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Journal articles on the topic 'Structure-based pharmacophore modeling'

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Published: 3 June 2025

Last updated: 31 July 2025

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1

Mortier, Jérémie, Pratik Dhakal, and Andrea Volkamer. "Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces." Molecules 23, no. 8 (2018): 1959. http://dx.doi.org/10.3390/molecules23081959.

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Pharmacophore models are an accurate and minimal tridimensional abstraction of intermolecular interactions between chemical structures, usually derived from a group of molecules or from a ligand-target complex. Only a limited amount of solutions exists to model comprehensive pharmacophores using the information of a particular target structure without knowledge of any binding ligand. In this work, an automated and customable tool for truly target-focused (T²F) pharmacophore modeling is introduced. Key molecular interaction fields of a macromolecular structure are calculated using the AutoGRID

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Kadu, Nilesh S., and Atul V. Ingle. "Three-Dimensional Pharmacophore Modeling of Betulonic Acid Derivatives as a Strong Inhibitor of Human Coronavirus-229E Replication." International Journal of Science and Healthcare Research 6, no. 2 (2021): 356–61. http://dx.doi.org/10.52403/ijshr.20210462.

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These-days, pharmacophore approaches have become one of the foremost tools in drug discovery after the past century’s development. Numerous ligand-based and structure-based strategies are developed for improved pharmacophore modeling with success and extensively applied in virtual screening, de novo design and lead improvement. Till now, there is little information on 3D-pharmacophore studies of 1,2,3-triazolo-fused betulonic acid derivatives as a strong inhibitor for human coronavirus-229E replication. Here, we tend to report the appliance of pharmacophore modeling for betulonic acid derivati

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Mansi, Iman A., Mahmoud A. Al-Sha'er, Nizar M. Mhaidat, Mutasem O. Taha, and Rand Shahin. "Investigation of Binding Characteristics of Phosphoinositide-dependent Kinase-1 (PDK1) Co-crystallized Ligands Through Virtual Pharmacophore Modeling Leading to Novel Anti-PDK1 Hits." Medicinal Chemistry 16, no. 7 (2020): 860–80. http://dx.doi.org/10.2174/1573406415666190724131048.

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Background: 3-Phosphoinositide Dependent Protein Kinase-1 (PDK1) is being lately considered as an attractive and forthcoming anticancer target. A Protein Data Bank (PDB) cocrystallized crystal provides not only rigid theoretical data but also a realistic molecular recognition data that can be explored and used to discover new hits. Objective: This incited us to investigate the co-crystallized ligands' contacts inside the PDK1 binding pocket via a structure-based receptor-ligand pharmacophore generation technique in Discovery Studio 4.5 (DS 4.5). Methods: Accordingly, 35 crystals for PDK1 were

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Simon, A., A. Bencsura, and J. Kardos. "Target Structure-based Modeling of the Glutamate Transporter Pharmacophore." Letters in Drug Design & Discovery 3, no. 5 (2006): 293–97. http://dx.doi.org/10.2174/157018006777574230.

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Kumar, Sivakumar Prasanth, and Prakash Chandra Jha. "Multi-Pharmacophore Modeling of Caspase-3 Inhibitors using Crystal, Dock and Flexible Conformation Schemes." Combinatorial Chemistry & High Throughput Screening 21, no. 1 (2018): 26–40. http://dx.doi.org/10.2174/1386207321666180102114917.

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Aim and Objective: Numerous caspase-3 drug discovery projects were found to have relied on single receptor as the template to recognize most promising small molecule candidates using docking approach. Alternatively, some researchers were contingent upon ligand-based alignment to build up an empirical relationship between ligand functional groups and caspase-3 inhibitory activity quantitatively. To connect both caspase-3 receptor details and its inhibitors chemical functionalities, this study was undertaken to develop receptor- and ligand-pharmacophore models based on different conformational s

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Rayevsky, O. V., O. M. Demchyk, P. A. Karpov та ін. "Structure-based virtual screening for new lead compounds targeted Plasmodium α-tubulin". Faktori eksperimental'noi evolucii organizmiv 28 (31 серпня 2021): 135–39. http://dx.doi.org/10.7124/feeo.v28.1389.

