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Zarrinzadeh G, Tajbakhsh M, Hosseinzadeh R, Khalilzadeh MA, Hosseinzadeh M. Biological Evaluation and Molecular Docking Study of Euparin and Its Maleic Anhydride and Semicarbazide Derivatives. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2015405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ghazaleh Zarrinzadeh
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Mahmood Tajbakhsh
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Rahman Hosseinzadeh
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Mohammad A. Khalilzadeh
- Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
- Department of Chemistry, College of Natural Resources, North Carolina State University, Raleigh, NC, USA
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Mittal A, Arora R, Kakkar R. Pharmacophore modeling, 3D-QSAR and molecular docking studies of quinazolines and aminopyridines as selective inhibitors of inducible nitric oxide synthase. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies have been performed on a dataset of thirty-two quinazoline and aminopyridine derivatives to get an insight into the important structural features required for binding to inducible nitric oxide synthase (iNOS). A four-point CPH (Common Pharmacophore Hypothesis), AHPR.29, with a hydrogen bond acceptor, hydrophobic group, positively charged ionizable group and an aromatic ring, has been obtained as the best pharmacophore model. Satisfactory statistical parameters of correlation ([Formula: see text]) and cross-validated ([Formula: see text]) correlation coefficients, 0.9288 and 0.6353, respectively, show high robustness and good predictive ability of our selected model. The contour maps have been developed from this model and the analysis has provided an interpretable explanation of the effect that various features and substituents have on the potency and selectivity of inhibitors towards iNOS. Docking studies have also been performed in order to analyze the interactions between the enzyme and the inhibitors. Our proposed model can thus be further used for screening a large database of compounds and design new iNOS inhibitors.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ritu Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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Arora R, Issar U, Kakkar R. Identification of novel urease inhibitors: pharmacophore modeling, virtual screening and molecular docking studies. J Biomol Struct Dyn 2018; 37:4312-4326. [PMID: 30580662 DOI: 10.1080/07391102.2018.1546620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pharmacophore modeling and atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR) have been developed on N-acylglycino- and hippurohydroxamic acid derivatives, which are known potential inhibitors of urease. This is followed by virtual screening and ADMET (absorption, distribution, metabolism, excretion and toxicity) studies on a large library of known drugs in order to get lead molecules as Helicobacter pylori urease inhibitors. A suitable three-featured pharmacophore model comprising one H-bond acceptor and two H-bond donor features (ADD.10) has been found to be the best QSAR model. An external library of compounds (∼3000 molecules), pre-filtered using Lipinski's rule of five, has been further screened using the pharmacophore model ADD.10. By analyzing the fitness of the hits with respect to the pharmacophore model and their binding interaction inside the urease active site, four molecules have been predicted to be extremely good urease inhibitors. Two of these have significant potential and should be taken up for further drug-designing process.
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Affiliation(s)
- Richa Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
| | - Upasana Issar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
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Garcia C, Burgain A, Chaillot J, Pic É, Khemiri I, Sellam A. A phenotypic small-molecule screen identifies halogenated salicylanilides as inhibitors of fungal morphogenesis, biofilm formation and host cell invasion. Sci Rep 2018; 8:11559. [PMID: 30068935 PMCID: PMC6070544 DOI: 10.1038/s41598-018-29973-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
A poorly exploited paradigm in the antimicrobial therapy field is to target virulence traits for drug development. In contrast to target-focused approaches, antivirulence phenotypic screens enable identification of bioactive molecules that induce a desirable biological readout without making a priori assumption about the cellular target. Here, we screened a chemical library of 678 small molecules against the invasive hyphal growth of the human opportunistic yeast Candida albicans. We found that a halogenated salicylanilide (N1-(3,5-dichlorophenyl)-5-chloro-2-hydroxybenzamide) and one of its analogs, Niclosamide, an FDA-approved anthelmintic in humans, exhibited both antifilamentation and antibiofilm activities against C. albicans and the multi-resistant yeast C. auris. The antivirulence activity of halogenated salicylanilides were also expanded to C. albicans resistant strains with different resistance mechanisms. We also found that Niclosamide protected the intestinal epithelial cells against invasion by C. albicans. Transcriptional profiling of C. albicans challenged with Niclosamide exhibited a signature that is characteristic of the mitochondria-to-nucleus retrograde response. Our chemogenomic analysis showed that halogenated salicylanilides compromise the potential-dependant mitochondrial protein translocon machinery. Given the fact that the safety of Niclosamide is well established in humans, this molecule could represent the first clinically approved antivirulence agent against a pathogenic fungus.
