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Karampuri A, Perugu S. A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches. FRONTIERS IN BIOINFORMATICS 2024; 3:1328262. [PMID: 38288043 PMCID: PMC10822965 DOI: 10.3389/fbinf.2023.1328262] [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: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024] Open
Abstract
Breast cancer is the most prevalent and heterogeneous form of cancer affecting women worldwide. Various therapeutic strategies are in practice based on the extent of disease spread, such as surgery, chemotherapy, radiotherapy, and immunotherapy. Combinational therapy is another strategy that has proven to be effective in controlling cancer progression. Administration of Anchor drug, a well-established primary therapeutic agent with known efficacy for specific targets, with Library drug, a supplementary drug to enhance the efficacy of anchor drugs and broaden the therapeutic approach. Our work focused on harnessing regression-based Machine learning (ML) and deep learning (DL) algorithms to develop a structure-activity relationship between the molecular descriptors of drug pairs and their combined biological activity through a QSAR (Quantitative structure-activity relationship) model. 11 popularly known machine learning and deep learning algorithms were used to develop QSAR models. A total of 52 breast cancer cell lines, 25 anchor drugs, and 51 library drugs were considered in developing the QSAR model. It was observed that Deep Neural Networks (DNNs) achieved an impressive R2 (Coefficient of Determination) of 0.94, with an RMSE (Root Mean Square Error) value of 0.255, making it the most effective algorithm for developing a structure-activity relationship with strong generalization capabilities. In conclusion, applying combinational therapy alongside ML and DL techniques represents a promising approach to combating breast cancer.
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Affiliation(s)
| | - Shyam Perugu
- Department of Biotechnology, National Institute of Technology, Warangal, India
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Ali A, Ali A, Warsi MH, Rahman MA, Ahsan MJ, Azam F. An Insight into the Structural Requirements and Pharmacophore Identification of Carbonic Anhydrase Inhibitors to Combat Oxidative Stress at High Altitudes: An In-Silico Approach. Curr Issues Mol Biol 2022; 44:1027-1045. [PMID: 35723291 PMCID: PMC8947748 DOI: 10.3390/cimb44030068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023] Open
Abstract
Carbonic anhydrases (CA) inhibitory action could be linked to the treatment of a number of ailments, including cancer, osteoporosis, glaucoma, and several neurological problems. For the development of effective CA inhibitors, a variety of heterocyclic rings have been investigated. Furthermore, at high altitudes, oxygen pressure drops, resulting in the formation of reactive oxygen and nitrogen species, and CA inhibitors having role in combating this oxidative stress. Acetazolamide contains thiadiazole ring, which has aroused researchers’ interest because of its CA inhibitory action. In the present study, we used a number of drug design tools, such as pharmacophore modeling, 3D QSAR, docking, and virtual screening on twenty-seven 1,3,4-thiadiazole derivatives that have been described as potential CA inhibitors in the literature. An atom-based 3D-QSAR analysis was carried out to determine the contribution of individual atoms to model generation, while a pharmacophore mapping investigation was carried out to find the common unique pharmacophoric properties required for biological activity. The coefficient of determination for both the training and test sets were statistically significant in the generated model. The best QSAR model was chosen based on the values of R2 (0.8757) and Q2 (0.7888). A molecular docking study was also conducted against the most potent analogue 4m, which has the highest SP docking score (−5.217) (PDB ID: 6g3v). The virtual screening revealed a number of promising compounds. The screened compound ZINC77699643 interacted with the amino acid residues, Pro201 and Thr199, in the virtual screening study (PDB ID: 6g3v). These interactions demonstrated the significance of the CA inhibitory activity of the compound. Furthermore, ADME study revealed useful information regarding compound’s drug-like properties. Therefore, the findings of the present investigation could aid in the development of more potent CA inhibitors, which could benefit the treatment of oxidative stress at high altitudes.
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Affiliation(s)
- Amena Ali
- High Altitude Research Center, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence:
| | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Musarrat Husain Warsi
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (M.H.W.); (M.A.R.)
| | - Mohammad Akhlaquer Rahman
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (M.H.W.); (M.A.R.)
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Ambabari Circle, Jaipur 302 039, Rajasthan, India;
| | - Faizul Azam
- Department of Pharmaceutical Chemistry & Pharmacognosy, Unaizah College of Pharmacy, Qassim University, P.O. Box 5888, Unaizah 51911, Saudi Arabia;
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Balachandran S, Binitha RN. An in silico approach to study the interaction of BHA with selected steroid hormone receptors and investigating it's agonistic and antagonistic properties. In Silico Pharmacol 2021; 9:16. [PMID: 33520595 DOI: 10.1007/s40203-020-00070-x] [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: 06/23/2020] [Accepted: 12/18/2020] [Indexed: 11/29/2022] Open
Abstract
Antioxidant food additives were routinely used for increasing the keeping quality of packaged food items. Butylated Hydroxyanisole (BHA) is one of the most widely used synthetic phenolic antioxidants of such kind. Although quantity of antioxidants in packaged eatables and admissible daily intake (ADI) per person per day are limited by laws, the urbanisation and changes in lifestyle has cross these limits. Although studies on BHA has been carried out, there exists a great deal of uncertainty about the exact molecular mechanism of interaction of BHA with various receptors in the body. Since earlier reports suggested BHA plausibly interferes with reproductive system development, we opted docking of critical receptors of endogenous hormones controlling growth and development of reproductive system with BHA. Nuclear receptors of estrogen (ER), androgen (AR) and progesterone (PR) were selected for this purpose. This manuscript describes the comparison of binding pattern of BHA towards AR, ER and PR along with their agonists and antagonist. Lamarckian Genetic Algorithm of AutoDock 4.0 was used for analysing the mode of binding of ligands with the receptors. It is evident form the docking studies that, BHA exhibited similar binding pattern` with antagonists of AR and agonists of ER. But the interaction of BHA with PR was not compatible with either agonists or antagonists. The docking patterns produced could reliably demonstrate the interactions of BHA with selected receptors and also predict its possible agonistic and antagonistic action.