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Aim. Search for new dinitroaniline and phosphorothioamide compounds, capable of selective binding with Plasmodium α-tubulin, affecting its mitotic apparatus. Methods. Structural biology methods of computational prediction of protein-ligand interaction: molecular docking, molecular dynamics and pharmacophore analysis. Selection of compounds based on pharmacophore characteristics and virtual screening results. Results. The protocol and required structural conditions for target (α-tubulin of P. falciparum) preparation and correct modeling of the ligand-protein interaction (docking and virtual scr

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Sugumar, Shobana. "VIRTUAL SCREENING, PHARMACOPHORE MODELING, AND QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP STUDIES ON HISTAMINE 4 RECEPTOR." Asian Journal of Pharmaceutical and Clinical Research 10, no. 12 (2017): 150. http://dx.doi.org/10.22159/ajpcr.2017.v10i12.19991.

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Objective: To find out novel inhibitors for histamine 4 receptor (H4R), the target for various allergic and inflammatory pathophysiological conditions.Methods: Homology modeling of H4R was performed using easy modeler and validated using structure analysis and verification server, and with the modeled structure, virtual screening, pharmacophore modeling, and quantitative structure activity relationship (QSAR) studies were performed using the Schrodinger 9.3 software.Results: Among all the synthetic and natural ligands, hesperidin, vitexin, and diosmin were found to have the highest dock score,

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Kundu, Sibsankar, and Sangwook Wu. "A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa." Molecules 26, no. 17 (2021): 5372. http://dx.doi.org/10.3390/molecules26175372.

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Blood coagulation is an essential physiological process for hemostasis; however, abnormal coagulation can lead to various potentially fatal disorders, generally known as thromboembolic disorders, which are a major cause of mortality in the modern world. Recently, the FDA has approved several anticoagulant drugs for Factor Xa (FXa) which work via the common pathway of the coagulation cascade. A main side effect of these drugs is the potential risk for bleeding in patients. Coagulation Factor IXa (FIXa) has recently emerged as the strategic target to ease these risks as it selectively regulates

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Khalaf, Reema A., Dalal Masalha, and Dima Sabbah. "DPP-IV Inhibitory Phenanthridines: Ligand, Structure-Based Design and Synthesis." Current Computer-Aided Drug Design 16, no. 3 (2020): 295–307. http://dx.doi.org/10.2174/1573409915666181211114743.

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Background: Lately, diabetes has become the main health concern for millions of people around the world. Dipeptidyl peptidase-IV (DPP-IV) inhibitors have emerged as a new class of oral antidiabetic agents. Formerly, acridines, N4-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives, and sulfamoyl-phenyl acid esters were designed and developed as new DPP-IV inhibitors. Objective: This study aims to develop a pharmacophore model of DPP-IV inhibitors and to evaluate phenanthridines as a novel scaffold for inhibiting DPP-IV enzyme. In addition, to assess their binding in

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Agrawal, Nikhil, Balakumar Chandrasekaran, and Amal Al-Aboudi. "Recent Advances in the In-silico Structure-based and Ligand-based Approaches for the Design and Discovery of Agonists and Antagonists of A2A Adenosine Receptor." Current Pharmaceutical Design 25, no. 7 (2019): 774–82. http://dx.doi.org/10.2174/1381612825666190306162006.

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A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family. Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/ docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed various molecular dynamics (MD) simulations studies o

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Chidambaram, Kumarappan. "Identification of BACE-1 Inhibitors against Alzheimer’s Disease through E-Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation Studies: An Insilco Approach." Life 13, no. 4 (2023): 952. http://dx.doi.org/10.3390/life13040952.

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Alzheimer is a severe memory and cognitive impairment neurodegenerative disease that is the most common cause of dementia worldwide and characterized by the pathological accumulation of tau protein and amyloid-beta peptides. In this study, we have developed E-pharmacophore modeling to screen the eMolecules database with the help of a reported co-crystal structure bound with Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE-1). Flumemetamol, florbetaben, and florbetapir are currently approved drugs for use in the clinical diagnosis of Alzheimer’s disease. Despite the benefits of comme

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Manhas, Anu, Sivakumar Prasanth Kumar, and Prakash Chandra Jha. "Molecular modeling of Plasmodium falciparum peptide deformylase and structure-based pharmacophore screening for inhibitors." RSC Advances 6, no. 35 (2016): 29466–85. http://dx.doi.org/10.1039/c6ra01071g.

