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Shaibuna M, Kuniyil MJK, Sreekumar K. Deep eutectic solvent assisted synthesis of dihydropyrimidinones/thiones via Biginelli reaction: theoretical investigations on their electronic and global reactivity descriptors. NEW J CHEM 2021. [DOI: 10.1039/d1nj03879f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DES 2 (ZrOCl2·8H2O-ethylene glycol at 1 : 2 ratio) was used as a catalyst for the synthesis of dihydropyrimidinones/thiones via a Biginelli reaction.
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Affiliation(s)
- M. Shaibuna
- Department of Applied Chemistry, Cochin University of Science and Technology, Cochin 682022, India
| | | | - K. Sreekumar
- Department of Applied Chemistry, Cochin University of Science and Technology, Cochin 682022, India
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2
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Ai Z, Xiao J, Li Y, Guo B, Du Y, Zhao K. Metal-free synthesis of 3-chalcogenyl chromones from alkynyl aryl ketones and diorganyl diselenides/disulfides mediated by PIFA. Org Chem Front 2020. [DOI: 10.1039/d0qo01175d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
3-Selenyl/sulfenyl chromones/thiochromones were conveniently synthesized from the PIFA-mediated reactions between alkynyl aryl ketones bearing an ortho-methoxy/methylthio group and diorganyl diselenides/disulfides.
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Affiliation(s)
- Zhenkang Ai
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jiaxi Xiao
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Yadong Li
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Boying Guo
- Department of Chemistry
- Monell Chemical Senses Center and Laboratory for Research on the Structure of Matter
- University of Pennsylvania
- Philadelphia
- USA
| | - Yunfei Du
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Kang Zhao
- State Key Laboratory of Microbial Technology
- Institute of Microbial Technology
- Shandong University
- Qingdao 266237
- China
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3
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Li H, Pan S, Xu X. Structure characteristics of flavonoids for cyclooxygenase-2 mRNA inhibition in lipopolysaccharide-induced inflammatory macrophages. Eur J Pharmacol 2019; 856:172416. [PMID: 31132359 DOI: 10.1016/j.ejphar.2019.172416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/11/2022]
Abstract
Flavonoids are natural active components. They distribute widely in edible plants with high activity of anti-inflammation. Inhibition of cyclooxygenase-2(COX-2) was determined by real-time fluorescent quantitative olymerase chain reaction (RTFQ-PCR). And structure characteristics of flavonoids for COX-2 inhibition were mainly analyzed by a quantitative structure activity relationship (QSAR) model. Descriptors such as SMR_VSA5, vsurf_DD12, reactive were the top three important independent variables to COX-2 mRNA inhibiton in RAW264.7. Low SMR_VSA5 value meant a lower molecular refractivity resulting in a lower COX-2 mRNA inhibition. High vsurf_DD12 value related to poor molecular balance and showed profound adverse to COX-2 mRNA inhibition. Reactive group in this paper referred to C2-C3 double bond contributed negatively to COX-2 mRNA inhibition. Glycosidic and C3-OH substitutions may lower SMR_VSA5 value. It indicated that flavanones such as hesperetin, naringenin, liquiritigenin were efficient to repress COX-2 mRNA and they were potential anti-inflammatory natural products. Further, substitution with a glucopyranosyl at C-6 resulted in a poorer molecule balance than that at C-8 and a lower COX-2 mRNA inhibiton accordingly. This may expain why orientin and vitexin exhibited better anti-inflammatory activity than their isomers homoorientin and isovitexin. Also, methoxyl groups at C-4' may also be a favorable flavonoid structural characteristic for COX-2 mRNA inhibiton. These results provide valuable information on understanding the high anti-inflammatory activity of flavonoids.
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Affiliation(s)
- Hui Li
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China.
