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Masand VH, Al-Hussain SA, Alzahrani AY, Al-Mutairi AA, Hussien RA, Samad A, Zaki MEA. Estrogen Receptor Alpha Binders for Hormone-Dependent Forms of Breast Cancer: e-QSAR and Molecular Docking Supported by X-ray Resolved Structures. ACS OMEGA 2024; 9:16759-16774. [PMID: 38617692 PMCID: PMC11007693 DOI: 10.1021/acsomega.4c00906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Cancer, a life-disturbing and lethal disease with a high global impact, causes significant economic, social, and health challenges. Breast cancer refers to the abnormal growth of cells originating from breast tissues. Hormone-dependent forms of breast cancer, such as those influenced by estrogen, prompt the exploration of estrogen receptors as targets for potential therapeutic interventions. In this study, we conducted e-QSAR molecular docking and molecular dynamics analyses on a diverse set of inhibitors targeting estrogen receptor alpha (ER-α). The e-QSAR model is based on a genetic algorithm combined with multilinear regression analysis. The newly developed model possesses a balance between predictive accuracy and mechanistic insights adhering to the OECD guidelines. The e-QSAR model pointed out that sp2-hybridized carbon and nitrogen atoms are important atoms governing binding profiles. In addition, a specific combination of H-bond donors and acceptors with carbon, nitrogen, and ring sulfur atoms also plays a crucial role. The results are supported by molecular docking, MD simulations, and X-ray-resolved structures. The novel results could be useful for future drug development for ER-α.
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Affiliation(s)
- Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati 444 602, Maharashtra, India
| | - Sami A Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail 61421, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Rania A Hussien
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha 65799, Kingdom of Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil 44001, Iraq
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
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2
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Gajęcka M, Brzuzan P, Otrocka-Domagała I, Zielonka Ł, Lisieska-Żołnierczyk S, Gajęcki MT. The Effect of 42-Day Exposure to a Low Deoxynivalenol Dose on the Immunohistochemical Expression of Intestinal ERs and the Activation of CYP1A1 and GSTP1 Genes in the Large Intestine of Pre-pubertal Gilts. Front Vet Sci 2021; 8:644549. [PMID: 34350223 PMCID: PMC8326516 DOI: 10.3389/fvets.2021.644549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/28/2021] [Indexed: 01/17/2023] Open
Abstract
Deoxynivalenol (DON) is a mycotoxin that contaminates various plant materials. Exposure to DON can disrupt hormonal homeostasis, decrease body weight gains and modulate the immune system in pigs. It can also cause diarrhea, vomiting, leukocytosis, hemorrhaging or even death. Prolonged exposure to low doses of DON can have serious health implications in mammals. This is the first in vivo study to show that per os administration of low DON doses probably contributes to specific dysfunctions in steroidogenesis processes by inducing the immunohistochemical expression of estrogen receptors alpha (ERα) in the entire gastrointestinal tract in strongly stained cells (3 points) and estrogen receptors beta (ERβ), but only in both investigated segments of the duodenum in pre-pubertal gilts. Therefore, the aim of this study was to determine whether a NOAEL dose of DON (12 μg DON/kg BW) administered per os over a period of 42 days induces changes in the immunohistochemical expression of ER in different intestinal segments and the transcriptional activation of CYP1A1 and GSTP1 genes in the large intestine of pre-pubertal gilts. This is the first report to demonstrate the expression of ER, in particular ERβ, with the associated consequences. The expression of ER was accompanied by considerable variations in the activation of CYP1A1 and GSTP1 genes, but it supported the maintenance of a stable consensus between the degree of mycotoxin exposure and the detoxifying effect in pre-pubertal gilts.