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Affiliation(s)
- Subin Balachandran
- Department of Zoology, Sacred Heart College, Thevara, Kochi-13, Kerala India
| | - R N Binitha
- Department of Zoology, Mar Athanasius College, Kothamangalam, Ernakulam, Kerala 686666 India
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular docking, 3D-QSAR, molecular dynamics, synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors. J Recept Signal Transduct Res 2019; 38:462-474. [PMID: 31038024 DOI: 10.1080/10799893.2019.1585453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3 D quantitative structure-activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.
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Affiliation(s)
- Ramesh Itteboina
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Srilata Ballu
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Sree Kanth Sivan
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Vijjulatha Manga
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
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Al-Sha'er MA, Al-Aqtash RA, Taha MO. Discovery of New Phosphoinositide 3-kinase Delta (PI3Kδ) Inhibitors via Virtual Screening using Crystallography-derived Pharmacophore Modelling and QSAR Analysis. Med Chem 2019; 15:588-601. [PMID: 30799792 DOI: 10.2174/1573406415666190222125333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND PI3Kδ is predominantly expressed in hematopoietic cells and participates in the activation of leukocytes. PI3Kδ inhibition is a promising approach for treating inflammatory diseases and leukocyte malignancies. Accordingly, we decided to model PI3Kδ binding. METHODS Seventeen PI3Kδ crystallographic complexes were used to extract 94 pharmacophore models. QSAR modelling was subsequently used to select the superior pharmacophore(s) that best explain bioactivity variation within a list of 79 diverse inhibitors (i.e., upon combination with other physicochemical descriptors). RESULTS The best QSAR model (r2 = 0.71, r2 LOO = 0.70, r2 press against external testing list of 15 compounds = 0.80) included a single crystallographic pharmacophore of optimal explanatory qualities. The resulting pharmacophore and QSAR model were used to screen the National Cancer Institute (NCI) database for new PI3Kδ inhibitors. Two hits showed low micromolar IC50 values. CONCLUSION Crystallography-based pharmacophores were successfully combined with QSAR analysis for the identification of novel PI3Kδ inhibitors.
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Affiliation(s)
- Mahmoud A Al-Sha'er
- Faculty of Pharmacy, Zarqa University, P.O. Box 132222, Zarqa, 13132, Jordan
| | - Rua'a A Al-Aqtash
- Faculty of Pharmacy, Zarqa University, P.O. Box 132222, Zarqa, 13132, Jordan
| | - Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
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The role of LasR active site amino acids in the interaction with the Acyl Homoserine Lactones (AHLs) analogues: A computational study. J Mol Graph Model 2018; 86:113-124. [PMID: 30352386 DOI: 10.1016/j.jmgm.2018.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/14/2018] [Accepted: 10/13/2018] [Indexed: 01/29/2023]
Abstract
The present work combines molecular docking calculations, 3D-QSAR, molecular dynamics simulations and free binding energy calculations (MM/PBSA and MM/GBSA) in a set of 28 structural analogues of acyl homoserine lactones with Quorum Sensing antagonist activity. The aim of this work is to understand how ligand binds and is affected by the molecular microenvironment in the active site of the LasR receptor for pseudomonas aeruginosa. We also study the stability of the interaction to find key structural characteristics that explain the antagonist activities of this set of ligands. This information is relevant for the rational modification or design of molecules and their identification as powerful LasR modulators. The analysis of molecular docking simulations shows that the 28 analogues have a similar binding mode compared to the native ligand. The carbonyl groups belonging to the lactone ring and the amide group of the acyl chain are oriented towards the amino acids forming hydrogen bond like interactions. The difference in antagonist activity is due to location and orientation of the LasR side chains within the hydrophobic pocket in its binding site. Additionally, we carried out molecular dynamics simulations to understand the conformational changes in the ligand-receptor interaction and the stability of each complex. Results show a direct relationship among the interaction energies of the ligands and the activities as an antagonist of the LasR receptor.
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Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct Res 2018; 38:61-70. [DOI: 10.1080/10799893.2018.1426607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Srilata Ballu
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Ramesh Itteboina
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Lima Costa AH, Clemente WS, Bezerra KS, Lima Neto JX, Albuquerque EL, Fulco UL. Computational biochemical investigation of the binding energy interactions between an estrogen receptor and its agonists. NEW J CHEM 2018. [DOI: 10.1039/c8nj03521k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present the energy profiles of estrogen receptor–agonist ligand interactions in atomic detail using a quantum biochemical approach.
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Affiliation(s)
- Aranthya H. Lima Costa
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Washington S. Clemente
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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9
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular modeling-driven approach for identification of Janus kinase 1 inhibitors through 3D-QSAR, docking and molecular dynamics simulations. J Recept Signal Transduct Res 2017; 37:453-469. [DOI: 10.1080/10799893.2017.1328442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ramesh Itteboina
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Srilata Ballu
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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10
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular docking, 3D QSAR and dynamics simulation studies of imidazo-pyrrolopyridines as janus kinase 1 (JAK 1) inhibitors. Comput Biol Chem 2016; 64:33-46. [DOI: 10.1016/j.compbiolchem.2016.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/16/2016] [Accepted: 04/26/2016] [Indexed: 01/30/2023]
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Niinivehmas SP, Manivannan E, Rauhamäki S, Huuskonen J, Pentikäinen OT. Identification of estrogen receptor α ligands with virtual screening techniques. J Mol Graph Model 2016; 64:30-39. [PMID: 26774287 DOI: 10.1016/j.jmgm.2015.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/16/2022]
Abstract
Utilization of computer-aided molecular discovery methods in virtual screening (VS) is a cost-effective approach to identify novel bioactive small molecules. Unfortunately, no universal VS strategy can guarantee high hit rates for all biological targets, but each target requires distinct, fine-tuned solutions. Here, we have studied in retrospective manner the effectiveness and usefulness of common pharmacophore hypothesis, molecular docking and negative image-based screening as potential VS tools for a widely applied drug discovery target, estrogen receptor α (ERα). The comparison of the methods helps to demonstrate the differences in their ability to identify active molecules. For example, structure-based methods identified an already known active ligand from the widely-used bechmarking decoy molecule set. Although prospective VS against one commercially available database with around 100,000 drug-like molecules did not retrieve many testworthy hits, one novel hit molecule with pIC50 value of 6.6, was identified. Furthermore, our small in-house compound collection of easy-to-synthesize molecules was virtually screened against ERα, yielding to five hit candidates, which were found to be active in vitro having pIC50 values from 5.5 to 6.5.