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4
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Nizami B, Sarasia EM, Momin MIK, Honarparvar B. Estrogenic Active Stilbene Derivatives as Anti-Cancer Agents: A DFT and QSAR Study. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:560-568. [PMID: 29990200 DOI: 10.1109/tcbb.2017.2779505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Exploring different quantum chemical quantities for lead compounds is an ongoing approach in identifying crucial structural activity related features that are contributing into their biological activities. Herein, activity-related quantum chemical calculations were performed for the selected estrogenic stilbene derivatives using density functional theory (DFT) with B3LYP functional and 6-311++G** basis set. In addition, specific activity-related geometry-independent drug-like properties are discussed for these derivatives. To obtain the mathematical model that correlates the chemical descriptors with their measured estrogenic activities, the quantitative structure activity relationship (QSAR) is established using multiple linear regression (MLR) and support vector regression (SVR) methods. Satisfactory fit with a reasonable regression correlation coefficient (${\rm{R}}^{2}= 0.78$R2=0.78) between predicted and experimental $pEC_{50}$pEC50 values is observed using MLR method. The present study identifies the essential physicochemical descriptors that effectively contribute in the estrogenic activity. The applied approach provides helpful insight into the designing novel estrogenic agents with improved anticancer activities.
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Honarparvar B, Kanchi S, Bisetty K. Theoretical insights into the competitive metal bioaffinity of lactoferrin as a metal ion carrier: a DFT study. NEW J CHEM 2019. [DOI: 10.1039/c9nj03786a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Metal–protein complexes, specifically lactoferrin (Lf), an iron-binding glycoprotein found naturally in milk and several other body fluids play a pivotal role in all living organisms.
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Affiliation(s)
- Bahareh Honarparvar
- Department of Chemistry
- Durban University of Technology
- Durban 4000
- South Africa
| | - Suvardhan Kanchi
- Department of Chemistry
- Durban University of Technology
- Durban 4000
- South Africa
| | - Krishna Bisetty
- Department of Chemistry
- Durban University of Technology
- Durban 4000
- South Africa
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Fang Y, Liang F, Liu K, Qaiser S, Pan S, Xu X. Structure characteristics for intestinal uptake of flavonoids in Caco-2 cells. Food Res Int 2018; 105:353-360. [DOI: 10.1016/j.foodres.2017.11.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 12/20/2022]
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7
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Fang Y, Cao W, Xia M, Pan S, Xu X. Study of Structure and Permeability Relationship of Flavonoids in Caco-2 Cells. Nutrients 2017; 9:nu9121301. [PMID: 29186068 PMCID: PMC5748751 DOI: 10.3390/nu9121301] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 01/23/2023] Open
Abstract
Flavonoids exhibit a broad range of biological activities. However, poor absorption of some flavonoids is a major limitation for use of flavonoids as nutraceuticals. To investigate the structure requirements for flavonoids intestinal absorption, transepithelial transport and cellular accumulation (CA) of 30 flavonoids were determined using the Caco-2 cell monolayer. The bilateral permeation of five types of flavonoids followed the order: flavanones ≥ isoflavones > flavones ≥ chalcones > flavonols. The concentration of flavonoids accumulated in cells did not correlate with cell penetration since the correlation coefficient between the apparent permeability coefficient (Papp) and their corresponding CA was poor (R2 < 0.3). Most flavonoids exhibited a ratio of 0.8–1.5 for Papp A to B/Papp B to A, suggesting passive diffusion pathways. However, luteolin, morin and taxifolin may involve the efflux mechanisms. The quantitative structure-permeability relationship (QSPR) study demonstrated that the intestinal absorption of flavonoids can be related to atomic charges on carbon 3′ (QC3′), molecule surface area (SlogP_V3), balance between the center of mass and position of hydrophobic region (vsurf_ID1) and solvation energy of flavonoids (E_sol). These results provide useful information for initially screening of flavonoids with high intestinal absorption.