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Affiliation(s)
- Magdalena Gajęcka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Paweł Brzuzan
- Department of Environmental Biotechnology, Faculty of Environmental Sciences and Fisheries, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Iwona Otrocka-Domagała
- Department of Pathological Anatomy, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Łukasz Zielonka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Sylwia Lisieska-Żołnierczyk
- Independent Public Health Care Center of the Ministry of the Interior and Administration and the Warmia and Mazury Oncology Center in Olsztyn, Olsztyn, Poland
| | - Maciej T Gajęcki
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Andreeva OV, Garifullin BF, Sharipova RR, Strobykina IY, Sapunova AS, Voloshina AD, Belenok MG, Dobrynin AB, Khabibulina LR, Kataev VE. Glycosides and Glycoconjugates of the Diterpenoid Isosteviol with a 1,2,3-Triazolyl Moiety: Synthesis and Cytotoxicity Evaluation. JOURNAL OF NATURAL PRODUCTS 2020; 83:2367-2380. [PMID: 32786882 DOI: 10.1021/acs.jnatprod.0c00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Several glycoconjugates of the diterpenoid isosteviol (16-oxo-ent-beyeran-19-oic acid) with a 1,2,3-triazolyl moiety were synthesized, and their cytotoxicity was evaluated against some human cancer and normal cell lines. Most of the synthesized compounds demonstrated weak inhibitory activities against the M-HeLa and MCF-7 human cancer cell lines. Three lead compounds, 54, 56 and 57, exhibited high selective cytotoxic activity against M-HeLa cells (IC50 = 1.7-1.9 μM) that corresponded to the activity of the anticancer drug doxorubicin (IC50 = 3.0 μM). Moreover, the lead compounds were not cytotoxic with respect to a Chang liver human normal cell line (IC50 > 100 μM), whereas doxorubicin was cytotoxic to this cell line (IC50 = 3.0 μM). It was found that cytotoxic activity of the lead compounds is due to induction of apoptosis proceeding along the mitochondrial pathway. The present findings suggest that 1,2,3-triazolyl-ring-containing glycoconjugates of isosteviol are a promising scaffold for the design of novel anticancer agents.
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Affiliation(s)
- Olga V Andreeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Bulat F Garifullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Radmila R Sharipova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Irina Yu Strobykina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Anastasiya S Sapunova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Alexandra D Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Mayya G Belenok
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Alexey B Dobrynin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Leysan R Khabibulina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
| | - Vladimir E Kataev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street, 8, Kazan, 420088, Russian Federation
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Lim NK, Cravillion T, Savage S, McClory A, Han C, Zhang H, DiPasquale A, Gosselin F. Synthesis of a Selective Estrogen Receptor Degrader via a Stereospecific Elimination Approach. Org Lett 2018; 20:1114-1117. [DOI: 10.1021/acs.orglett.8b00035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ngiap-Kie Lim
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Theresa Cravillion
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Scott Savage
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Andrew McClory
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Chong Han
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Haiming Zhang
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Antonio DiPasquale
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process
Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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5
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Zafar A, Ahmad S, Naseem I. Insight into the structural stability of coumestrol with human estrogen receptor α and β subtypes: a combined approach involving docking and molecular dynamics simulation studies. RSC Adv 2015. [DOI: 10.1039/c5ra14745j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structural stability of coumestrol with human estrogen receptor α and β subtypes.
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Affiliation(s)
- Atif Zafar
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Sabahuddin Ahmad
- Department of Computer Science
- Faculty of Natural Sciences
- New Delhi 110025
- India
| | - Imrana Naseem
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh 202002
- India
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6
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Gu WG, Liu BN, Yuan JF. Virtual-screening targeting Human Immunodeficiency Virus type 1 integrase-lens epithelium-derived growth factor/p75 interaction for drug development. J Drug Target 2014; 23:134-9. [DOI: 10.3109/1061186x.2014.959020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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7
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Ng HW, Perkins R, Tong W, Hong H. Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:8709-42. [PMID: 25162709 PMCID: PMC4198987 DOI: 10.3390/ijerph110908709] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/20/2022]
Abstract
The estrogen receptors (ERs) are a group of versatile receptors. They regulate an enormity of processes starting in early life and continuing through sexual reproduction, development, and end of life. This review provides a background and structural perspective for the ERs as part of the nuclear receptor superfamily and discusses the ER versatility and promiscuity. The wide repertoire of ER actions is mediated mostly through ligand-activated transcription factors and many DNA response elements in most tissues and organs. Their versatility, however, comes with the drawback of promiscuous interactions with structurally diverse exogenous chemicals with potential for a wide range of adverse health outcomes. Even when interacting with endogenous hormones, ER actions can have adverse effects in disease progression. Finally, how nature controls ER specificity and how the subtle differences in receptor subtypes are exploited in pharmaceutical design to achieve binding specificity and subtype selectivity for desired biological response are discussed. The intent of this review is to complement the large body of literature with emphasis on most recent developments in selective ER ligands.
