Herein, the molecular design and structural features of innovative HPPD inhibitors are reviewed to guide the development of new HPPD inhibitors possessing an enhanced biological efficacy.
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Affiliation(s)
- Tengfei Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
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Leng XY, Pang QF, Ma YF, Ye BW, Ye F, Fu Y. Integrated Virtual Screening and Validation toward Potential HPPD Inhibition Herbicide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4587-4595. [PMID: 38408430 DOI: 10.1021/acs.jafc.3c06312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) is one of the most widely studied herbicide targets and has gained significant attention. To identify potential effective HPPD inhibitors, a rational multistep virtual screening workflow was built, which included CBP models (based on the receptor-ligand interactions in the crystal complex), Hypogen models with activity prediction ability (according to the derivation of structure-activity relationships from a set of molecules with reported activity values), and a consensus docking procedure (consisting of LibDock, Glide, and CDOCKER). About 1 million molecules containing diketone or β-keto-enol substructures were filtered by Lipinski's rules, CBP model, and Hypogen model. A total of 12 compounds with similar docking postures were generated by consensus docking. Eventually, four molecules were screened based on the specific binding pattern and affinity of the HPPD inhibitor. The biological evaluation in vivo displayed that compounds III-1 and III-2 exhibited comparable herbicidal activity to isoxaflutole and possessed superior safety on various crops (wheat, rice, sorghum, and maize). The ADMET prediction (absorption, distribution, metabolism, excretion, and toxicity) showed that compound III possessed relatively good toxicological results. This work provides a theoretical basis and valuable reference for the virtual screening and molecular design of novel HPPD inhibition herbicides.
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Affiliation(s)
- Xin-Yu Leng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Qi-Fan Pang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yi-Fan Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Bo-Wen Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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Leng XY, Gao S, Ma YF, Zhao LX, Wang M, Ye F, Fu Y. Discovery of novel HPPD inhibitors: Virtual screening, molecular design, structure modification and biological evaluation. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105390. [PMID: 37105629 DOI: 10.1016/j.pestbp.2023.105390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD, a Fe(II)/α-ketoglutarate dependent oxygenases), is a popular herbicide target. In this work, two pharmacophore models based on common molecular characteristics (HipHop) and receptor-ligand complex (CBP) were generated for virtual screening for HPPD inhibitors. About 1,000,000 molecules containing diketone structure from PubChem were filtered by Lipinski's rules to build a 3D database. Then the database was screened through combining HipHop model, CBP model, ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction and molecular docking. Subsequently, based on the specific binding mode and affinity of HPPD inhibitors, 4 molecules with high -CDOCKER energy, good aqueous solubility and human safety predicative properties values were screened. From the screening results and combined with previous work, three novel HPPD inhibitors were designed and synthesized through fragment splicing and bioisosterism strategies. Compound IV-a exhibited similar inhibition of Arabidopsis thaliana HPPD (AtHPPD) and herbicidal activity as mesotrione. Crop selectivity showed that compound IV-a had better crop safety than mesotrione. Comparing the molecular properties, ADMET and molecular docking studies indicated that compounds IV-a exhibited better properties than mesotrione, which could be further modified as novel HPPD inhibitor herbicides.
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Affiliation(s)
- Xin-Yu Leng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yi-Fan Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Meng Wang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China.
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China.
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Fu Y, Liu YX, Yi KH, Li MQ, Li JZ, Ye F. Quantitative Structure Activity Relationship Studies and Molecular Dynamics Simulations of 2-(Aryloxyacetyl)cyclohexane-1,3-Diones Derivatives as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Front Chem 2019; 7:556. [PMID: 31482084 PMCID: PMC6710436 DOI: 10.3389/fchem.2019.00556] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/22/2019] [Indexed: 11/17/2022] Open
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a significant enzyme in the biosynthesis of plastoquinone and tocopherol. Moreover, it is also a potential target to develop new herbicide. The technology of computer-aided drug design (CADD) is a useful tool in the efficient discovery of new HPPD inhibitors. Forty-three compounds with known activities were used to generate comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models based on common framework and molecular docking. The structural contribution to the activity was determined, which provided further information for the design of novel inhibitors. Molecular docking was used to explain the changes in activity caused by the binding mode between ligand and protein. The molecular dynamics (MD) results indicated that the electrostatic energy was the major driving force for ligand–protein interaction and the Phe403 made the greatest contribution to the binding. The present work has provided useful information for the rational design of novel HPPD inhibitors with improved activity.