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Affiliation(s)
- Sanna P Niinivehmas
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Finland
| | - Elangovan Manivannan
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Finland; School of Pharmacy, Devi Ahilya University, Indore 452001, Madhya Pradesh, India
| | - Sanna Rauhamäki
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Finland
| | - Juhani Huuskonen
- Department of Chemistry & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Finland
| | - Olli T Pentikäinen
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Finland.
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Substrate-Binding Site of Family 11 Xylanase fromBacillus firmusK-1 by Molecular Docking. Biosci Biotechnol Biochem 2014; 73:833-9. [DOI: 10.1271/bbb.80731] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pires DEV, de Melo-Minardi RC, da Silveira CH, Campos FF, Meira W. aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. ACTA ACUST UNITED AC 2013; 29:855-61. [PMID: 23396119 DOI: 10.1093/bioinformatics/btt058] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design. RESULTS We propose a novel graph-based-binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor's techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario. AVAILABILITY AND IMPLEMENTATION Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Douglas E V Pires
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, Brazil.
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Figueroa-Valverde L, Díaz-Cedillo F, López-Ramos M, Garcia-Cervera E, Rivero-Rosado V. Synthesis and theoretical QSAR study of a naphthalene–androsterone derivative. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wang JH, Hou QQ, Tang K, Cheng XL, Dong LH, Liu YJ, Liu CB. Receptor-based QSAR study for a series of 3,3-disubstituted-5-aryl oxindoles and 6-aryl benzimidazol-2-ones derivatives as progesterone receptor inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:775-799. [PMID: 22004567 DOI: 10.1080/1062936x.2011.623324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Receptor-based comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of 54 progesterone receptor (PR) inhibitors. The established CoMFA model from the training set gives statistically significant results with the cross-validated q (2) of 0.534 and non-cross-validated [Formula: see text] of 0.947. The best CoMSIA model was derived by the combination of steric field and hydrophobic field with a q (2) of 0.615 and [Formula: see text] of 0.954. A test set of 18 compounds was used to validate the predictive ability of the two models. The predicted correlation coefficients [Formula: see text] are 0.681 and 0.677 for CoMFA and CoMSIA models, respectively. Based on the CoMFA maps, the key structural characters of progesterone receptor inhibitors are identified. Moreover, the binding modes of oxindoles and benzimidazol-2-ones are also given by the quantum mechanical/molecular mechanical (QM/MM) calculations. This may provide useful information for drug design.
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Affiliation(s)
- J H Wang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
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Graham LA, Shaw IC. Does the oestrogen receptor encourage oestrogenicity in environmental pollutants? The case of 4-nonylphenol. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:329-350. [PMID: 21598197 DOI: 10.1080/1062936x.2011.569899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A computer-aided docking study was conducted to explore in detail the binding interactions between the structurally unlikely environmental oestrogen 4-nonylphenol (4NP) and three of its metabolites with the human oestrogen receptor alpha (hERα). Docking was done within the Schrodinger Suite 2008 using both a conventional rigid receptor with flexible ligand and the induced-fit docking protocol. Induced-fit docking allows side-chain and backbone movement in the receptor to accommodate the ligand. This study has revealed unconventional interactions between the ligands and the hERα binding pocket that could explain the observed oestrogen-like behaviour of 4NP and suggests some of the metabolites of 4NP may also be oestrogenic.
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Affiliation(s)
- L A Graham
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Structure-based quantitative structure–activity relationship modeling of estrogen receptor β-ligands. Future Med Chem 2011; 3:933-45. [DOI: 10.4155/fmc.11.49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: A variety of chemotypes have been studied as estrogen receptor (ER) β-selective ligands for potential drugs against various indications, including neurodegenerative diseases. Their structure–activity relationship data and the x-ray structures of the ERβ ligand-binding domain bound with different ligands have become available. Thus, it is vitally important for future development of ERβ-selective ligands that robust quantitative structure–activity relationship (QSAR) models be built. Methods/results: We employed a newly developed structure-based QSAR method (structure-based pharmacophore keys QSAR) that utilizes both the structure–activity relationship data and the 3D structural information of ERβ, as well as a robust QSAR workflow to analyze 37 ligands. Four sets of QSAR models were obtained, among which approximately 30 models afforded high (>0.60) training-r2 and test set-R2 statistics. Conclusion: We have obtained an ensemble of predictive models of ERβ ligands that will be useful in the future discovery of novel ERβ-selective molecules.
