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Cheng XR, Yu BT, Song J, Ma JH, Chen YY, Zhang CX, Tu PH, Muskat MN, Zhu ZG. The Alleviation of Dextran Sulfate Sodium (DSS)-Induced Colitis Correlate with the log P Values of Food-Derived Electrophilic Compounds. Antioxidants (Basel) 2022; 11:antiox11122406. [PMID: 36552614 PMCID: PMC9774124 DOI: 10.3390/antiox11122406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Food-derived electrophilic compounds (FECs) are small molecules with electrophilic groups with potential cytoprotective effects. This study investigated the differential effects of six prevalent FECs on colitis in dextran sodium sulfate (DSS)-induced mice and the underlying relationship with molecular characteristics. Fumaric acid (FMA), isoliquiritigenin (ISO), cinnamaldehyde (CA), ferulic acid (FA), sulforaphane (SFN), and chlorogenic acid (CGA) exhibited varying improvements in colitis on clinical signs, colonic histopathology, inflammatory and oxidative indicators, and Nrf2 pathway in a sequence of SFN, ISO > FA, CA > FMA, CGA. Representative molecular characteristics of the “penetration-affinity−covalent binding” procedure, logP value, Keap1 affinity energy, and electrophilic index of FECs were theoretically calculated, among which logP value revealed a strong correlation with colitis improvements, which was related to the expression of Nrf2 and its downstream proteins. Above all, SFN and ISO possessed high logP values and effectively improving DSS-induced colitis by activating the Keap1−Nrf2 pathway to alleviate oxidative stress and inflammatory responses.
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Affiliation(s)
- Xiang-Rong Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bu-Tao Yu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jie Song
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jia-Hui Ma
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Yu-Yao Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Chen-Xi Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Piao-Han Tu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Mitchell N Muskat
- School of Pharmacy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ze-Gang Zhu
- Jinhua Academy of Agricultural Sciences, Jinhua 321000, China
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Khurm M, Wang X, Zhang H, Hussain SN, Qaisar MN, Hayat K, Saqib F, Zhang X, Zhan G, Guo Z. The genus Cassia L.: Ethnopharmacological and phytochemical overview. Phytother Res 2021; 35:2336-2385. [PMID: 33617115 DOI: 10.1002/ptr.6954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/16/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022]
Abstract
Nature gifts medicinal plants with the untapped and boundless treasure of active chemical constituents with significant therapeutic potential that makes these plants a beneficial source in the development of phytomedicines. Genus Cassia, with approximately 500 species, is a large group of flowering plants in the family Fabaceae. Cassia species are widely distributed throughout different regions mainly tropical Asia, North America, and East Africa. In the folk medicinal history, these plants are used as laxative and purgative agents. In the Ayurveda system of medicine, they are used to cure headache and fever. Cassia plants exhibit pharmacological activities at large scales such as antimicrobial, anticancer, antiinflammatory, antioxidant, hypoglycemic, hyperglycemic, antimutagenic, and antivirals. The phytochemical investigations of genus Cassia demonstrate the presence of more than 200 chemical compounds, including piperidine alkaloids, anthracene derivatives (anthraquinones), flavonoids, pentacyclic triterpenoids, sterols, phenylpropanoids, and γ-naphthopyrones. The literature illustrated anthraquinones and flavonoids as major secondary metabolites from this genus. However, some Cassia plants, with rich contents of anthraquinones, still show toxicology properties. As Cassia plants are used extensively in the herbal system of medicine, but only senna dosage forms have achieved the status of the pharmaceutical market as standard laxative agents. In conclusion, further investigations on isolating newer biologically active constituents, unknown underlying mechanisms, toxicology profiles, and clinical studies of Cassia species are needed to be explored. This review article specifies the systematic breach existing between the current scientific knowledge and the fundamentals for the marketization of genus Cassia products.