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Affiliation(s)
- Yajing Fang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weiwei Cao
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mengmeng Xia
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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8
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Adeowo FY, Honarparvar B, Skelton AA. Density Functional Theory Study on the Complexation of NOTA as a Bifunctional Chelator with Radiometal Ions. J Phys Chem A 2017; 121:6054-6062. [PMID: 28737914 DOI: 10.1021/acs.jpca.7b01017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1,4,7-Triazacyclononane-1,4,7-triacetic acid (NOTA) is a key bifunctional chelator utilized for the complexation of metal ions in radiopharmaceutical applications; the ability of these chelators depends on the strength of their binding with ions. The focus of the present work is to evaluate the complexation of Cu2+, Ga3+, Sc3+, and In3+ radiometal ions with NOTA using density functional theory (B3LYP functional) and 6-311+G(2d,2p)/DGDZVP basis sets. The significant role of ion-water interactions in the chelation interaction energies in solution reflects the competition between ion-water and NOTA-ion interaction in the chelation process. There is reasonable agreement between experimental and theoretical binding constants, geometries, and 1H NMR chemical shifts. Chelation interaction energies, Gibbs free energies, and entropies in solution show that the NOTA-Ga3+ and NOTA-Cu2+ are the most and least stable complexes, respectively. The natural atomic charges and second order perturbation analysis reveal charge transfer between NOTA and radiometal ions. The theoretical 1H NMR chemical shifts of NOTA are in good agreement with experiment; these values are influenced by the presence of the ions, which have a deshielding effect on the protons of NOTA. Global scalar properties such as EHOMO/ELUMO, ΔELUMO-HOMO, and chemical hardness/softness confirm that the NOTA-Cu2+ complex, which has a singly occupied molecular orbital, has the lowest ΔELUMO-HOMO value, the least chemical hardness, and the highest chemical softness. The significant variation of the hardness and ΔELUMO-HOMO values of the complexes can be attributed to the different positions of the metal ions on the periodic table. This study affirms that, among the radiometal ions, Ga3+ can be used to effectively radiolabel NOTA chelator for radiopharmaceutical usage as it binds most stably with NOTA.
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Affiliation(s)
- F Y Adeowo
- School of Health Sciences, Discipline of Pharmacy, University of KwaZulu-Natal , Durban 4001, South Africa
| | - B Honarparvar
- School of Health Sciences, Discipline of Pharmacy, University of KwaZulu-Natal , Durban 4001, South Africa
| | - A A Skelton
- School of Health Sciences, Discipline of Pharmacy, University of KwaZulu-Natal , Durban 4001, South Africa
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9
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Beheshti A, Hashemi F, Behavndi F, Zahedi M, Kolahi M, Motamedi H, Mayer P. Synthesis, structural characterization, QSAR and docking studies of a new binuclear nickel (II) complex based on the flexible tetradentate N-donor ligand as a potent antibacterial and anticancer agent. Int J Biol Macromol 2017; 104:1107-1123. [PMID: 28663150 DOI: 10.1016/j.ijbiomac.2017.06.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 10/19/2022]
Abstract
A new nickel (II)complex namely [Ni2(Lt)Cl4] derived from the NiCl2.6H2O and 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl)propane (Lt) has been synthesized and fully characterized by the single crystal X-ray diffraction, elemental analysis, FT-IR, UV-vis, density functional theory (DFT) calculations, antibacterial and anticancer activities. In the title complex, each of the Ni(II) atoms is tetrahedrally coordinated by two N atoms from one of the chelating bidentate bis(3,5-dimethylpyrazolyl)methane units of the Lt ligand and two Cl as terminal ligands. The neighboring [Ni2(Lt)Cl4] molecules are linked together by the intermolecular CH⋯Cl hydrogen bonds to generate a 1D chain structure. The chains are further stabilized by the intermolecular CH⋯π interactions to form a two-dimensional non-covalent bonded structure. The antibacterial activity of the free Lt ligand and its Ni (II) complex shows that the ability of these compounds to inhibit growth of the tested bacteria increase from the Lt to binuclear nickel (II) complex. Scanning probe microscopy (SPM) study of the treated B. subtilis and E. coli bacteria was implemented to understand the structural changes caused by the interactions between the nickel (II) complex and the target bacteria. The cytotoxicity test of the Lt ligand and its complex was evaluated against the human carcinoma cell line (Caco-2) using the MTT assay. The results indicate that the Lt ligand and its complex display cytotoxicity against Caco-2 with the IC50 values of 36.29μM and 12.97μM, respectively. Therefore, the complex can be nominated as a potential anticancer agent. Molecular docking investigations on the five standard antibiotic, five standard anticancer drugs, free Lt ligand, title complex and twelve receptors were performed by Autodock vina function. The results of docking and DFT calculations are in line with the in vitro data obtained via the antibacterial and anticancer activity of Lt ligand and its made-complex.