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Gao J, Cheng Y, Cui W, Chen Q, Zhang F, Du Y, Ji M. 3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9672-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Sivan SK, Manga V. Multiple receptor conformation docking and dock pose clustering as tool for CoMFA and CoMSIA analysis - a case study on HIV-1 protease inhibitors. J Mol Model 2011; 18:569-82. [PMID: 21547550 DOI: 10.1007/s00894-011-1048-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 03/18/2011] [Indexed: 11/25/2022]
Abstract
Multiple receptors conformation docking (MRCD) and clustering of dock poses allows seamless incorporation of receptor binding conformation of the molecules on wide range of ligands with varied structural scaffold. The accuracy of the approach was tested on a set of 120 cyclic urea molecules having HIV-1 protease inhibitory activity using 12 high resolution X-ray crystal structures and one NMR resolved conformation of HIV-1 protease extracted from protein data bank. A cross validation was performed on 25 non-cyclic urea HIV-1 protease inhibitor having varied structures. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were generated using 60 molecules in the training set by applying leave one out cross validation method, r (loo) (2) values of 0.598 and 0.674 for CoMFA and CoMSIA respectively and non-cross validated regression coefficient r(2) values of 0.983 and 0.985 were obtained for CoMFA and CoMSIA respectively. The predictive ability of these models was determined using a test set of 60 cyclic urea molecules that gave predictive correlation (r (pred) (2) ) of 0.684 and 0.64 respectively for CoMFA and CoMSIA indicating good internal predictive ability. Based on this information 25 non-cyclic urea molecules were taken as a test set to check the external predictive ability of these models. This gave remarkable out come with r (pred) (2) of 0.61 and 0.53 for CoMFA and CoMSIA respectively. The results invariably show that this method is useful for performing 3D QSAR analysis on molecules having different structural motifs.
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Affiliation(s)
- Sree Kanth Sivan
- Department of Chemistry, Nizam College, Osmania University, Hyderabad 500001, India
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Sadeghian H, Seyedi SM, Attaran N, Jabbari A, Jafari Z. Synthesis and SAR comparative studies of 2-allyl-4-methoxy-1-alkoxybenzenes as 15-lipoxygenase inhibitors. J Enzyme Inhib Med Chem 2011; 26:238-44. [PMID: 20939767 DOI: 10.3109/14756366.2010.495717] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A group of 2-alkoxy-5-methoxyallylbenzene were designed, synthesised and evaluated as potential inhibitors of the soybean 15-lipoxygenase (SLO) on the basis of the eugenol and esteragol structures. Compound 4d showed the best half maximal inhibitory concentration (IC₅₀) for SLO inhibition (IC₅₀ = 5.9 ± 0.6 µM). All the compounds were docked in the SLO active site retrieved from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB entry: 1IK3) and showed that the allyl group of the synthetic compounds similar to the linoleic acid double bond, were oriented toward the Fe³+-OH moiety in the active site of the enzyme and this conformation was especially fixed by the hydrophobic interaction of the 2-alkoxy group with Leu⁵¹⁵, Trp⁵¹⁹, Val⁵⁶⁶ and Ile⁵⁷². It was concluded that the molecular volume and shape of the alkoxy moiety was a major factor in the inhibitory potency variation of the synthetic compounds.
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Affiliation(s)
- Hamid Sadeghian
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, IR Iran
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21
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Yi P, Di YT, Liu W, Hao XJ, Ming Y, Huang DS, Yang J, Yi ZZ, Li ZJ, Yang RD, Zhang JC. Protein-based alignment in 3D-QSAR of FBPase inhibitors. Eur J Med Chem 2011; 46:885-92. [DOI: 10.1016/j.ejmech.2010.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/07/2010] [Accepted: 12/31/2010] [Indexed: 10/18/2022]
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22
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Wang J, Tang K, Hou Q, Cheng X, Dong L, Liu Y, Liu C. 3D-QSAR Studies on C24-Monoalkylated Vitamin D3 26,23-Lactones and their C2α-Modified Derivatives with Inhibitory Activity to Vitamin D Receptor. Mol Inform 2010; 29:621-32. [PMID: 27463456 DOI: 10.1002/minf.201000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 09/03/2010] [Indexed: 11/09/2022]
Abstract
The ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) for 82 inhibitors of 25-dehydro-1α-hydroxyvitamin D3 -26,23-lactone analogs has been studied by using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models. The established CoMFA model in training set gives a cross-validated q(2) value of 0.516 and a non-cross-validated rncv (2) value of 0.667, while the CoMSIA model results in q(2) =0.517 and rncv (2) =0.632. In general, the predictive ability of the CoMFA model is superior to that of the CoMSIA model, with rpred (2) =0.639 for the CoMFA and rpred (2) =0.619 for the CoMSIA model. Based on the CoMFA contour maps, some key structural characters of vitamin D3 analogs responsible for inhibitory activity are identified, and some new C2α-modified 24-alkylvitamin D3 lactone analogs with high predicted pIC50 values are designed. The ligand functional group mutations by FEP simulation and docking studies reveal the rationality of the molecular design.
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Affiliation(s)
- Jinhu Wang
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464
| | - Ke Tang
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464
| | - Qianqian Hou
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464
| | - Xueli Cheng
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464
| | - Lihua Dong
- School of Chemistry and Chemical Engineering, Taishan Medical University, Taian, Shandong 271000, P. R. China
| | - Yongjun Liu
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464.
| | - Chengbu Liu
- Key Lab of Collid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China telephone: +86-531-88365576, fax: +86-531-88564464
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Sadeghian H, Seyedi SM, Saberi MR, Nick RS, Hosseini A, Bakavoli M, Mansouri SMT, Parsaee H. Design, synthesis and pharmacological evaluation of 6-hydroxy-4-methylquinolin-2(1H)-one derivatives as inotropic agents. J Enzyme Inhib Med Chem 2010; 24:918-29. [PMID: 19555170 DOI: 10.1080/14756360802448063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Selective PDE3 inhibitors improve cardiac contractility and may be used in congestive heart failure. However, their proarrhythmic potential is the most important side effect. In this research we designed, synthesized and evaluated the potential cardiotonic activity of thirteen PDE3 inhibitors (4-[(4-methyl-2-oxo-1,2-dihydro-6-quinolinyl)oxy]butanamide analogs) using the spontaneously beating atria model. The design strategy was based on the structure of cilostamide, a selective PDE3 inhibitor. In each experiment, atrium of reserpine-treated rat was isolated and the contractile and chronotropic effects of a synthetic compounds were assessed. All experiments were carried out in comparison with IBMX, amrinone and cilostamide as standard compounds. The results showed that, among the new compounds, the best pharmacological profile was obtained with the compound 6-[4-(4-methylpiperazine-1-yl)-4-oxobutoxy]-4-methylquinolin-2(1H)-one, 4j, which displayed selectivity for increasing the force of contraction (165 +/- 4% change over the control) rather than the frequency rate (115 +/- 7% change over the control) at 100 microM and potent inhibitory activity of PDE3 with IC(50) = 0.20 microM.