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Affiliation(s)
- Muhammad Khurm
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Xingbin Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Hui Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | | | | | - Khezar Hayat
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Xinxin Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Guanqun Zhan
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengjun Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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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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Flavonol 7- O-Glucoside Herbacitrin Inhibits HIV-1 Replication through Simultaneous Integrase and Reverse Transcriptase Inhibition. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:1064793. [PMID: 30853999 PMCID: PMC6378053 DOI: 10.1155/2019/1064793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/31/2018] [Accepted: 01/14/2019] [Indexed: 11/17/2022]
Abstract
Here we report the evaluation of the antiretroviral effect of two flavonoid 7-O-glucosides, herbacitrin (1) and gossypitrin (2), together with quercetin (3), a well-studied flavonol. Antiviral activity of the flavonoids was assessed by analyzing HIV-1 p24 core protein levels in the supernatants of HIV-1 infected MT-4 and MT-2 cell cultures. The compounds showed mild to weak cytotoxic activities on the host cells; herbacitrin was the strongest in this regard (CC50=27.8 and 63.64 μM on MT-4 and MT-2 cells, respectively). In nontoxic concentrations, herbacitrin and quercetin reduced HIV-1 replication, whereas gossypitrin was ineffective. Herbacitrin was found to inhibit reverse transcriptase at 21.5 μM, while it was a more potent integrase inhibitor already active at 2.15 μM. Therefore, our observations suggest that herbacitrin exerts antiretroviral activity through simultaneously acting on these two targets of HIV-1 and that integrase inhibition might play a major role in this activity.
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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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Alshammari MB, Geesi MH, Anouar EH, Al-Salahi R, Alharthi AI, Elnakady Y, Marzouk M. Quantum Chemical Calculations and Statistical Analysis: Structural Cytotoxicity Relationships of some Synthesized 2-thiophen-naphtho(benzo)oxazinone Derivatives. Cell Biochem Biophys 2018; 76:377-389. [PMID: 30062659 DOI: 10.1007/s12013-018-0848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022]
Abstract
Twenty-two 2-thiophen-naphtho(benzo)oxazinone derivatives are prepared using 3-amino-2-naphthoic and 5-nitroanthranilic acids as building blocks. The target compounds (1-22) were evaluated quantitatively for their cytotoxic effects in vitro against three cancer cell lines, including the lung A549, the hepatocyte HepG2, and the breast MCF-7 carcinoma cells. Compounds 1, 12, 14, and 21 were found to exhibit remarkable cytotoxicity against the tested cancer cell lines. Compound 21 has shown the highest activity against A549 and MCF-7 (IC50: 9.8 & 3.6 µg mL-1) whereas 1 (IC50: 5.9 µg mL-1) and 5 (3.6 µg mL-1) were the most active against HepG2. To elucidate the structure-cytotoxicity relationships of the synthesized compounds, a number of their chemical descriptors are determined including electronic, steric and hydrophobicity descriptors. The electronic properties were calculated through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d,p). The impact of the chosen descriptors is evaluated statistically through simple and multiple linear regression analyses (SLR and MLR). SLR analyses reveal that the impact of each descriptor on the cell lines are relatively weak except for MCF-7, where hardness and softness show moderate correlations with correlation coefficients higher than 60%. The correlations were improved by considering MLR analyses (R2 ≥ 90%), which showed that the cytotoxicity of synthesized compounds is correlated with their combined descriptors hardness, softness, electrophiliciy and hydrophobicity (LogP).
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Affiliation(s)
- Mohammed B Alshammari
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al kharj, 11942, Saudi Arabia
| | - Mohammed H Geesi
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al kharj, 11942, Saudi Arabia
| | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al kharj, 11942, Saudi Arabia
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman I Alharthi
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al kharj, 11942, Saudi Arabia
| | - Yasser Elnakady
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed Marzouk
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al kharj, 11942, Saudi Arabia. .,Chemistry of Natural Products Group, Center of Excellence for Advanced Sciences, National Research Center, Dokki, Cairo, 12622, Egypt.
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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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8
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Mihailovs I, Kampars V, Turovska B, Rutkis M. Rational computing of energy levels for organic electronics: the case of 2-benzylidene-1,3-indandiones. RSC Adv 2016. [DOI: 10.1039/c6ra16456k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To compute ionization potential and electron affinity (HOMO & LUMO levels by tradition), diffuse functions are redundant, while range-separated hybrid DFT is not always better than B3LYP. Solvent modelling is essential and can be cheap with CPCM.