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Affiliation(s)
- Azizolla Beheshti
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Faezeh Hashemi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Fatemeh Behavndi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Chemistry, Shahid Beheshti University, G. C. Tehran, 19839, Evin, P.O. Box 19395-4716, Iran
| | - Maryam Kolahi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hossein Motamedi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran; Biotechnology and Biological Science Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Peter Mayer
- Department Chemie Butenandtstr, LMU München University, München, Germany
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10
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Bentz EN, Pomilio AB, Lobayan RM. Donor-acceptor interactions as descriptors of the free radical scavenging ability of flavans and catechin. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Zermeño-Macías MDLÁ, González-Chávez MM, Méndez F, González-Chávez R, Richaud A. Theoretical Reactivity Study of Indol-4-Ones and Their Correlation with Antifungal Activity. Molecules 2017; 22:molecules22030427. [PMID: 28282898 PMCID: PMC6155404 DOI: 10.3390/molecules22030427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/02/2017] [Indexed: 12/03/2022] Open
Abstract
Chemical reactivity descriptors of indol-4-ones obtained via density functional theory (DFT) and hard–soft acid–base (HSAB) principle were calculated to prove their contribution in antifungal activity. Simple linear regression was made for global and local reactivity indexes. Results with global descriptors showed a strong relationship between antifungal activity vs. softness (S) (r = 0.98) for series I (6, 7a–g), and for series II (8a–g) vs. chemical potential (µ), electronegativity (χ) and electrophilicity (ω) (r = 0.86), p < 0.05. Condensed reactivity descriptors sk+, ωk− for different fragments had strong relationships for series I and II (r = 0.98 and r = 0.92). Multiple linear regression was statistically significant for S (r = 0.98), η (r = 0.91), and µ/ω (r = 0.91) in series I. Molecular electrostatic potential maps (MEP) showed negative charge accumulation around oxygen of carbonyl group and positive accumulation around nitrogen. Fukui function isosurfaces showed that carbons around nitrogen are susceptible to electrophilic attack, whereas the carbon atoms of the carbonyl and phenyl groups are susceptible to nucleophilic attack for both series. The above suggest that global softness in conjunction with softness and electrophilicity of molecular fragments in enaminone systems and pyrrole rings contribute to antifungal activity of indol-4-ones.
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Affiliation(s)
| | - Marco Martín González-Chávez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava No. 6 Zona Universitaria, 78210 San Luis Potosí, Mexico.
| | - Francisco Méndez
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana, Unidad Iztapalapa, 09340 Ciudad de México, Mexico.
| | - Rodolfo González-Chávez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava No. 6 Zona Universitaria, 78210 San Luis Potosí, Mexico.
| | - Arlette Richaud
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana, Unidad Iztapalapa, 09340 Ciudad de México, Mexico.
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12
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Adeowo FY, Honarparvar B, Skelton AA. The interaction of NOTA as a bifunctional chelator with competitive alkali metal ions: a DFT study. RSC Adv 2016. [DOI: 10.1039/c6ra20203a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This work investigates NOTA–alkali metal (Li+, Na+ and K+ and Rb+) complexation using density functional theory.