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Affiliation(s)
- Hamid Sadeghian
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, IR Iran
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24
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Nikpour M, Sadeghian H, Saberi MR, Nick RS, Seyedi SM, Hosseini A, Parsaee H, Bozorg ATD. Design, synthesis and biological evaluation of 6-(benzyloxy)-4-methylquinolin-2(1H)-one derivatives as PDE3 inhibitors. Bioorg Med Chem 2010; 18:855-62. [DOI: 10.1016/j.bmc.2009.11.044] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 11/19/2009] [Accepted: 11/20/2009] [Indexed: 11/28/2022]
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25
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Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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Costanzi S, Tikhonova IG, Harden TK, Jacobson KA. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands. J Comput Aided Mol Des 2009; 23:747-54. [PMID: 18483766 PMCID: PMC2789990 DOI: 10.1007/s10822-008-9218-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 04/22/2008] [Indexed: 11/24/2022]
Abstract
Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.
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Affiliation(s)
- Stefano Costanzi
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Sadeghian H, Sadeghian A, Pordel M, Rahimizadeh M, Jahandari P, Orafaie A, Bakavoli M. Design, synthesis, and structure–activity relationship study of 5-amido-1-(2,4-dinitrophenyl)-1H-4-pyrazolecarbonitrils as DD-carboxypeptidase/penicillin-binding protein inhibitors with Gram-positive antibacterial activity. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9175-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Jyrkkärinne J, Windshügel B, Rönkkö T, Tervo AJ, Küblbeck J, Lahtela-Kakkonen M, Sippl W, Poso A, Honkakoski P. Insights into ligand-elicited activation of human constitutive androstane receptor based on novel agonists and three-dimensional quantitative structure-activity relationship. J Med Chem 2009; 51:7181-92. [PMID: 18983136 DOI: 10.1021/jm800731b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The human constitutive androstane receptor (CAR, NR1I3) is an important regulator of xenobiotic metabolism and other physiological processes. So far, only few CAR agonists are known and no explicit mechanism has been proposed for their action. Thus, we aimed to generate a 3D QSAR model that could explain the molecular determinants of CAR agonist action. To obtain a sufficient number of agonists that cover a wide range of activity, we applied a virtual screening approach using both structure- and ligand-based methods. We identified 27 novel human CAR agonists on which a 3D QSAR model was generated. The model, complemented by coregulator recruitment and mutagenesis results, suggests a potential activation mechanism for human CAR and may serve to predict potential activation of CAR for compounds emerging from drug development projects or for chemicals undergoing toxicological risk assessment.
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Affiliation(s)
- Johanna Jyrkkärinne
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
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29
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Celik L, Davey J, Lund D, Schiøtt B. Exploring interactions of endocrine-disrupting compounds with different conformations of the human estrogen receptor alpha ligand binding domain: a molecular docking study. Chem Res Toxicol 2009; 21:2195-206. [PMID: 18921983 DOI: 10.1021/tx800278d] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Endocrine-disrupting compounds (EDCs) accumulating in nature are known to interact with nuclear receptors. Especially important is the human estrogen receptor alpha (hERalpha), and several EDCs are either known or suspected to influence the activity of the ligand-binding domain (LBD). We here present a comparative docking study of both well-known hERalpha ligands and small organic compounds, including selected polychlorinated biphenyls (PCBs), plasticizers, and pesticides, that are all potentially endocrine-disrupting,into different conformations of the hERalpha LBD. Three newly found quasi-stable structures of the hERalhpa LBD are examined along with three crystallographic conformations of the protein, either theapo structure or using a protein structure with a bound agonist or antagonist ligand. The possible interactions between the protein and the potentially EDCs are described. It is found that most suspected EDCs can bind in the steroid binding cavity, interacting with at least one of the two hydrophilic ends of the steroid binding site. DDE, DDT, and HPTE are predicted to bind most strongly to the hERalpha LBD. It is predicted that these compounds can interact with the three conformations of hERalpha LBD with comparable affinities.The metabolic hydroxylation of aromatic compounds is found to lead to an increase in the binding affinity of PCBs as well as DDT. Docking into the quasi-stable conformations of the hERalpha LBD leads to computed binding affinities similar to or better than those calculated for the three X-ray structures, revealing that the new structures may be of importance for assessing the function of the influence of EDCs on nuclear receptors.
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Affiliation(s)
- Leyla Celik
- iNANO and inSPIN Centers, Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark
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30
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Sadeghian H, Attaran N, Jafari Z, Saberi MR, Seyedi SM, Eshghi H, Pordel M, Riazi MM. Design and synthesis of 4-methoxyphenylacetic acid esters as 15-lipoxygenase inhibitors and SAR comparative studies of them. Bioorg Med Chem 2009; 17:2327-35. [PMID: 19251422 DOI: 10.1016/j.bmc.2009.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 01/18/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022]
Abstract
A group of 4-methoxyphenylacetic acid esters were designed, synthesized and evaluated as potential inhibitors of soybean 15-lipoxygenase (SLO) on the basis of eugenol and esteragol structures. Compounds 7d-e showed the best IC(50) in SLO inhibition (IC(50)=3.8 and 1.9 microM, respectively). All compounds were docked in SLO active site and showed that carbonyl group of compounds is oriented toward the Fe(III)-OH moiety in the active site of enzyme and fixed by hydrogen bonding with hydroxyl group. It is assumed that lipophilic interaction of ligand-enzyme would be in charge of inhibiting the enzyme activity. The selectivity of the synthetic esters in inhibiting of 15-HLOb was also compared with 15-HLOa by molecular modeling and multiple alignment techniques.