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Affiliation(s)
- Igors Mihailovs
- Institute of Solid State Physics
- University of Latvia
- Riga
- Latvia
- Institute of Applied Chemistry
| | - Valdis Kampars
- Institute of Applied Chemistry
- Riga Technical University
- Riga
- Latvia
| | | | - Martins Rutkis
- Institute of Solid State Physics
- University of Latvia
- Riga
- Latvia
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Hamdi OAA, Anouar EH, Shilpi JA, Trabolsy ZBKA, Zain SBM, Zakaria NSS, Zulkefeli M, Weber JFF, Malek SNA, Rahman SNSA, Awang K. A Quantum Chemical and Statistical Study of Cytotoxic Activity of Compounds Isolated from Curcuma zedoaria. Int J Mol Sci 2015; 16:9450-68. [PMID: 25923077 PMCID: PMC4463598 DOI: 10.3390/ijms16059450] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/10/2015] [Accepted: 02/17/2015] [Indexed: 11/23/2022] Open
Abstract
A series of 21 compounds isolated from Curcuma zedoaria was subjected to cytotoxicity test against MCF7; Ca Ski; PC3 and HT-29 cancer cell lines; and a normal HUVEC cell line. To rationalize the structure-activity relationships of the isolated compounds; a set of electronic; steric and hydrophobic descriptors were calculated using density functional theory (DFT) method. Statistical analyses were carried out using simple and multiple linear regressions (SLR; MLR); principal component analysis (PCA); and hierarchical cluster analysis (HCA). SLR analyses showed that the cytotoxicity of the isolated compounds against a given cell line depend on certain descriptors; and the corresponding correlation coefficients (R2) vary from 0%-55%. MLR results revealed that the best models can be achieved with a limited number of specific descriptors applicable for compounds having a similar basic skeleton. Based on PCA; HCA and MLR analyses; active compounds were classified into subgroups; which was in agreement with the cell based cytotoxicity assay.
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Affiliation(s)
- Omer Abdalla Ahmed Hamdi
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - El Hassane Anouar
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA Kampus Puncak Alam, Bandar Puncak Alam 42300, Malaysia.
| | - Jamil A Shilpi
- Centre for Natural Products and Drug Discovery (CENAR), University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Zuhra Bashir Khalifa Al Trabolsy
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA Kampus Puncak Alam, Bandar Puncak Alam 42300, Malaysia.
| | - Sharifuddin Bin Md Zain
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Nur Shahidatul Shida Zakaria
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA Kampus Puncak Alam, Bandar Puncak Alam 42300, Malaysia.
| | - Mohd Zulkefeli
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA Kampus Puncak Alam, Bandar Puncak Alam 42300, Malaysia.
| | - Jean-Frédéric F Weber
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA Kampus Puncak Alam, Bandar Puncak Alam 42300, Malaysia.
| | - Sri Nurestri A Malek
- Institue of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | | | - Khalijah Awang
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- Centre for Natural Products and Drug Discovery (CENAR), University of Malaya, Kuala Lumpur 50603, Malaysia.
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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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de Campos LJ, de Melo EB. Modeling structure–activity relationships of prodiginines with antimalarial activity using GA/MLR and OPS/PLS. J Mol Graph Model 2014; 54:19-31. [DOI: 10.1016/j.jmgm.2014.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 08/02/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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12
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Singh M, Kaur M, Silakari O. Flavones: an important scaffold for medicinal chemistry. Eur J Med Chem 2014; 84:206-39. [PMID: 25019478 DOI: 10.1016/j.ejmech.2014.07.013] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/03/2014] [Accepted: 07/05/2014] [Indexed: 01/31/2023]
Abstract
Flavones have antioxidant, anti-proliferative, anti-tumor, anti-microbial, estrogenic, acetyl cholinesterase, anti-inflammatory activities and are also used in cancer, cardiovascular disease, neurodegenerative disorders, etc. Also, flavonoids are found to have an effect on several mammalian enzymes like protein kinases that regulate multiple cell signaling pathways and alterations in multiple cellular signaling pathways are frequently found in many diseases. Flavones have been an indispensable anchor for the development of new therapeutic agents. The majority of metabolic diseases are speculated to originate from oxidative stress, and it is therefore significant that recent studies have shown the positive effect of flavones on diseases related to oxidative stress. Due to the wide range of biological activities of flavones, their structure-activity relationships have generated interest among medicinal chemists. The outstanding development of flavones derivatives in diverse diseases in very short span of time proves its magnitude for medicinal chemistry research. The present review gives detail about the structural requirement of flavone derivatives for various pharmacological activities. This information may provide an opportunity to scientists of medicinal chemistry discipline to design selective, optimize as well as poly-functional flavone derivatives for the treatment of multi-factorial diseases.
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Affiliation(s)
- Manjinder Singh
- Molecular Modeling Lab, Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Maninder Kaur
- Molecular Modeling Lab, Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Om Silakari
- Molecular Modeling Lab, Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India.