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Affiliation(s)
- F. Y. Adeowo
- School of Health Sciences
- School of Pharmacy and Pharmacology
- Discipline of Pharmacy
- University of KwaZulu-Natal
- Durban 4001
| | - B. Honarparvar
- School of Health Sciences
- School of Pharmacy and Pharmacology
- Discipline of Pharmacy
- University of KwaZulu-Natal
- Durban 4001
| | - A. A. Skelton
- School of Health Sciences
- School of Pharmacy and Pharmacology
- Discipline of Pharmacy
- University of KwaZulu-Natal
- Durban 4001
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13
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Md. Abdur Rauf S, Arvidsson PI, Albericio F, Govender T, Maguire GEM, Kruger HG, Honarparvar B. The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study. Org Biomol Chem 2015; 13:9993-10006. [DOI: 10.1039/c5ob01565k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of the cis/trans amide conformational energy barrier (EA).
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Affiliation(s)
- Shah Md. Abdur Rauf
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Per I. Arvidsson
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Fernando Albericio
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
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14
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Antioxidant activity of flavonoids: a QSAR modeling using Fukui indices descriptors. J Mol Model 2014; 20:2476. [DOI: 10.1007/s00894-014-2476-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 09/21/2014] [Indexed: 10/24/2022]
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15
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Wu T, He M, Zang X, Zhou Y, Qiu T, Pan S, Xu X. A structure-activity relationship study of flavonoids as inhibitors of E. coli by membrane interaction effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2751-6. [PMID: 23938956 DOI: 10.1016/j.bbamem.2013.07.029] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/24/2013] [Accepted: 07/29/2013] [Indexed: 11/26/2022]
Abstract
Flavonoids exhibit a broad range of biological activities including antibacterial activity. However, the mechanism of their antibacterial activity has not been fully investigated. The antibacterial activity and membrane interaction of 11 flavonoids (including 2 polymethoxyflavones and 4 isoflavonoids) against Escherichia coli were examined in this study. The antibacterial capacity was determined as flavonoids>polymethoxyflavones>isoflavonoids. Using fluorescence, it was observed that the 5 flavonoids rigidified the liposomal membrane, while the polymethoxyflavones and isoflavonoids increased membrane fluidity. There was a significant positive correlation between antibacterial capacity and membrane rigidification effect of the flavonoids. A quantitative structure-activity relationship (QSAR) study demonstrated that the activity of the flavonoid compounds can be related to molecular hydrophobicity (CLogP) and charges on C atom at position3 (C3). The QSAR model could be used to predict the antibacterial activity of flavonoids which could lead to natural compounds having important use in food and medical industry.
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Affiliation(s)
- Ting Wu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, PR China
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16
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Kuo CM, Bezuidenhoudt BCB, Conradie J. Determination of the relationship between theoretical vibrational frequencies and experimental IR absorbance bands in organic molecules: computational study of oxane, chromane and flavan. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chen-Miao Kuo
- Department of Chemistry; University of the Free State; PO Box 339; Bloemfontein; 9300; South Africa
| | | | - Jeanet Conradie
- Department of Chemistry; University of the Free State; PO Box 339; Bloemfontein; 9300; South Africa
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17
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Chakraborty A, Pan S, Chattaraj PK. Biological Activity and Toxicity: A Conceptual DFT Approach. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Świderek K, Martí S, Moliner V. Theoretical studies of HIV-1 reverse transcriptase inhibition. Phys Chem Chem Phys 2012; 14:12614-24. [DOI: 10.1039/c2cp40953d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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LIAO SIYAN, XU LIANCAI, QIAN LI, ZHENG KANGCHENG. QSAR AND ACTION MECHANISM OF TROXACITABINE PRODRUGS WITH ANTITUMOR ACTIVITY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607003428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The quantitative structure–activity relationship (QSAR) of troxacitabine prodrugs with antitumor activity has been studied by using the density functional theory (DFT), molecular mechanics (MM2), and statistical methods. The established QSAR model shows not only significant statistical quality, but also predictive ability, with the square of adjusted correlation coefficient [Formula: see text] and the square of the cross-validation coefficient (q2 = 0.807). The antitumor activity is expressed as p IC50, which is defined as the negative value of the logarithm of necessary molar concentration of a compound to cause 50% growth inhibition against the human non-small-cell lung cancer cell line SW1573. It appears to be mainly governed by two factors (or original variables), i.e. the calculated hydrophobic coefficient (C log P) of whole molecule and the net charges of the first atom of substituent R (Q FR ), although three descriptors, i.e. C log P, (C log P)2, and Q FR , were selected in our multiple linear regression model. The factor C log P shows parabolic relation to p IC50 and its suitable range is around 5.6, and the other factor Q FR shows a significant negative correlation with p IC50. In this paper, a detailed discussion on these two factors was carried out, and their close correlation with the action mechanism of these prodrugs was reasonably revealed. Such results can offer some useful theoretical references for understanding the action mechanism and directing the molecular design of this kind of compound with antitumor activity.