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S, Janardhan, та Padmanabha Reddy Y. "Molecular Modeling Studies of β-aminoacyl containing Homopiperazine derivatives as DPP4 Inhibitors". International Journal of Drug Design and Discovery 2, № 3 (2024): 533–47. https://doi.org/10.37285/ijddd.2.3.4.

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Dipeptidyl peptidase IV (DPP4) is a promising target for developing novel anti-diabetic and anti-obesity drugs. Pharmacophore based three dimensional quantitative structure activity relationship studies (3D-QSAR) and molecular docking were performed on a series of 56 β-aminoacyl-containing homopiperazine derivatives of DPP4 inhibitors to find out the structural relationship with the activity. The best predictive 3D-QSAR model with pharmacophore based alignment resulted in R2 (training set) value of 0.9407, Q2 (internal test set) value of 0.9053, Pearson-R value of 0.9517 and root mean square e

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Kalva, Sukesh, Nikhil Agrawal, Adam A. Skelton, and Lilly M. Saleena. "Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation." Molecular BioSystems 12, no. 8 (2016): 2519–31. http://dx.doi.org/10.1039/c6mb00066e.

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Alnabulsi, Soraya M., and Nizar A. Al-shar’i. "Hit identification of SMYD3 enzyme inhibitors using structure-based pharmacophore modeling." Future Medicinal Chemistry 11, no. 10 (2019): 1107–17. http://dx.doi.org/10.4155/fmc-2018-0462.

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Valasani, Koteswara Rao, Michael O. Chaney, Victor W. Day, and Shirley ShiDu Yan. "Acetylcholinesterase Inhibitors: Structure Based Design, Synthesis, Pharmacophore Modeling, and Virtual Screening." Journal of Chemical Information and Modeling 53, no. 8 (2013): 2033–46. http://dx.doi.org/10.1021/ci400196z.

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17

Torimoto-Katori, Nao, Ruili Huang, Harutoshi Kato, Rikiya Ohashi, and Menghang Xia. "In Silico Prediction of hPXR Activators Using Structure-Based Pharmacophore Modeling." Journal of Pharmaceutical Sciences 106, no. 7 (2017): 1752–59. http://dx.doi.org/10.1016/j.xphs.2017.03.004.

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18

Vadlakonda, Rajashekar, Sreenivas Enaganti, and Raghunandan Nerella. "INSILICO DISCOVERY OF HUMAN AURORA B KINASE INHIBITORS BY MOLECULAR DOCKING, PHARMACOPHORE VALIDATION AND ADMET STUDIES." Asian Journal of Pharmaceutical and Clinical Research 10, no. 2 (2017): 165. http://dx.doi.org/10.22159/ajpcr.2017.v10i2.14974.

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Objectives: To predict the anticancer potentiality of some newly designed azaindole derivatives gainst human Aurora B kinase and to identify the critical features important for their activity.Methods: Initially, the derivatives of azaindoles, (Z)-2-(oxo-1 H-pyrrolo [2,3-b] pyridine-3 (2H)-ylidene)-N-(p-substituted) hydrazine carbothioamide (scaffold A), (E)-3-((E)-substituted benzylidene hydrazono)-1H-pyrrolo[2,3-b]pyridine-2(3H)-one (scaffold B), and 1-(2-substituted acetyl)-1H- pyrrolo [2,3-b]pyridine-2,3-dione are synthesized and sketched using ACD/ChemSketch (12.0). With the 3D converted c

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Li, Na, Lin Yin, Xi Chen, et al. "Combination of Docking-Based and Pharmacophore-Based Virtual Screening Identifies Novel Agonists That Target the Urotensin Receptor." Molecules 27, no. 24 (2022): 8692. http://dx.doi.org/10.3390/molecules27248692.