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Affiliation(s)
- Carlos Garcia
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Anaïs Burgain
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Julien Chaillot
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Émilie Pic
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Inès Khemiri
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Adnane Sellam
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada.
- Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
- Big Data Research Centre (BDRC-UL), Université Laval, Faculty of Sciences and engineering, Quebec City, QC, Canada.
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Ramachandran R, Piramanyagam S. Pharmacophore modeling, atom based 3D-QSAR and Molecular docking approaches to screen C-X-C chemokine receptor type 4 antagonists as microbicides for human immunodeficiency virus-1. Virusdisease 2018; 28:272-280. [PMID: 29291213 DOI: 10.1007/s13337-017-0397-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/28/2017] [Indexed: 01/10/2023] Open
Abstract
The C-X-C chemokine receptor type 4 receptor CXCR4 which acts as a co-receptor for human immunodeficiency virus-1, expressed in the later stages of infection is considered as an attractive and new target for drug design. Microbicides acting as co-receptor blockers are highly significant as these drugs block HIV lifecycle at early stage itself. The urgent need for a safe and effective microbicide urges to explore new CXCR4 antagonists which could be developed as microbicides. The pharmacophore based 3D-QSAR models and docking models were developed using PHASE and GLIDE modules of Schrodinger software. Three-dimensional quantitative structure-activity relationships (3D-QSAR) studies and pharmacophore modelling was carried out on a dataset of 114 CXCR4 antagonists with the intention of exploring entry inhibitors with better therapeutic potential. A training set of 43 compounds was used to create 3D-QSAR models and they were validated using a test set of 28 compounds. CXCR4 antagonists with good inhibitory activity could be designed and structurally modified based upon the QSAR model developed with necessary pharmacophore features. The results revealed that the common pharmacophore hypothesis ADHPR.1 was used for 3D-QSAR model development and the most active compound, CXCR4 antagonist no.44 which is a imidazopyridine-tetrahydro-8-quinolinamine derivative interacted with the CXCR4 receptor residue ASP 97 by the formation of a hydrogen bond. Also, the docking studies were carried out for the dataset for analyzing the binding conformation of CXCR4 and 114 antagonists. The results obtained from the 3D-QSAR studies and docking simulation can be used for designing new and potent CXCR4 antagonists. The compound identified from this study can be taken up further for validation by in vitro/in vivo studies.
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Affiliation(s)
- Radhika Ramachandran
- Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu 641 046 India
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Badhani B, Kakkar R. In silico studies on potential MCF-7 inhibitors: a combination of pharmacophore and 3D-QSAR modeling, virtual screening, molecular docking, and pharmacokinetic analysis. J Biomol Struct Dyn 2016; 35:1950-1967. [PMID: 27401212 DOI: 10.1080/07391102.2016.1202863] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gallic acid and its derivatives exhibit a diverse range of biological applications, including anti-cancer activity. In this work, a data-set of forty-six molecules containing the galloyl moiety, and known to show anticarcinogenic activity against the MCF-7 human cancer cell line, have been chosen for pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies. A tree-based partitioning algorithm has been used to find common pharmacophore hypotheses. The QSAR model was generated for three, four, and five featured hypotheses with increasing PLS factors and analyzed. Results for five featured hypotheses with three acceptors and two aromatic rings were the best out of all the possible combinations. On analyzing the results, the most robust (R2 = .8990) hypothesis with a good predictive power (Q2 = .7049) was found to be AAARR.35. A good external validation (R2 = .6109) was also obtained. In order to design new MCF-7 inhibitors, the QSAR model was further utilized in pharmacophore-based virtual screening of a large database. The predicted IC50 values of the identified potential MCF-7 inhibitors were found to lie in the micromolar range. Molecular docking into the colchicine domain of tubulin was performed in order to examine one of the probable mechanisms. This revealed various interactions between the ligand and the active site protein residues. The present study is expected to provide an effective guide for methodical development of potent MCF-7 inhibitors.