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Affiliation(s)
- Ying Fu
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Yong-Xuan Liu
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Ke-Han Yi
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Ming-Qiang Li
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fei Ye
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
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Fu Y, Sun YN, Yi KH, Li MQ, Cao HF, Li JZ, Ye F. 3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors. Molecules 2017; 22:molecules22060959. [PMID: 28598377 PMCID: PMC6152767 DOI: 10.3390/molecules22060959] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 06/05/2017] [Indexed: 11/16/2022] Open
Abstract
p-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only the useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical herbicides. A combined in silico structure-based pharmacophore and molecular docking-based virtual screening were performed to identify novel potential HPPD inhibitors. The complex-based pharmacophore model (CBP) with 0.721 of ROC used for screening compounds showed remarkable ability to retrieve known active ligands from among decoy molecules. The ChemDiv database was screened using CBP-Hypo2 as a 3D query, and the best-fit hits subjected to molecular docking with two methods of LibDock and CDOCKER in Accelrys Discovery Studio 2.5 (DS 2.5) to discern interactions with key residues at the active site of HPPD. Four compounds with top rankings in the HipHop model and well-known binding model were finally chosen as lead compounds with potential inhibitory effects on the active site of target. The results provided powerful insight into the development of novel HPPD inhibitors herbicides using computational techniques.
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Affiliation(s)
- Ying Fu
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yi-Na Sun
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Ke-Han Yi
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Ming-Qiang Li
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Hai-Feng Cao
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, 199 West Donggang Rd., Lanzhou 730000, China.
| | - Fei Ye
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
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Jiang DP, Zhu CC, Shao XS, Cheng JG, Li Z. Bioactive conformation analysis of anthranilic diamide insecticides: DFT-based potential energy surface scanning and 3D-QSAR investigations. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhang M, Xie P, Zhao W, Niu B, Wu W, Bian Z, Pittman CU, Zhou A. Cascade Couplings of N-Alkyl-N-methacryloyl Benzamides with Ethers and Benzenesulfonohydrazides To Generate Isoquinoline-1,3(2H,4H)-dione Derivatives. J Org Chem 2015; 80:4176-83. [DOI: 10.1021/acs.joc.5b00158] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Min Zhang
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Ping Xie
- Scientific
Information Research Institute, Jiangsu University (Library), Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Wannian Zhao
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Ben Niu
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Wei Wu
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Zhaogang Bian
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
| | - Charles U. Pittman
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Aihua Zhou
- Pharmacy
School, Jiangsu University, Xuefu Road 301, Zhenjiang City, Jiangsu, China 212013
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Tautomerism and multiple modelling enhance the efficacy of QSAR: antimalarial activity of phosphoramidate and phosphorothioamidate analogues of amiprophos methyl. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1043-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhao W, Xie P, Zhang M, Niu B, Bian Z, Pittman C, Zhou A. Synthesis of isoquinoline-1,3(2H,4H)-dione derivatives via cascade reactions of N-alkyl-N-methacryloyl benzamide with aryl aldehydes. Org Biomol Chem 2014; 12:7690-3. [DOI: 10.1039/c4ob01442a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A cascade reaction between N-alkyl-N-methacryloylbenzamide and aryl aldehydes was developed to generate isoquinoline-1,3(2H,4H)-dione derivatives.
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Affiliation(s)
- Wannian Zhao
- Pharmacy School
- Jiangsu University
- Zhenjiang City, China
| | - Ping Xie
- Scientific Information Research Institute
- Jiangsu University (Library)
- Zhenjiang City, China
| | - Min Zhang
- Pharmacy School
- Jiangsu University
- Zhenjiang City, China
| | - Ben Niu
- Pharmacy School
- Jiangsu University
- Zhenjiang City, China
| | - Zhaogang Bian
- Pharmacy School
- Jiangsu University
- Zhenjiang City, China
| | | | - Aihua Zhou
- Pharmacy School
- Jiangsu University
- Zhenjiang City, China
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Masand VH, Mahajan DT, Ben Hadda T, Jawarkar RD, Alafeefy AM, Rastija V, Ali MA. Does tautomerism influence the outcome of QSAR modeling? Med Chem Res 2013. [DOI: 10.1007/s00044-013-0776-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Natesan S, Balaz S. Rigorous incorporation of tautomers, ionization species, and different binding modes into ligand-based and receptor-based 3D-QSAR methods. Curr Pharm Des 2013; 19:4316-22. [PMID: 23170882 PMCID: PMC3778504 DOI: 10.2174/1381612811319230013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/19/2012] [Indexed: 11/22/2022]
Abstract
Speciation of drug candidates and receptors caused by ionization, tautomerism, and/or covalent hydration complicates ligandand receptor-based predictions of binding affinities by 3-dimensional structure-activity relationships (3D-QSAR). The speciation problem is exacerbated by tendency of tautomers to bind in multiple conformations or orientations (modes) in the same binding site. New forms of the 3D-QSAR correlation equations, capable of capturing this complexity, can be developed using the time hierarchy of all steps that lie behind the monitored biological process - binding, enzyme inhibition or receptor activity. In most cases, reversible interconversions of individual ligand and receptor species can be treated as quickly established equilibria because they are finished in a small fraction of the exposure time that is used to determine biological effects. The speciation equilibria are satisfactorily approximated by invariant fractions of individual ligand and receptor species for buffered experimental or in vivo conditions. For such situations, the observed drug-receptor association constant of a ligand is expressed as the sum of products, for each ligand and receptor species pair, of the association microconstant and the fractions of involved species. For multiple binding modes, each microconstant is expressed as the sum of microconstants of individual modes. This master equation leads to new 3D-QSAR correlation equations integrating the results of all molecular simulations or calculations, which are run for each ligand-receptor species pair separately. The multispecies, multimode 3D-QSAR approach is illustrated by a ligand-based correlation of transthyretin binding of thyroxine analogs and by a receptor-based correlation of inhibition of MK2 by benzothiophenes and pyrrolopyrimidines.