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Affiliation(s)
- SI YAN LIAO
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
| | - LIAN CAI XU
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
| | - LI QIAN
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
| | - KANG CHENG ZHENG
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
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Balaban Gündüzalp A, Özbek N, Karacan N. Synthesis, characterization, and antibacterial activity of the ligands including thiophene/furan ring systems and their Cu(II), Zn(II) complexes. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9878-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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21
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Comparative study on antioxidant capacity of flavonoids and their inhibitory effects on oleic acid-induced hepatic steatosis in vitro. Eur J Med Chem 2011; 46:4548-58. [PMID: 21824690 DOI: 10.1016/j.ejmech.2011.07.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 07/17/2011] [Accepted: 07/18/2011] [Indexed: 01/22/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease and its incidence is rising worldwide. We compared the antioxidant capacity of seventeen flavonoids with their inhibitory effects on oleic acid-induced triglyceride (TG) over-accumulation in HepG2 cells. The results showed significant correlations (P < 0.01) between the inhibition of intracellular TG levels and the suppression effects on reactive oxygen species. Nevertheless, the radical-reducing activities of flavonoids assessed by chemical assays (cyclic voltammetry and Folin-Ciocalteu reagent assay) were poorly correlated with their intracellular TG inhibitory effects. The relationships between structural properties of flavonoids and their inhibitory effects on TG over-accumulation were discussed.
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Aparicio S. A systematic computational study on flavonoids. Int J Mol Sci 2010; 11:2017-38. [PMID: 20559499 PMCID: PMC2885091 DOI: 10.3390/ijms11052017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/27/2010] [Accepted: 04/27/2010] [Indexed: 11/29/2022] Open
Abstract
17 selected flavones derivatives, flavonoids, were analyzed through a systematic B3LYP/6-311++G** computational study with the aim of understanding the molecular factors that determine their structural and energetic properties in gas phase. Flavonoids were selected in a systematic way to infer the effect of the number and relative positions of hydroxyl groups on molecular properties. Different conformers for each flavonoid were analyzed and the strength and topology of the intramolecular hydrogen bonds studied through the computation of the corresponding torsional profiles. Atoms in a Molecule, and Natural Bond Orbital methodology was applied to the analysis of charge distribution along the studied molecules, and the intramolecular hydrogen bonds. Molecular shapes were studied through full geometry optimization, and the position of the catechol ring analyzed through dihedral scans.