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Abstract
Frequent failure of drug candidates during development stages remains the major deterrent for an early introduction of new drug molecules. The drug toxicity is the major cause of expensive late-stage development failures. An early identification/optimization of the most favorable molecule will naturally save considerable cost, time, human efforts and minimize animal sacrifice. (Quantitative) Structure Activity Relationships [(Q)SARs] represent statistically derived predictive models correlating biological activity (including desirable therapeutic effect and undesirable side effects) of chemicals (drugs/toxicants/environmental pollutants) with molecular descriptors and/or properties. (Q)SAR models which categorize the available data into two or more groups/classes are known as classification models. Numerous techniques of diverse nature are being presently employed for development of classification models. Though there is an increasing use of classification models for prediction of either biological activity or toxicity, the future trend will naturally be towards the development of classification models capable of simultaneous prediction of biological activity, toxicity, and pharmacokinetic parameters so as to accelerate development of bioavailable safe drug molecules.
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POM as a quick bioinformatic platform to select flavonoids and their metabolites as potential and efficient HIV-1 integrase inhibitors. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0679-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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de Melo EB, Ferreira MMC. Four-dimensional structure-activity relationship model to predict HIV-1 integrase strand transfer inhibition using LQTA-QSAR methodology. J Chem Inf Model 2012; 52:1722-32. [PMID: 22657398 DOI: 10.1021/ci300039a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite highly active antiretroviral therapy (HAART) implementation, there is a continuous need to search for new anti-HIV agents. HIV-1 integrase (HIV-1 IN) is a recently validated biological target for AIDS therapy. In this work, a four-dimensional quantitative structure-activity relationship (4D-QSAR) study using the new methodology named LQTA-QSAR approach with a training set of 85 HIV-1 IN strand transfer inhibitors (INSTI), containing the β-diketo acid (DKA) substructure, was carried out. The GROMACS molecular dynamic package was used to obtain a conformational ensemble profile (CEP) and LQTA-QSAR was employed to calculate Coulomb and Lennard-Jones potentials and to generate the field descriptors. The partial least-squares (PLS) regression model using 14 field descriptors and 8 latent variables (LV) yielded satisfactory statistics (R2= 0.897, SEC = 0.270, and F = 72.827), good performance in internal (QLOO2 = 0.842 and SEV = 0.314) and external prediction (Rpred2 = 0.839, SEP = 0.384, AREpred = 4.942%, k = 0.981, k′ = 1.016, and |R02 – R0′2 = 0.0257). The QSAR model was shown to be robust (leave-N-out cross validation; average QLNO2 = 0.834) and was not built by chance (y-randomization test; R2 intercept = 0.109; Q2 intercept = -0.398). Fair chemical interpretation of the model could be traced, including descriptors related to interaction with the metallic cofactors and the hydrophobic loop. The model obtained has a good potential for aid in the design of new INSTI, and it is a successful example of application of LQTA-QSAR as an useful tool to be used in computer-aided drug design (CADD).
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Affiliation(s)
- Eduardo B de Melo
- Theoretical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Parana State University-Unioeste, 2069 Universitaria St, Cascavel, PR 85819-110, Brazil
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Affiliation(s)
- Pratim Kumar Chattaraj
- Department of Chemistry, Center for Theoretical Studies, Indian Institute of Technology, Kharagpur, India
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Faizi S, Dar A, Siddiqi H, Naqvi S, Naz A, Bano S. Bioassay-guided isolation of antioxidant agents with analgesic properties from flowers of Tagetes patula. PHARMACEUTICAL BIOLOGY 2011; 49:516-25. [PMID: 21284510 DOI: 10.3109/13880209.2010.523006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CONTEXT Tagetes patula L. is one of the French marigold group of the Asteraceae family. It is recognized in folklore for its medicinal and pesticidal properties. OBJECTIVE In search of more effective, but non-toxic compounds with antioxidative potential led to the bioassay guided isolation studies on the extracts of T. patula. MATERIALS AND METHODS The bioassay on Tagetes patula flowers were carried out guided by in vitro antioxidant activity using DPPH assay. A minor but proven plant constituent methyl protocatechuate (1) was isolated by column chromatography, while patuletin (2) and patulitrin (3) obtained in bulk by employing solvent partition of methanol extract. Derivatization of patuletin into benzoyl, cinnamoyl and methyl was conducted to establish the structure activity relationship (SAR). Analgesic activity of compound 2 was evaluated using acetic acid-induced writhing test and hot-plate test in mice. The toxicity of methanol extract and compound 2 were also determined. RESULTS Polar extracts, fractions and phases demonstrated better antioxidant activity. The synthetic methyl protocatechuate (1) showed IC(50) value of 2.8 ± 0.2 μg/mL, whereas patuletin (2) (IC(50) = 4.3 ± 0.25 µg/mL) was comparable to quercetin and rutin but significantly better than patulitrin (3) (IC(50) = 10.17 ± 1.16 µg/mL). Toxicity test for the methanol extract and compound 2 did not elicit any behavioral changes or cause mortality in mice. Compound 2 also demonstrated mild analgesic property. DISCUSSION AND CONCLUSION These findings demonstrate that the plant polar extracts and fractions possess significant antioxidant property with non-toxic effect. Compound 1 is a genuine plant constituent of T. patula.