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Affiliation(s)
- Hamid Sadeghian
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad 91389-13131, Iran.
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31
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Seyedi SM, Jafari Z, Attaran N, Sadeghian H, Saberi MR, Riazi MM. Design, synthesis and SAR studies of 4-allyoxyaniline amides as potent 15-lipoxygensae inhibitors. Bioorg Med Chem 2009; 17:1614-22. [DOI: 10.1016/j.bmc.2008.12.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 12/26/2008] [Accepted: 12/30/2008] [Indexed: 10/21/2022]
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32
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Agatonovic-Kustrin S, Turner J, Glass B. Molecular structural characteristics as determinants of estrogen receptor selectivity. J Pharm Biomed Anal 2008; 48:369-75. [DOI: 10.1016/j.jpba.2008.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 04/07/2008] [Accepted: 04/07/2008] [Indexed: 12/01/2022]
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33
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Development of predictive in silico model for cyclosporine- and aureobasidin-based P-glycoprotein inhibitors employing receptor surface analysis. J Mol Graph Model 2008; 27:439-51. [PMID: 18789739 DOI: 10.1016/j.jmgm.2008.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/21/2022]
Abstract
P-glycoprotein (Pgp) is implicated in multiple drug resistance (MDR) exhibited by several types of cancer against a multitude of anticancer chemotherapeutic agents. This problem prompted several research groups to search for effective P-gp inhibitors. Cyclosporine A (CsA), aureobasidin A (AbA) and related analogues were reported to possess potent inhibitory actions against Pgp. In this work we employed receptor surface analysis (RSA) to construct two satisfactory receptor surface models (RSMs) for cyclosporine- and aureobasidin-based Pgp inhibitors. These pseudoreceptors were combined to achieve satisfactory three-dimensional quantitative structure activity relationship (3D-QSAR) for 68 different cyclosporine and aureobasidin derivatives. Upon validation against an external set of 16 randomly selected Pgp inhibitors, the optimal 3D-QSAR was found to be self-consistent and predictive (r(LOO)(2)=0.673, r(PRESS)(2)=0.600). The resulting 3D-QSAR was employed to probe the structural factors that control the inhibitory activities of cyclosporine and aureobasidin analogues against Pgp.
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34
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Pharmacophore search for anti-fertility and estrogenic potencies of estrogen analogs. J Mol Model 2008; 14:1071-82. [DOI: 10.1007/s00894-008-0338-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
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35
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Knox AJS, Yang Y, Lloyd DG, Meegan MJ. Virtual screening of the estrogen receptor. Expert Opin Drug Discov 2008; 3:853-66. [DOI: 10.1517/17460441.3.8.853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Andrew JS Knox
- Postdoctoral Research Fellow School of Biochemistry and Immunology, Molecular Design Group, Trinity College Dublin, Ireland ;
| | - Yidong Yang
- PhD Candidate School of Biochemistry and Immunology, Molecular Design Group, Trinity College Dublin, Ireland
| | - David G Lloyd
- Hitachi Senior Lecturer in Advanced Computing School of Biochemistry and Immunology, Molecular Design Group, Trinity College Dublin, Ireland
| | - Mary J Meegan
- Associate Professor School of Pharmacy and Pharmaceutical Sciences, Centre for Synthesis and Chemical Biology, Trinity College Dublin, Ireland
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36
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Bakavoli M, Sadeghian H, Tabatabaei Z, Rezaei E, Rahimizadeh M, Nikpour M. SAR comparative studies on pyrimido[4,5-b][1,4] benzothiazine derivatives as 15-lipoxygenase inhibitors, using ab initio calculations. J Mol Model 2008; 14:471-8. [PMID: 18425541 DOI: 10.1007/s00894-008-0298-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
Abstract
The enzyme inhibitory activity of a new group of 2-substituted pyrimido[4,5-b][1,4]benzothiazines on soybean 15-lipoxygenase (15-LO) was evaluated and compared with those of their 4-methyl analogs using ab initio calculations. The results of these studies showed that the lack of 4-methyl substituent in the pyrimido[4,5-b][1,4] benzothiazine molecules greatly reduces their 15-LO inhibitory activities.
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Affiliation(s)
- Mehdi Bakavoli
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad 91775-1436, Iran.
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37
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Receptor guided 3D-QSAR: a useful approach for designing of IGF-1R inhibitors. J Biomed Biotechnol 2008; 2008:837653. [PMID: 18385815 PMCID: PMC2276912 DOI: 10.1155/2008/837653] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 12/17/2007] [Indexed: 01/03/2023] Open
Abstract
Research by other investigators has established that insulin-like growth factor‐1 receptor (IGF-1R) is a key oncological target, and that derivatives of 1, 3-disubstituted-imidazo[1,5-α] pyrazine are potent IGF-1R inhibitors. In this paper, we report on our three-dimensional quantitative structure activity relationship (3D-QSAR) studies for this series of compounds. We validated the 3D-QSAR models by the comparison of two major alignment schemes, namely, ligand-based (LB) and receptor-guided (RG) alignment schemes. The latter scheme yielded better 3D-QSAR models for both comparative molecular field analysis (CoMFA) (q2 = 0.35, r2 = 0.95) and comparative molecular similarity indices analysis (CoMSIA) (q2 = 0.51, r2 = 0.86). We submit that this might arise from the more accurate inhibitor alignment that results from using the structural information of the active site. We conclude that the receptor-guided 3D-QSAR may be helpful to design more potent IGF-1R inhibitors, as well as to understand their binding affinity with the receptor.