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The urotensin receptor (UT receptor), a G-protein-coupled receptor mediating urotensin-II and urotensin-II-related peptide signaling in the urotensinergic system, has multiple pharmacological activities. However, there is no drug targeting the UT receptor currently in clinical use, and the discovery of new leads is still important. The complete crystal structure of the UT receptor has not yet been resolved and a screening strategy combining multiple methods can improve the accuracy and efficiency of drug screening. This study aimed to identify novel UT receptor agonists using a combination of

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Kirkpatrick, D. Lynn, Shawndra Watson, and Saraj Ulhaq. "Structure-Based Drug Design: Combinatorial Chemistry and Molecular Modeling." Combinatorial Chemistry & High Throughput Screening 2, no. 4 (1999): 211–21. http://dx.doi.org/10.2174/1386207302666220204193511.

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Abstract: Drug discovery efforts are shifting to include the rapid synthetic procedures of combinatorial chemistry and the elegance of rational library design. The wealth of computational methods which explore both the receptor structure and the ultimate pharmacophore complementarity, provide novel avenues for chemists to discover new lead compounds or design virtual libraries for screening prior to the synthetic stage. This mini-review provides an overview of a few current methodologies of library generation, highlighting docking procedures which have utility in both the discovery and optimiz

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Culletta, Giulia, Maria Rita Gulotta, Ugo Perricone, Maria Zappalà, Anna Maria Almerico, and Marco Tutone. "Exploring the SARS-CoV-2 Proteome in the Search of Potential Inhibitors via Structure-Based Pharmacophore Modeling/Docking Approach." Computation 8, no. 3 (2020): 77. http://dx.doi.org/10.3390/computation8030077.

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To date, SARS-CoV-2 infectious disease, named COVID-19 by the World Health Organization (WHO) in February 2020, has caused millions of infections and hundreds of thousands of deaths. Despite the scientific community efforts, there are currently no approved therapies for treating this coronavirus infection. The process of new drug development is expensive and time-consuming, so that drug repurposing may be the ideal solution to fight the pandemic. In this paper, we selected the proteins encoded by SARS-CoV-2 and using homology modeling we identified the high-quality model of proteins. A structu

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De, Baishakhi, Koushik Bhandari, Francisco J. B. Mendonça, Marcus T. Scotti, and Luciana Scotti. "Computational Studies in Drug Design Against Cancer." Anti-Cancer Agents in Medicinal Chemistry 19, no. 5 (2019): 587–91. http://dx.doi.org/10.2174/1871520618666180911125700.

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Background: The application of in silico tools in the development of anti cancer drugs. Objective: The summing of different computer aided drug design approaches that have been applied in the development of anti cancer drugs. Methods: Structure based, ligand based, hybrid protein-ligand pharmacophore methods, Homology modeling, molecular docking aids in different steps of drug discovery pipeline with considerable saving in time and expenditure. In silico tools also find applications in the domain of cancer drug development. Results: Structure-based pharmacophore modeling aided in the identific

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Sanders, Marijn P. A., Ross McGuire, Luc Roumen, et al. "From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling." MedChemComm 3, no. 1 (2012): 28–38. http://dx.doi.org/10.1039/c1md00210d.

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Protein structure-based pharmacophore (SBP) models derive the molecular features a ligand must contain to be biologically active by conversion of protein properties to reciprocal ligand space. SBPs improve molecular understanding of ligand–protein interactions and can be used as valuable tools for hit and lead optimization, compound library design, and target hopping.

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Mathpal, Deepti, Tahani M. Almeleebia, Kholoud M. Alshahrani, et al. "Identification of 3-((1-(Benzyl(2-hydroxy-2-phenylethyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamoyl)pyrazine-2-carboxylic Acid as a Potential Inhibitor of Non-Nucleosidase Reverse Transcriptase Inhibitors through InSilico Ligand- and Structure-Based Approaches." Molecules 26, no. 17 (2021): 5262. http://dx.doi.org/10.3390/molecules26175262.