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Affiliation(s)
- Bharti Badhani
- a Computational Chemistry Laboratory, Department of Chemistry , University of Delhi , Delhi 110007 , India
| | - Rita Kakkar
- a Computational Chemistry Laboratory, Department of Chemistry , University of Delhi , Delhi 110007 , India
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Pourbasheer E, Shokouhi Tabar S, Masand VH, Aalizadeh R, Ganjali MR. 3D-QSAR and docking studies on adenosine A2A receptor antagonists by the CoMFA method. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:461-477. [PMID: 26055215 DOI: 10.1080/1062936x.2015.1049666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Parkinson's disease affects millions of people around the world. Recently, adenosine A2A receptor antagonists have been identified as a drug target for the treatment of Parkinson's disease. Consequently, there is an immediate need to develop new classes of A2A receptor antagonists. In the present analysis, three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on a series of pyrimidines, using comparative molecular field analysis (CoMFA). The best prediction was obtained with a CoMFA standard model (q(2) = 0.475, r(2) = 0.977) and a CoMFA region focusing model (q(2) = 0.637, r(2) = 0.976) combined with steric and electrostatic fields. The structural insights derived from the contour maps helped to better interpret the structure-activity relationships. Also, to understand the structure-activity correlation of A2A receptor antagonists, we have carried out molecular docking analysis. Based on the results obtained from the present 3D-QSAR and docking studies, we have identified some key features for increasing the activity of compounds, which have been used to design new A2A receptor antagonists. The newly designed molecules showed high activity with the obtained models.
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Affiliation(s)
- E Pourbasheer
- a Department of Chemistry , Payame Noor University (PNU) , Tehran , Iran
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Recent Advances in The Discovery ofN-Myristoyltransferase Inhibitors. ChemMedChem 2014; 9:2425-37. [DOI: 10.1002/cmdc.201402174] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/17/2014] [Indexed: 01/08/2023]
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Pharmacophore modeling, 3D-QSAR, and molecular docking study on naphthyridine derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0383-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Leng Y, Lu T, Yuan HL, Liu HC, Lu S, Zhang WW, Jiang YL, Chen YD. QSAR studies on imidazopyrazine derivatives as Aurora A kinase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:705-730. [PMID: 22971111 DOI: 10.1080/1062936x.2012.719541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Aurora kinases have emerged as attractive targets for the development of novel anti-cancer agents. A combined study of molecular docking, pharmacophore modelling and 3D-QSAR was performed on a series of imidazo [1, 2-a] pyrazines as novel Aurora kinase inhibitors to gain insights into the structural determinants and their structure-activity relationship. An ensemble of conformations based on molecular docking was used for PHASE pharmacophore studies. The developed best-fitted pharmacophore model was validated by diverse chemotypes of Aurora A kinase inhibitors and was consistent with the structural requirements for the docked binding mechanism. Subsequently, the pharmacophore-based alignment was used to develop PHASE and comparative molecular similarity indices analysis (CoMSIA) 3D-QSAR models. The best CoMSIA model showed good statistics (q (2 )= 0.567, r (2 )= 0.992), and the predictive ability of the model was validated using an external test set of 13 compounds giving a satisfactory prediction ([Formula: see text]). The 3D contour maps provided insight into the binding mechanism and highlighted key structural features that are essential to the inhibitory activity. Based on the PHASE and CoMSIA 3D-QSAR results, a set of novel Aurora A inhibitors were designed that showed excellent potencies.