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38
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Fischer B, Fukuzawa K, Wenzel W. Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery. Proteins 2008; 70:1264-73. [PMID: 17876816 DOI: 10.1002/prot.21607] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The adaptation of forcefield-based scoring function to specific receptors remains an important challenge for in-silico drug discovery. Here we compare binding energies of forcefield-based scoring functions with models that are reparameterized on the basis of large-scale quantum calculations of the receptor. We compute binding energies of eleven ligands to the human estrogen receptor subtype alpha (ERalpha) and four ligands to the human retinoic acid receptor of isotype gamma (RARgamma). Using the FlexScreen all-atom receptor-ligand docking approach, we compare docking simulations parameterized by quantum-mechanical calculation of a large protein fragment with purely forcefield-based models. The use of receptor flexibility in the FlexScreen permits the treatment of all ligands in the same receptor model. We find a high correlation between the classical binding energy obtained in the docking simulation and quantum mechanical binding energies and a good correlation with experimental affinities R=0.81 for ERalpha and R=0.95 for RARgamma using the quantum derived scoring functions. A significant part of this improvement is retained, when only the receptor is treated with quantum-based parameters, while the ligands are parameterized with a purely classical model.
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Affiliation(s)
- Bernhard Fischer
- Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany
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39
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Murumkar PR, Giridhar R, Yadav MR. 3D-quantitative structure-activity relationship studies on benzothiadiazepine hydroxamates as inhibitors of tumor necrosis factor-alpha converting enzyme. Chem Biol Drug Des 2008; 71:363-73. [PMID: 18284555 DOI: 10.1111/j.1747-0285.2008.00639.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A set of 29 benzothiadiazepine hydroxamates having selective tumor necrosis factor-alpha converting enzyme inhibitory activity were used to compare the quality and predictive power of 3D-quantitative structure-activity relationship, comparative molecular field analysis, and comparative molecular similarity indices models for the atom-based, centroid/atom-based, data-based, and docked conformer-based alignment. Removal of two outliers from the initial training set of molecules improved the predictivity of models. Among the 3D-quantitative structure-activity relationship models developed using the above four alignments, the database alignment provided the optimal predictive comparative molecular field analysis model for the training set with cross-validated r(2) (q(2)) = 0.510, non-cross-validated r(2) = 0.972, standard error of estimates (s) = 0.098, and F = 215.44 and the optimal comparative molecular similarity indices model with cross-validated r(2) (q(2)) = 0.556, non-cross-validated r(2) = 0.946, standard error of estimates (s) = 0.163, and F = 99.785. These models also showed the best test set prediction for six compounds with predictive r(2) values of 0.460 and 0.535, respectively. The contour maps obtained from 3D-quantitative structure-activity relationship studies were appraised for activity trends for the molecules analyzed. The comparative molecular similarity indices models exhibited good external predictivity as compared with that of comparative molecular field analysis models. The data generated from the present study helped us to further design and report some novel and potent tumor necrosis factor-alpha converting enzyme inhibitors.
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Affiliation(s)
- Prashant R Murumkar
- Pharmacy Department, Faculty of Technology and Engineering, The M.S. University of Baroda, Vadodara 390001, Gujarat, India
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40
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San Juan AA. 3D-QSAR models on clinically relevant K103N mutant HIV-1 reverse transcriptase obtained from two strategic considerations. Bioorg Med Chem Lett 2008; 18:1181-94. [DOI: 10.1016/j.bmcl.2007.11.134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 11/02/2007] [Accepted: 11/30/2007] [Indexed: 10/22/2022]
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41
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Sadeghian H, Seyedi SM, Saberi MR, Arghiani Z, Riazi M. Design and synthesis of eugenol derivatives, as potent 15-lipoxygenase inhibitors. Bioorg Med Chem 2008; 16:890-901. [PMID: 17998164 DOI: 10.1016/j.bmc.2007.10.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 09/22/2007] [Accepted: 10/09/2007] [Indexed: 11/28/2022]
Abstract
A group of 4-allyl-2-methoxyphenol (eugenol) esters were designed, synthesized, and evaluated as potential inhibitors of soybean 15-lipoxygenase (SLO). Compounds 4c, 4d 4f, 4p, and 4q showed the best IC(50) in SLO inhibition (IC(50)=1.7, 2.3, 2.1, 2.2, and 0.017microM, respectively). All compounds were docked into SLO active site and showed that allyl group of compounds is oriented toward the iron atom in the active site of SLO. It is assumed that lipophilic interaction of ligand-enzyme would be in charge of inhibiting the enzyme activity. The selectivity of eugenol derivatives in inhibiting 15-HLOb was also compared with 15-HLOa by molecular modeling and multiple alignment techniques.
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Affiliation(s)
- Hamid Sadeghian
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad 91775-1436, Iran
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Roncaglioni A, Benfenati E. In silico-aided prediction of biological properties of chemicals: oestrogen receptor-mediated effects. Chem Soc Rev 2008; 37:441-50. [DOI: 10.1039/b616276m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Bichlmaier I, Finel M, Sippl W, Yli-Kauhaluoma J. Stereochemical and Steric Control of the UDP-Glucuronosyltransferase-Catalyzed Conjugation Reaction: A Rational Approach for the Design of Inhibitors for the Human UGT2B7. ChemMedChem 2007; 2:1730-40. [DOI: 10.1002/cmdc.200700122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Muthas D, Sabnis YA, Lundborg M, Karlén A. Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. J Mol Graph Model 2007; 26:1237-51. [PMID: 18203638 DOI: 10.1016/j.jmgm.2007.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 11/16/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
Abstract
We have investigated the influence of post-filtering virtual screening results, with pharmacophoric features generated from an X-ray structure, on enrichment rates. This was performed using three docking softwares, zdock+, Surflex and FRED, as virtual screening tools and pharmacophores generated in UNITY from co-crystallized complexes. Sets of known actives along with 9997 pharmaceutically relevant decoy compounds were docked against six chemically diverse protein targets namely CDK2, COX2, ERalpha, fXa, MMP3, and NA. To try to overcome the inherent limitations of the well-known docking problem, we generated multiple poses for each compound. The compounds were first ranked according to their scores alone and enrichment rates were calculated using only the top scoring pose of each compound. Subsequently, all poses for each compound were passed through the different pharmacophores generated from co-crystallized complexes and the enrichment factors were re-calculated based on the top-scoring passing pose of each compound. Post-filtering with a pharmacophore generated from only one X-ray complex was shown to increase enrichment rates in all investigated targets compared to docking alone. This indicates that this is a general method, which works for diverse targets and different docking softwares.