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Affiliation(s)
- Senthil Natesan
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Colchester, VT 05446
| | - Stefan Balaz
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Colchester, VT 05446
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Clark RD. A perspective on the role of quantitative structure-activity and structure-property relationships in herbicide discovery. PEST MANAGEMENT SCIENCE 2012; 68:513-8. [PMID: 22323389 DOI: 10.1002/ps.3256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 11/13/2011] [Accepted: 12/20/2011] [Indexed: 05/26/2023]
Abstract
BACKGROUND For the last 15 years the agrochemical industry has focused on using genetic modification to put genes that confer resistance to existing commercial herbicides into crop plants rather than on discovering new herbicides with novel modes of action. The widespread appearance of weeds resistant to those herbicides is now causing the industry to revive their herbicide discovery programs. RESULTS Elucidation of quantitative structure-activity relationships (QSARs) played a major role in the discovery and development of existing commercial herbicides, but the advent of genetically modified crops has caused published work (at least) in the area to drift from the industrial arena into academic studies. The focus has also turned inward, to refining models for established herbicide targets instead of elucidating new ones. CONCLUSION This perspective highlights the importance of QSARs and quantitative structure-property relationships (QSPRs) to herbicide discovery in an historical context and provides some guidance as to how they might profitably be applied going forward.
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Hashimoto Y, Matsumoto Y, Noguchi-Yachide T, Nakamura M, Mita Y, Numadate A. Specific Inhibitors of Puromycin-Sensitive Aminopeptidase with a 3-(Halogenated Phenyl)-2,4(1H,3H)-quinazolinedione Skeleton. HETEROCYCLES 2012. [DOI: 10.3987/com-12-s(n)109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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QSAR modeling of anxiolytic activity taking into account the presence of keto- and enol-tautomers by balance of correlations with ideal slopes. OPEN CHEM 2011. [DOI: 10.2478/s11532-011-0064-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractOptimal descriptors calculated with simplified molecular input line entry system (SMILES) have been examined as a tool for prediction of anxiolytic activity. Descriptors calculated with SMILES (a) of keto-isomers; (b) of enol-isomers; and (c) of both keto-isomers together with enol-isomers have been studied. Three approaches have been compared: 1. classic’ training-test’ system 2. balance of correlations and 3. balance of correlations with ideal slopes. The best statistical characteristics for the external validation set took place for optimal descriptors calculated with SMILES of both keto-form and enol-form (i.e., molecular structure was represented in the format: ’sMILES of keto-form. SMILES of enol-form’) by means of balance of correlations with ideal slopes. The predictive potential of this model was checked with three random splits.
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Quantitative Structure–Retention Relationship Study on Nitrogen-Containing Polycyclic Aromatic Compounds by Using Molecular Electronegativity Interaction Vector. Chromatographia 2011. [DOI: 10.1007/s10337-011-2078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Liao L, Qing D, Li J, Lei G. Structural characterization and Kovats retention index prediction for oxygen-containing organic compounds. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Chen CYC. Bioinformatics, chemoinformatics, and pharmainformatics analysis of HER2/HSP90 dual-targeted inhibitors. J Taiwan Inst Chem Eng 2010. [DOI: 10.1016/j.jtice.2009.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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