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Affiliation(s)
- Y Leng
- Laboratory of Molecular Design and Drug Discovery, School of Basic Science, China Pharmaceutical University, Nanjing, China
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Mustyala KK, Chitturi AR, Naikal James PS, Vuruputuri U. Pharmacophore mapping and in silico screening to identify new potent leads for A2Aadenosine receptor as antagonists. J Recept Signal Transduct Res 2012; 32:102-13. [DOI: 10.3109/10799893.2012.660532] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Taha MO, Qandil AM, Al-Haraznah T, Khalaf RA, Zalloum H, Al-Bakri AG. Discovery of New Antifungal Leads via Pharmacophore Modeling and QSAR Analysis of Fungal N-Myristoyl Transferase Inhibitors Followed by In Silico Screening. Chem Biol Drug Des 2011; 78:391-407. [PMID: 21679375 DOI: 10.1111/j.1747-0285.2011.01160.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3D-QSAR and docking-based combined in silico study on C-5 methyl substituted 4-arylthio and 4-aryloxy-3-iodopyridin-2-(1H)-one as HIV-1 RT inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9720-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Telvekar VN, Patel KN. Pharmacophore development and docking studies of the hiv-1 integrase inhibitors derived from N-methylpyrimidones, Dihydroxypyrimidines, and bicyclic pyrimidinones. Chem Biol Drug Des 2011; 78:150-60. [PMID: 21518263 DOI: 10.1111/j.1747-0285.2011.01130.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To elucidate the crucial structural features for the HIV-1 integrase inhibitors, a three-dimensional pharmacophore model was developed based on N-methyl pyrimidones, dihydroxypyrimidines, and bicyclic pyrimidinones derivatives using Phase. N-methyl pyrimidone derivative raltegravir, the first US-FDA approved drug by Merck, belongs to this series. The best-fitted common pharmacophore hypothesis was characterized by two acceptor, two hydrophobic, and two ring features having a correlation coefficient of 0.895, cross-validated Q(2) value of 0.631, and survival score of 8.862, suggesting that a highly predictive pharmacophore model was developed. The cross-validation studies using 23 test set molecules and fifteen structurally diverse HIV-integrase inhibitors give extra confidence about the correctness of the pharmacophore model. The cross-validation studies proved that our developed model can successfully differentiate between active and inactive HIV-integrase inhibitors. The docking studies were also carried out wherein the molecules were docked against the active site of HIV integrase to analyze the binding mode and the necessary structural requirement for their respective enzymatic inhibition. The results obtained from our studies provide a valuable tool for designing of new lead molecules with potent activity.
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Affiliation(s)
- Vikas N Telvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga (E), Mumbai, India.
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Sharma H, Patil S, Sanchez TW, Neamati N, Schinazi RF, Buolamwini JK. Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorg Med Chem 2011; 19:2030-45. [PMID: 21371895 DOI: 10.1016/j.bmc.2011.01.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/16/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
HIV-1 integrase is one of the three most important enzymes required for viral replication and is therefore an attractive target for anti retroviral therapy. We herein report the design and synthesis of 3-keto salicylic acid chalcone derivatives as novel HIV-1 integrase inhibitors. The most active compound, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) was selectively active against integrase strand transfer, with an IC(50) of 3.7 μM. While most of the compounds exhibited strand transfer selectivity, a few were nonselective, such as 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15), which was active against both 3'-processing and strand transfer with IC(50) values of 11±4 and 5±2 μM, respectively. The compounds also inhibited HIV replication with potencies comparable with their integrase inhibitory potencies. Thus, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) and 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15) inhibited HIV-1 replication with EC(50) values of 7.3 and 8.7 μM, respectively. A PHASE pharmacophore hypothesis was developed and validated by 3D-QSAR, which gave a predictive r(2) of 0.57 for an external test set of ten compounds. Phamacophore derived molecular alignments were used for CoMFA and CoMSIA 3D-QSAR modeling. CoMSIA afforded the best model with q(2) and r(2) values of 0.54 and 0.94, respectively. This model predicted all the ten compounds of the test set within 0.56 log units of the actual pIC(50) values; and can be used to guide the rational design of more potent novel 3-keto salicylic acid integrase inhibitors.
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Affiliation(s)
- Horrick Sharma
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 847 Monroe Avenue, Suite 327, TN 38163, USA
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Telvekar VN, Patel DJ, Jadhav NC, Mishra SJ. Three-dimensional QSAR and pharmacophore mapping of biphenyl benzoic acid derivatives as selective human β3-adrenergic receptor agonists. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9261-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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