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Affiliation(s)
- Shaheen Faizi
- International Center for Chemical and Biological Sciences, H E J Research Institute of Chemistry, University of Karachi, Karachi, Pakistan.
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Upadhyay A, Chompoo J, Kishimoto W, Makise T, Tawata S. HIV-1 integrase and neuraminidase inhibitors from Alpinia zerumbet. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:2857-2862. [PMID: 21306110 DOI: 10.1021/jf104813k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
AIDS and influenza are viral pandemics and remain one of the leading causes of human deaths worldwide. The increasing resistance of these diseases to synthetic drugs demands the search for novel compounds from plant-based sources. In this regard, the leaves and rhizomes of Alpinia zerumbet, a traditionally important economic plant in Okinawa, were investigated for activity against HIV-1 integrase (IN) and neuraminidase (NA). The aqueous extracts of leaves and rhizomes had IN inhibitory activity with IC(50) values of 30 and 188 μg/mL, whereas against NA they showed 50% inhibition at concentrations of 43 and 57 μg/mL, respectively. 5,6-Dehydrokawain (DK), dihydro-5,6-dehydrokawain (DDK), and 8(17),12-labdadiene-15,16-dial (labdadiene) were isolated from the rhizomes and were tested for enzyme inhibitions. DK and DDK strongly inhibited IN with IC(50) of 4.4 and 3.6 μg/mL, respectively. Against NA, DK, DDK, and labdadiene exhibited mixed type of inhibition with respective IC(50) values of 25.5, 24.6, and 36.6 μM and K(i) values ranging from 0.3 to 2.8 μM. It was found that DDK is a slow and time-dependent reversible inhibitor of NA, probably with a methoxy group as its functionally active site. These results suggest that alpinia could be used as a source of bioactive compounds against IN and NA and that DK and DDK may have possibilities in the design of drugs against these viral diseases.
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Affiliation(s)
- Atul Upadhyay
- Department of Biochemistry and Applied Bioscience, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
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Liu L, Ma H, Yang N, Tang Y, Guo J, Tao W, Duan J. A series of natural flavonoids as thrombin inhibitors: structure-activity relationships. Thromb Res 2010; 126:e365-78. [PMID: 20828797 DOI: 10.1016/j.thromres.2010.08.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 11/15/2022]
Abstract
A series of natural flavonoids has been evaluated as potential inhibitors of thrombin using the optimized method of thrombin time. Myricetin and quercetin have shown to be the best thrombin inhibitors tested. In order to investigate the thrombin recognition of the most active and selective compounds, a molecular modeling study has been performed using available Protein Data Bank (PDB) structures as receptor models for docking experiments. Structure-activity relationships of flavonoids (SARs) on thrombin would facilitate the design of chemical compounds with higher potency to serve as potential thrombin inhibitors, and provide information for the exploitation and utilization of flavonoids as thrombin inhibitors for thrombotic disease treatment.