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Affiliation(s)
- Hui Wen Ng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Roger Perkins
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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8
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Adler S, Basketter D, Creton S, Pelkonen O, van Benthem J, Zuang V, Andersen KE, Angers-Loustau A, Aptula A, Bal-Price A, Benfenati E, Bernauer U, Bessems J, Bois FY, Boobis A, Brandon E, Bremer S, Broschard T, Casati S, Coecke S, Corvi R, Cronin M, Daston G, Dekant W, Felter S, Grignard E, Gundert-Remy U, Heinonen T, Kimber I, Kleinjans J, Komulainen H, Kreiling R, Kreysa J, Leite SB, Loizou G, Maxwell G, Mazzatorta P, Munn S, Pfuhler S, Phrakonkham P, Piersma A, Poth A, Prieto P, Repetto G, Rogiers V, Schoeters G, Schwarz M, Serafimova R, Tähti H, Testai E, van Delft J, van Loveren H, Vinken M, Worth A, Zaldivar JM. Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010. Arch Toxicol 2011; 85:367-485. [PMID: 21533817 DOI: 10.1007/s00204-011-0693-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 03/03/2011] [Indexed: 01/09/2023]
Abstract
The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.
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Affiliation(s)
- Sarah Adler
- Centre for Documentation and Evaluation of Alternatives to Animal Experiments (ZEBET), Federal Institute for Risk Assessment (BfR), Berlin, Germany
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9
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Probing the structural requirements of A-type Aurora kinase inhibitors using 3D-QSAR and molecular docking analysis. J Mol Model 2011; 18:1107-22. [DOI: 10.1007/s00894-011-1042-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/14/2011] [Indexed: 02/02/2023]
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10
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Xu X, Yang W, Wang X, Li Y, Wang Y, Ai C. Dynamic communication between androgen and coactivator: Mutually induced conformational perturbations in androgen receptor ligand-binding domain. Proteins 2011; 79:1154-71. [DOI: 10.1002/prot.22951] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/09/2010] [Accepted: 11/16/2010] [Indexed: 11/10/2022]
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11
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Yan Y, Li Y, Zhang S, Ai C. Studies of tricyclic piperazine/piperidine furnished molecules as novel integrin αvβ3/αIIbβ3 dual antagonists using 3D-QSAR and molecular docking. J Mol Graph Model 2011; 29:747-62. [PMID: 21273104 DOI: 10.1016/j.jmgm.2010.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 12/10/2010] [Accepted: 12/20/2010] [Indexed: 10/18/2022]
Abstract
The development of injectable integrin α(v)β(3)/α(IIb)β(3) dual antagonists attracts much attention of research for treating of acute ischemic diseases in recent years. In this work, based on a dataset composed of 102 tricyclic piperazine/piperidine furnished dual α(v)β(3) and α(IIb)β(3) antagonists, a variety of in silico modeling approaches including the comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), and molecular docking were applied to reveal the requisite 3D structural features impacting the biological activities. Our statistical results show that the ligand-based 3D-QSAR models for both the α(v)β(3) and α(IIb)β(3) studies exhibited satisfactory internal and external predictability, i.e., for the CoMFA models, results of Q(2)=0.48, R(ncv)(2)=0.87, R(pred)(2)=0.71 for α(v)β(3) and Q(2)=0.50, R(ncv)(2)=0.85, R(pred)(2)=0.72 for α(IIb)β(3) analysis were obtained, and for the CoMSIA ones, the outcomes of Q(2)=0.55, R(ncv)(2)=0.90, R(pred)(2)=0.72 for α(v)β(3) and Q(2)=0.52, R(ncv)(2)=0.88, R(pred)(2)=0.74 for α(IIb)β(3) were achieved