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Affiliation(s)
- Daniel Muthas
- Department of Medicinal Chemistry, Division of Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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Korhonen SP, Tuppurainen K, Asikainen A, Laatikainen R, Peräkylä M. SOMFA on Large Diverse Xenoestrogen Dataset: The Effect of Superposition Algorithms and External Regression Tools. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200610003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Dezi C, Brea J, Alvarado M, Raviña E, Masaguer CF, Loza MI, Sanz F, Pastor M. Multistructure 3D-QSAR studies on a series of conformationally constrained butyrophenones docked into a new homology model of the 5-HT2A receptor. J Med Chem 2007; 50:3242-55. [PMID: 17579386 DOI: 10.1021/jm070277a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study is part of a long-term research project aiming to gain insight into the mechanism of action of atypical antipsychotics. Here we describe a 3D-QSAR study carried out on a series of butyrophenones with affinity for the serotonin-2A receptor, aligned by docking into the binding site of a receptor model. The series studied has two peculiarities: (i) all the compounds have a chiral center and can be represented by two enantiomeric structures, and (ii) many of the structures can bind the receptor in two alternative orientations, posing the problem of how to select a single representative structure for every compound. We have used an original solution consisting of the simultaneous use of multiple structures, representing different configurations, binding conformations, and positions. The final model showed good statistical quality (n = 426, r2 = 0.84, q2LOO = 0.81) and its interpretation provided useful information, not obtainable from the simple inspection of the ligand-receptor complexes.
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Affiliation(s)
- Cristina Dezi
- Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
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Holder S, Lilly M, Brown ML. Comparative molecular field analysis of flavonoid inhibitors of the PIM-1 kinase. Bioorg Med Chem 2007; 15:6463-73. [PMID: 17637507 DOI: 10.1016/j.bmc.2007.06.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2006] [Revised: 05/23/2007] [Accepted: 06/12/2007] [Indexed: 12/31/2022]
Abstract
The PIM-1 protein, the product of the pim-1 oncogene, is a serine/threonine kinase. Dysregulation of the PIM-1 kinase has been implicated in the development of human malignancies including lymphomas, leukemias, and prostate cancer. Comparative molecular field analysis (CoMFA) is a 3-D QSAR technique that has been widely used, with notable success, to correlate biological activity with the steric and electrostatic properties of ligands. We have used a set of 15 flavonoid inhibitors of the PIM-1 kinase, aligned de novo by common substructure, to generate a CoMFA model for the purpose of elucidating the steric and electrostatic properties involved in flavonoid binding to the PIM-1 kinase. Partial least squares correlation between observed and predicted inhibitor potency (expressed as -logIC50), using a non-cross-validated partial least squares analysis, generated a non-cross-validated q2=0.805 for the training set (n=15) of flavonoids. The CoMFA generated steric map indicated that the PIM-1-binding site was sterically hindered, leading to more efficient binding of planar molecules over (R) or (S) compounds. The electrostatic map identified that positive charges near the flavonoid atom C8 and negative charges near C4' increased flavonoid binding. The CoMFA model accurately predicted the potency of a test set of flavonoids (n=6), generating a correlation between observed and predicted potency of q2=0.825. CoMFA models generated from additional alignment rules, which were guided by co-crystal structure ligand orientations, did not improve the correlative value of the model. Superimposing the PIM-1 kinase crystal structure onto the CoMFA contours validated the steric and electrostatic maps, elucidating the amino acid residues that potentially contribute to the CoMFA fields. Thus we have generated the first predictive model that may be used for the rational design of small-molecule inhibitors of the PIM-1 kinase.
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Affiliation(s)
- Sheldon Holder
- Center for Molecular Biology & Gene Therapy, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA
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Du L, Li M, You Q, Xia L. A novel structure-based virtual screening model for the hERG channel blockers. Biochem Biophys Res Commun 2007; 355:889-94. [PMID: 17331468 DOI: 10.1016/j.bbrc.2007.02.068] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 02/09/2007] [Indexed: 11/15/2022]
Abstract
The hERG potassium channel is a key effector of cardiac repolarization and the blockade of this channel could cause arrhythmia. Thus, hERG channel blockade plays an important role for the potential pro-arrhythmic liability. In this report, binding of blockers to the hERG potassium channel is investigated using a combination of homology modeling, molecular docking, and molecular simulations, where blockade activities are evaluated using the linear regression model of GoldScore fitness. This structure-based virtual screening model is able to estimate the pIC(50) value of a wide range of ligands for the hERG potassium channel. The docked poses for ligands are also consistent with published mutation. Therefore, this model for the prediction of hERG channel blockade has the potential to provide cost-effective virtual screening tools for the evaluation of the cardiac liability of new chemical entities.
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Affiliation(s)
- Lupei Du
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
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Abu Hammad AM, Afifi FU, Taha MO. Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions. J Mol Graph Model 2007; 26:443-56. [PMID: 17360207 DOI: 10.1016/j.jmgm.2007.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 02/05/2007] [Accepted: 02/06/2007] [Indexed: 11/15/2022]
Abstract
In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors.
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Affiliation(s)
- Areej M Abu Hammad
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Queen Rania Street, Amman 11942, Jordan
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Huang SY, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006; 27:1876-82. [PMID: 16983671 DOI: 10.1002/jcc.20505] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native-like binding modes under the criterion of rmsd < or = 2 A for each top-ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein-ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge-based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure-based drug design.
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Affiliation(s)
- Sheng-You Huang
- Department of Biochemistry, Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA
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