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Non-nucleosidase reverse transcriptase inhibitors (NNRTIs) are highly promising agents for use in highly effective antiretroviral therapy. We implemented a rational approach for the identification of promising NNRTIs based on the validated ligand- and structure-based approaches. In view of our state-of-the-art techniques in drug design and discovery utilizing multiple modeling approaches, we report here, for the first time, quantitative pharmacophore modeling (HypoGen), docking, and in-house database screening approaches in the identification of potential NNRTIs. The validated pharmacophore mo

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Shiri, Fereshteh, Somayeh Pirhadi, and Jahan B. Ghasemi. "Dynamic structure based pharmacophore modeling of the Acetylcholinesterase reveals several potential inhibitors." Journal of Biomolecular Structure and Dynamics 37, no. 7 (2018): 1800–1812. http://dx.doi.org/10.1080/07391102.2018.1468281.

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Ebalunode, Jerry O., Xialan Dong, Zheng Ouyang, Jie Liang, Roderic G. Eckenhoff, and Weifan Zheng. "Structure-based shape pharmacophore modeling for the discovery of novel anesthetic compounds." Bioorganic & Medicinal Chemistry 17, no. 14 (2009): 5133–38. http://dx.doi.org/10.1016/j.bmc.2009.05.060.

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Yoo, Jakyung, and José L. Medina-Franco. "Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase." Journal of Computer-Aided Molecular Design 25, no. 6 (2011): 555–67. http://dx.doi.org/10.1007/s10822-011-9441-1.

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Crisan, Luminita, Daniela Varga, and Liliana Pacureanu. "Pharmacophore Modeling and Docking Study of Pyrazolylaminoquinazoline Derivatives as Highly Potent Fibroblast Growth Factor Receptor Inhibitors2 (FGFR2)." Revista de Chimie 70, no. 3 (2019): 790–96. http://dx.doi.org/10.37358/rc.19.3.7008.

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In this study pharmacophore modeling and molecular docking investigations have been performed on pyrazolylaminoquinazoline derivatives, highly potent fibroblast growth factor receptor2 (FGFR2) inhibitors. The best pharmacophore hypotheses displaying five features (ADHRR.2051 and AADHR.798) were generated using a set of 28 compounds. The associated 3D atom-based quantitative structure � activity relationships (QSAR) models were statistically robust showing high correlation coefficients (R-squared = 0.981 / 0.982), and cross validation coefficients (Q-squared = 0.645 / 0.671). The R-Pearson valu

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Langer, Thierry, and G. Wolber. "Virtual combinatorial chemistry and in silico screening: Efficient tools for lead structure discovery?" Pure and Applied Chemistry 76, no. 5 (2004): 991–96. http://dx.doi.org/10.1351/pac200476050991.

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In this article, an overview of the most common ligand-based in silico screening techniques is given together with an example on the recent successful application of combined use of pharmacophore modeling, database mining, and biological assays. Additionally, a new approach for structure-based high-throughput pharmacophore model generation is presented. The LigandScout program contains an automated method for creating pharmacophore models from experimentally determined structure data, e.g., publicly available from the Brookhaven Protein Databank (PDB). In a first step, known algorithms were im

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Munir, Anum, Shaukat I. Malik, and Khalid A. Malik. "De-Novo Ligand Design against Mutated Huntington Gene by Ligand-based Pharmacophore Modeling Approach." Current Computer-Aided Drug Design 16, no. 2 (2020): 134–44. http://dx.doi.org/10.2174/1573409915666181207104437.

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Background: Huntington's disease is characterized by three side effects, including motor disturbances, psychiatric elements, and intellectual weakness. The onset for HD has nonlinear converse associations with the number of repeat sequences of the polyglutamine mutations, so that younger patients have a tendency for longer repeats length. This HD variation is because of the development of a polyglutamine (CAG) repeats in the exon 1 of the Huntingtin protein. Methods: In the present study, a few derivatives utilized as a part of the treatment of HD, are used to create the pharmacophore model an

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Audat, Suaad A., Nizar A. Al-Shar’i, Buthina A. Al-Oudat, et al. "Identification of Human Leukotriene A4 Hydrolase Inhibitors Using Structure-Based Pharmacophore Modeling and Molecular Docking." Molecules 25, no. 12 (2020): 2871. http://dx.doi.org/10.3390/molecules25122871.