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Affiliation(s)
- Santiago Aparicio
- Department of Chemistry, University of Burgos, 09001 Burgos, Spain; E-Mail: ; Tel.: +34-947-258-062
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Haghdadi M, Fatemi MH. Quantitative Structure–Toxicity Prediction of log(1/EC50) for Some Benzene Derivatives from Their Density Functional Theory Calculated Molecular Descriptors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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The lipophilicity indices of flavonoids estimated by reversed-phase liquid chromatography using different computation methods. J Sep Sci 2009; 32:2066-74. [DOI: 10.1002/jssc.200900106] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hemmateenejad B, Mehdipour AR, Popelier PLA. Quantum Topological QSAR Models based on the MOLMAP Approach. Chem Biol Drug Des 2008; 72:551-63. [DOI: 10.1111/j.1747-0285.2008.00731.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lameira J, Alves C, Santos L, Santos A, de Almeida Santos R, Souza J, Silva C, da Silva A. A combined X-ray and theoretical study of flavonoid compounds with anti-inflammatory activity. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.04.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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QSAR modeling for lipid peroxidation inhibition potential of flavonoids using topological and structural parameters. OPEN CHEM 2008. [DOI: 10.2478/s11532-008-0014-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractIn the present study, Quantitative Structure-Activity Relationship (QSAR) modeling has been carried out for lipid peroxidation (LPO)-inhibition potential of a set of 27 flavonoids, using structural and topological parameters. For the development of models, three methods were used: (1) stepwise regression, (2) factor analysis followed by multiple linear regressions (FA-MLR) and (3) partial least squares (PLS) analysis. The best equation was obtained from stepwise regression analysis (Q2 = 0.626) considering the leave-oneout prediction statistics.
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Liao S, Qian L, Lu H, Shen Y, Zheng K. A Combined 2D‐ and 3D‐QSAR Study on Analogues of ARC‐111 with Antitumor Activity. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200730154] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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QSAR modeling of antiradical and antioxidant activities of flavonoids using electrotopological state (E-State) atom parameters. OPEN CHEM 2007. [DOI: 10.2478/s11532-007-0047-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractIn the present paper QSAR modeling using electrotopological state atom (E-state) parameters has been attempted to determine the antiradical and the antioxidant activities of flavonoids in two model systems reported by Burda et al. (2001). The antiradical property of a methanolic solution of 1, 1-diphenyl-2-picrylhydrazyl (DPPH) and the antioxidant activity of flavonoids in a β-carotenelinoleic acid were the two model systems studied. Different statistical tools used in this communication are stepwise regression analysis, multiple linear regressions with factor analysis as the preprocessing step for variable selection (FA-MLR) and partial least squares analysis (PLS). In both the activities the best equation is obtained from stepwise regression analysis, considering, both equation statistics and predictive ability (antiradical activity: R 2 = 0.927, Q2 = 0.871 and antioxidant activity: R 2 = 0.901, Q2 = 0.841).
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QSAR, action mechanism and molecular design of flavone and isoflavone derivatives with cytotoxicity against HeLa. Eur J Med Chem 2007; 43:2159-70. [PMID: 18082913 DOI: 10.1016/j.ejmech.2007.10.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 10/26/2007] [Accepted: 10/29/2007] [Indexed: 11/20/2022]
Abstract
The quantitative structure-activity relationship (QSAR) of 32 flavone and isoflavone derivatives with cytotoxicity expressed as pGC50, which is defined as the negative value of the logarithm of necessary molar concentration of this series of compounds to cause 50% growth inhibition against the human cervical epithelioid carcinoma cell line (HeLa), has been studied by using the density functional theory (DFT), molecular mechanics (MM2) and statistical methods. In order to obtain QSAR model with high predictive ability, the original dataset was randomly divided into a training set comprising 26 compounds and a test set comprising the rest 6 compounds. An optimal model for the training set with significant statistical quality (RA2=0.852) and predictive ability (q2=0.818) was established. The same model was further applied to predict pGC50 values of the 6 compounds in the test set, and the resulting predictive correlation coefficient Rpred2 reaches 0.738, further showing that this QSAR model has high predictive ability. It is very interesting to find that the cytotoxicities of these compounds against HeLa appear to be mainly governed by two quantum-chemical factors, i.e., the energy (ELUMO) of the lowest unoccupied molecular orbital (LUMO) and the net charges of C atom at site 6 on aromatic rings (QC6). Here the possible action mechanism of these compounds was analyzed and discussed in detail, in particular, the fact why the flavone derivatives have considerably higher cytotoxicity than isoflavone derivatives was reasonably explained. Based on this QSAR equation, 5 new compounds with higher cytotoxicity have been theoretically designed. Such results can offer useful theoretical references for experimental works.