respectively. In addition, through a comparison between 3D-QSAR contour maps and docking results, it is revealed that that the most crucial interactions occurring between the tricyclic piperazine/piperidine derivatives and α(v)β(3)/α(IIb)β(3) receptor ligand binding pocket are H-bonding, and the key amino acids impacting the interactions are Arg214, Asn215, Ser123, and Lys253 for α(v)β(3), but Arg214, Asn215, Ser123 and Tyr190 for α(IIb)β(3) receptors, respectively. Halogen-containing groups at position 15 and 16, benzene sulfonamide substituent at position 23, and the replacement of piperazine with 4-aminopiperidine of ring B may increase the α(v)β(3)/α(IIb)β(3) antagonistic activity. The potencies for antagonists to inhibit isolated α(v)β(3) and α(IIb)β(3) are linear correlated, indicating that similar interaction mechanisms may exist for the series of molecules. To our best knowledge this is the first report on 3D-QSAR modeling of these dual α(v)β(3)/α(IIb)β(3) antagonists. The results obtained should provide information for better understanding of the mechanism of antagonism and thus be helpful in design of novel potent dual α(v)β(3)/α(IIb)β(3) antagonists.
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Affiliation(s)
- Yulian Yan
- School of Chemical Engineering, Dalian University of Technology, Dalian, 116012, Liaoning, China
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12
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3D-QSAR and molecular docking studies on derivatives of MK-0457, GSK1070916 and SNS-314 as inhibitors against Aurora B kinase. Int J Mol Sci 2010; 11:4326-47. [PMID: 21151441 PMCID: PMC3000085 DOI: 10.3390/ijms11114326] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 09/21/2010] [Accepted: 09/29/2010] [Indexed: 12/30/2022] Open
Abstract
Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q2 = 0.605, r2pred = 0.826), (q2 = 0.52, r2pred = 0.798) and (q2 = 0.582, r2pred = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors.
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13
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In silico prediction of estrogen receptor subtype binding affinity and selectivity using statistical methods and molecular docking with 2-arylnaphthalenes and 2-arylquinolines. Int J Mol Sci 2010; 11:3434-58. [PMID: 20957105 PMCID: PMC2956105 DOI: 10.3390/ijms11093434] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 08/23/2010] [Accepted: 08/27/2010] [Indexed: 11/24/2022] Open
Abstract
Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ERα and ERβ inhibitory activities was built, and quantitative structure-activity relationship (QSAR) methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR) and a nonlinear statistical method (Bayesian regularized neural network, BRNN) were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ERα and ERβ, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ERα: for MLR, Rtr2 = 0.72, Qte2 = 0.63; for PLSR, Rtr2 = 0.92, Qte2 = 0.84. ERβ: for MLR, Rtr2 = 0.75, Qte2 = 0.75; for PLSR, Rtr2 = 0.98, Qte2 = 0.80). The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in Rtr2 = 0.74 and Qte2 = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ERα and ERβ is more correlated with the atom fragment type, polarity, electronegativites and hydrophobicity. The substitutent in position 8 of the naphthalene or the quinoline plane and the space orientation of these two planes contribute the most to the subtype selectivity on the basis of similar hydrogen bond interactions between binding ligands and both ER subtypes. The QSAR models built together with the docking procedure should be of great advantage for screening and designing ER ligands with improved affinity and subtype selectivity property.
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