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Leukotriene B4 (LTB4) is a potent, proinflammatory lipid mediator implicated in the pathologies of an array of inflammatory diseases and cancer. The biosynthesis of LTB4 is regulated by the leukotriene A4 hydrolase (LTA4H). Compounds capable of limiting the formation of LTB4, through selective inhibition of LTA4H, are expected to provide potent anti-inflammatory and anti-cancer agents. The aim of the current study is to obtain potential LTA4H inhibitors using computer-aided drug design. A hybrid 3D structure-based pharmacophore model was generated based on the crystal structure of LTA4H in com

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Lee, Myeong, Anand Balupuri, Ye-rim Jung, et al. "Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches." Molecules 23, no. 12 (2018): 3136. http://dx.doi.org/10.3390/molecules23123136.

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Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositio

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Durai, Prasannavenkatesh, Young-Joon Ko, Jin-Chul Kim, Cheol-Ho Pan, and Keunwan Park. "Identification of Tyrosinase Inhibitors and Their Structure-Activity Relationships via Evolutionary Chemical Binding Similarity and Structure-Based Methods." Molecules 26, no. 3 (2021): 566. http://dx.doi.org/10.3390/molecules26030566.

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Tyrosinase is an enzyme that plays a crucial role in the melanogenesis of humans and the browning of food products. Thus, tyrosinase inhibitors that are useful to the cosmetic and food industries are required. In this study, we have used evolutionary chemical binding similarity (ECBS) to screen a virtual chemical database for human tyrosinase, which resulted in seven potential tyrosinase inhibitors confirmed through the tyrosinase inhibition assay. The tyrosinase inhibition percentage for three of the new actives was over 90% compared to 61.9% of kojic acid. From the structural analysis throug

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Al-Sayed, Ahmad Mansour, Belal O. Al-Najjar, and Ashok Shakya. "Novel glucokinase activators: A structure-based pharmacophore modeling, QSAR analysis, and molecular dynamics approach." Pharmacia 71 (August 30, 2024): 1–9. https://doi.org/10.3897/pharmacia.71.e131072.

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Glucokinase (GK) activators are promising candidates for type 2 diabetes treatment. This study utilized structure-based pharmacophore modeling and QSAR analysis to identify novel activators. Virtual screening of a 250,000-compound library yielded eight new candidates with significant <i>in vitro</i> activity (over 50% activation at 25 µg/mL) and diverse structures. Molecular dynamics simulations revealed a potential mechanism involving a transient loop flip in the GK allosteric site, aligning with known activator behavior. The leading candidate, NSC12516, displayed superior hydrogen bonding wi

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Basak, Subhash C., and Apurba K. Bhattacharjee. "Computational Approaches for the Design of Mosquito Repellent Chemicals." Current Medicinal Chemistry 27, no. 1 (2020): 32–41. http://dx.doi.org/10.2174/0929867325666181029165413.

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Background: In view of many current mosquito-borne diseases there is a need for the design of novel repellents. Objective: The objective of this article is to review the results of the researches carried out by the authors in the computer-assisted design of novel mosquito repellents. Methods: Two methods in the computational design of repellents have been discussed: a) Quantitative Structure Activity Relationship (QSAR) studies from a set of repellents structurally related to DEET using computed mathematical descriptors, and b) Pharmacophore based modeling for design and discovery of novel rep

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Ostopovici-Halip, Liliana, and Ramona Rad-Curpan. "Modeling of ligand binding to dopamine D2 receptor." Journal of the Serbian Chemical Society 79, no. 2 (2014): 175–83. http://dx.doi.org/10.2298/jsc130208046o.

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The dopaminic receptors have been for long time the major targets for developing new small molecules with high affinity and selectivity to treat psychiatric disorders, neurodegeneration, drug abuse, and other therapeutic areas. In the absence of a 3D structure for the human D2 dopamine (HDD2) receptor, the efforts for discovery and design of new potential drugs rely on comparative models generation, docking and pharmacophore development studies. To get a better understanding of the HDD2 receptor binding site and the ligand-receptor interactions a homology model of HDD2 receptor based on the X-

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Daoud, Safa, Shada J. Alabed, and Lina A. Dahabiyeh. "Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies." Acta Pharmaceutica 71, no. 2 (2020): 163–74. http://dx.doi.org/10.2478/acph-2021-0016.