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Affiliation(s)
- Li Liu
- Jiangsu Key Laboratory for TCM Formulae Research, Nanjing University of Chinese Medicine, Nanjing 210046, China
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Structure–activity relationship of dihydroxy-4-methylcoumarins as powerful antioxidants: Correlation between experimental & theoretical data and synergistic effect. Biochimie 2010; 92:1089-100. [DOI: 10.1016/j.biochi.2010.06.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 06/11/2010] [Indexed: 11/21/2022]
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Zhang X, Li Y, Chen P, Han T, Zhao W. Sodium quercetin-8-sulfonate trihydrate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:m1036-7. [PMID: 21588109 PMCID: PMC3007453 DOI: 10.1107/s1600536810029570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/25/2010] [Indexed: 11/10/2022]
Abstract
The organic anion of the title compound, {[Na(C(15)H(9)O(10)S)(H(2)O)(2)]·H(2)O}(n) {systematic name: poly[[diaqua-[μ-2-(3,4-dihy-droxy-phen-yl)-3,5,7-trihy-droxy-4-oxo-4H-chromene-8-sulfon-ato]-sodium] monohydrate]}, has a nearly planar structure. The Na atom is six-coordinated by O atoms, two from water mol-ecules and four from the anion. The dihedral angle between the ring systems in the anion is 10.1 (1)°. Intra-molecular O-H⋯S and O-H⋯O inter-actions occur. In the crystal structure, an extensive network of classical inter-molecular O-H⋯S and O-H⋯O hydrogen bonds forms layers along the c axis.
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Affiliation(s)
- Xian Zhang
- School of Pharmaceutical Science and Technology, Dalian Unversity of Technology, PO Box 90, Zhongshan Road 158, Dalian 116012, People's Republic of China
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22
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Borges de Melo E, Ataide Martins JP, Marinho Jorge TC, Friozi MC, Castro Ferreira MM. Multivariate QSAR study on the antimutagenic activity of flavonoids against 3-NFA on Salmonella typhimurium TA98. Eur J Med Chem 2010; 45:4562-9. [PMID: 20696502 DOI: 10.1016/j.ejmech.2010.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 03/29/2010] [Accepted: 07/10/2010] [Indexed: 10/19/2022]
Abstract
A quantitative structure-activity relationship (QSAR) study of twenty flavonoid derivatives with antimutagenic activity against 3-nitrofluoranthene (3-NFA) was performed by Partial Least Squares (PLS), using Ordered Predictors Selection (OPS) algorithm for variable selection. Four descriptors (PJI2, Mor27m, G1e and R4u+) were selected and a good model (n = 19; R(2) = 0.747; SEC = 0.332; PRESS(cal) = 1.768; F((2,27)) = 23.585; Q(LOO)(2) = 0.590; SEV = 0.388; PRESS(val) = 2.858; R(pred)(2) = 0.591; SEP = 0.394; ARE(pred) = 5.230%; k = 1.005; k' = 0.990; |R(02) - R'(02)| = 0.109) was built with two latent variables describing 83.410% of the original information. Leave-N-out cross validation (LNO) and y-randomization were performed in order to confirm the robustness of the model. The topological descriptors selected indicate that the antimutagenic activity against 3-NFA depends on molecular size, shape and Sanderson electronegativity of flavonoids. The proposed model may provide a better understanding of the antimutagenic activity of flavonoids and can be used as a guidance for proposition of new chemopreventive agents.
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Affiliation(s)
- Eduardo Borges de Melo
- Curso de Farmácia, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná - Unioeste, Cascavel, PR, Brazil
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Faizi S, Siddiqi H, Naz A, Bano S, Lubna. Specific Deuteration in Patuletin and Related FlavonoidsviaKeto-Enol Tautomerism: Solvent- and Temperature-Dependent1H-NMR Studies. Helv Chim Acta 2010. [DOI: 10.1002/hlca.200900249] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wang S, Yan J, Wang X, Yang Z, Lin F, Zhang T. Synthesis and evaluation of the alpha-glucosidase inhibitory activity of 3-[4-(phenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one derivatives. Eur J Med Chem 2009; 45:1250-5. [PMID: 20045223 DOI: 10.1016/j.ejmech.2009.12.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 12/08/2009] [Accepted: 12/12/2009] [Indexed: 10/20/2022]
Abstract
In the course of studies directed toward the discovery of novel non-sugar alpha-glucosidase inhibitors for the treatment of diabetes, a series of 3-[4-(phenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one derivatives was synthesized and evaluated as alpha-glucosidase inhibitors. Most compounds showed good inhibitory activity with IC(50) values ranging from 0.0645 microM to 26.746 microM. 7-Hydroxy-6-methoxy-3-[4-(4-methylphenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one 7u manifested the most potent inhibitory activity with an IC(50) value of 0.0645 microM.
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Affiliation(s)
- Shaojie Wang
- Key Laboratory of New Drugs Design and Discovery of Liaoning Province, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China.