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A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid. Biophys J 2007; 94:2443-51. [PMID: 17981909 DOI: 10.1529/biophysj.107.107623] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy for wild-type and N155S mutant HIV-1 IN, both complexed with a DKA. This hybrid methodology has the advantage of the inclusion of quantum effects such as ligand polarization upon binding, which can be very important when highly polarizable groups are embedded in anisotropic environments, for example in metal-containing active sites. Furthermore, an energy terms decomposition analysis was performed to determine contributions of individual residues to the enzyme-inhibitor interactions. The results reveal that there is a strong interaction between the Lys-159, Lys-156, and Asn-155 residues and Mg(2+) cation and the DKA inhibitor. Our calculations show that the binding energy is higher in wild-type than in the N155S mutant, in accordance with the experimental results. The role of the mutated residue has thus been checked as maintaining the structure of the ternary complex formed by the protein, the Mg(2+) cation, and the inhibitor. These results might be useful to design compounds with more interesting anti-HIV-1 IN activity on the basis of its three-dimensional structure.
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Reis M, Lobato B, Lameira J, Santos AS, Alves CN. A theoretical study of phenolic compounds with antioxidant properties. Eur J Med Chem 2006; 42:440-6. [PMID: 17227686 DOI: 10.1016/j.ejmech.2006.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Revised: 11/15/2006] [Accepted: 11/17/2006] [Indexed: 11/28/2022]
Abstract
Quantum chemical calculations at the DFT/B3LYP, HF, and AM1 and PM3 semiempirical levels were employed to calculate a set of molecular properties for 41 phenol compounds with antioxidant activity. The significant molecular descriptors related to the compounds were the vertical ionization potentials (IPvs) and the charge on oxygen atom 7. The IPv has been calculated using Koopman's theorem IPv=-epsilon(HOMO(DFT)), IPv=-epsilon(HOMO(HF)) and as the difference of energy calculations for the corresponding cation and for the neutral form IPv(E(cation)-E(neutral)) obtained with the DFT/B3LYP method. The best model obtained showed not only the statistical significance but also predictive ability.
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Affiliation(s)
- Mauro Reis
- Departamento de Química, Centro de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110 Belém, PA, Brazil
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Lameira J, Medeiros IG, Reis M, Santos AS, Alves CN. Structure–activity relationship study of flavone compounds with anti-HIV-1 integrase activity: A density functional theory study. Bioorg Med Chem 2006; 14:7105-12. [PMID: 16890444 DOI: 10.1016/j.bmc.2006.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/23/2006] [Accepted: 07/01/2006] [Indexed: 11/24/2022]
Abstract
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Flavone compounds have been very much studied due to their activity during the inhibition process of HIV-1 IN. In this study, we employed density functional theory (DFT) using the B3LYP hybrid functional to calculate a set of molecular properties for 32 flavonoid compounds with anti-HIV-1 IN activity. The stepwise discriminant analysis (SDA), principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods were employed to reduce dimensionality and investigate possible relationship between the calculated properties and the anti-HIV-1 IN activity. These analyses showed that the molecular hydrophobicity (ClogP), charge on atom 11 and electrophilic index (omega) are responsible for the separation between anti-HIV-1 IN active and inactive compounds.
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Affiliation(s)
- J Lameira
- Departamento de Química, Centro de Ciências Exatas e Naturais, Universidade Federal do Pará, Av. Augusto Corrêa 01, CP 11101, 66075-110, Belém, PA, Brazil
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