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Anouar E, Calliste CA, Košinová P, Di Meo F, Duroux JL, Champavier Y, Marakchi K, Trouillas P. Free Radical Scavenging Properties of Guaiacol Oligomers: A Combined Experimental and Quantum Study of the Guaiacyl-Moiety Role. J Phys Chem A 2009; 113:13881-91. [DOI: 10.1021/jp906285b] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Anouar
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - C. A. Calliste
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - P. Košinová
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - F. Di Meo
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - J. L. Duroux
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - Y. Champavier
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - K. Marakchi
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
| | - P. Trouillas
- Université de Limoges, EA 4021, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges, France, Université Mohammed V, Laboratoire de Chimie Théorique, Faculté des Sciences, B.P 1014 Rabat, Morocco, and Service commun de RMN, Université de Limoges, 2 rue du Docteur Marcland, 87025 Limoges, France
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Multivariate QSAR study of 4,5-dihydroxypyrimidine carboxamides as HIV-1 integrase inhibitors. Eur J Med Chem 2009; 44:3577-83. [DOI: 10.1016/j.ejmech.2009.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/02/2009] [Indexed: 11/17/2022]
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27
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Camargo LTFM, Sena MM, Camargo AJ. A quantum chemical and chemometrical study of indolo[2,1-b]quinazoline and their analogues with cytotoxic activity against breast cancer cells. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2009; 20:537-549. [PMID: 19916113 DOI: 10.1080/10629360903278800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Some indolo[2,1-b]quinalozine (tryptanthrin) analogues present cytotoxic activity against human breast cancer cells. In this work, chemometric methods were applied in the search for building discriminant models between active and inactive analogues, based on the correlations among their in vitro cytotoxic activities and their electronic and geometric molecular descriptors. From 88 descriptors calculated with density functional theory with the exchange correlation functional B3LYP and the basis set 6-31G* (Gaussian 03), 29 were pre-selected based on their Fisher weights, and finally five descriptors (partial charge on atom 15, bond orders between atoms 12-13, 17-25 and 18-26, and energy difference between frontier molecular orbitals) were selected for principal component analysis. This analysis was able to discriminate 12 inactive from 22 active analogues by using only one principal component, accounting for 49% of the total variance and allowing us to better understand the influence of these electronic descriptors in the cytotoxic activity. In addition, a supervised partial least-squares discriminant model was build and successfully used to discriminate tryptanthrin analogues. The model was validated through an independent test set and considered robust to overfitting.
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Affiliation(s)
- L T F M Camargo
- Unidade Universitária de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Anápolis, GO, Brazil
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28
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Xu F, Guan H, Li G, Liu H. LC Method for Analysis of Three Flavonols in Rat Plasma and Urine after Oral Administration of Polygonum aviculare Extract. Chromatographia 2009. [DOI: 10.1365/s10337-009-1088-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Chattaraj PK, Giri S. Electrophilicity index within a conceptual DFT framework. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b802832j] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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31
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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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Affiliation(s)
- Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, IndiaThis is a Chemical Reviews Perennial Review. The root paper of this title was published in 2006 (Chattaraj, P. K.; Sarkar, U.; Roy, D. R. Chem. Rev. 2006, 106, 2065). Updates to the text appear in red type
| | - Debesh Ranjan Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, IndiaThis is a Chemical Reviews Perennial Review. The root paper of this title was published in 2006 (Chattaraj, P. K.; Sarkar, U.; Roy, D. R. Chem. Rev. 2006, 106, 2065). Updates to the text appear in red type
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Veljkovic V, Mouscadet JF, Veljkovic N, Glisic S, Debyser Z. Simple criterion for selection of flavonoid compounds with anti-HIV activity. Bioorg Med Chem Lett 2006; 17:1226-32. [PMID: 17189684 DOI: 10.1016/j.bmcl.2006.12.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2006] [Revised: 12/04/2006] [Accepted: 12/05/2006] [Indexed: 11/16/2022]
Abstract
Flavonoid compounds represent an important natural source of antiretrovirals for AIDS therapy due to their significant anti-HIV-1 activity and low toxicity. Here we propose a simple theoretical criterion to discriminate active from inactive flavonoids that is suitable for rapid in silico screening of flavonoid libraries, and selection and optimization of lead compounds with anti-HIV-1 activity.
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Affiliation(s)
- Veljko Veljkovic
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, PO Box 522, 11001 Belgrade, Serbia.
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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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