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Abstract The current outbreak of novel coronavirus (COVID-19) infections urges the need to identify potential therapeutic agents. Therefore, the repurposing of FDA-approved drugs against today’s diseases involves the use of de-risked compounds with potentially lower costs and shorter development timelines. In this study, the recently resolved X-ray crystallographic structure of COVID-19 main protease (Mpro) was used to generate a pharmacophore model and to conduct a docking study to capture antiviral drugs as new promising COVID-19 main protease inhibitors. The developed pharmacophore successf

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Agrawal, Neetu. "Pharmacophore modeling and 3D-QSAR studies of 2,4-disubstituted pyrimidine derivatives as Janus kinase 3 inhibitors." Journal of Theoretical and Computational Chemistry 19, no. 01 (2020): 2050001. http://dx.doi.org/10.1142/s0219633620500017.

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A robust pharmacophore model was developed and the structure-activity relationship was analyzed using 71 pyrimidine derivatives reported for covalent Janus Kinase 3 (JAK3) inhibition. Pharmacophore modeling developed a five featured pharmacophore: one H-bond acceptor, two H-bond donors, one hydrophobic, and one aromatic ring features. The atom-based three-dimensional QSAR models with statistical significance were generated using the training set of 52 compounds. The excellent predictive correlation coefficients were obtained for 3D models determined using a test set of 19 molecules. The genera

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Owono Owono, Luc Calvin, Melalie Keita, Eugene Megnassan, Vladimir Frecer, and Stanislav Miertus. "Design of Thymidine Analogues Targeting Thymidilate Kinase ofMycobacterium tuberculosis." Tuberculosis Research and Treatment 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/670836.

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We design here new nanomolar antituberculotics, inhibitors ofMycobacterium tuberculosisthymidine monophosphate kinase (TMPKmt), by means of structure-based molecular design. 3D models of TMPKmt-inhibitor complexes have been prepared from the crystal structure of TMPKmtcocrystallized with the natural substrate deoxythymidine monophosphate (dTMP) (1GSI) for a training set of 15 thymidine analogues (TMDs) with known activity to prepare a QSAR model of interaction establishing a correlation between the free energy of complexation and the biological activity. Subsequent validation of the predictabi

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Al-Sayed Ahmad, Mansour, Belal O. Al-Najjar, and Ashok Shakya. "Novel glucokinase activators: A structure-based pharmacophore modeling, QSAR analysis, and molecular dynamics approach." Pharmacia 71 (August 30, 2024): 1–9. http://dx.doi.org/10.3897/pharmacia.71.e131072.

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Glucokinase (GK) activators are promising candidates for type 2 diabetes treatment. This study utilized structure-based pharmacophore modeling and QSAR analysis to identify novel activators. Virtual screening of a 250,000-compound library yielded eight new candidates with significant in vitro activity (over 50% activation at 25 µg/mL) and diverse structures. Molecular dynamics simulations revealed a potential mechanism involving a transient loop flip in the GK allosteric site, aligning with known activator behavior. The leading candidate, NSC12516, displayed superior hydrogen bonding with key

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Luo, Lianxiang, Ai Zhong, Qu Wang, and Tongyu Zheng. "Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products." Marine Drugs 20, no. 1 (2021): 29. http://dx.doi.org/10.3390/md20010029.

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Background: In the past decade, several antibodies directed against the PD-1/PD-L1 interaction have been approved. However, therapeutic antibodies also exhibit some shortcomings. Using small molecules to regulate the PD-1/PD-L1 pathway may be another way to mobilize the immune system to fight cancer. Method: 52,765 marine natural products were screened against PD-L1(PDBID: 6R3K). To identify natural compounds, a structure-based pharmacophore model was generated, following by virtual screening and molecular docking. Then, the absorption, distribution, metabolism, and excretion (ADME) test was c

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Sun, Hao-Peng, Jia Zhu, Fei-Hong Chen, and Qi-Dong You. "Structure-Based Pharmacophore Modeling from Multicomplex: a Comprehensive Pharmacophore Generation of Protein Kinase CK2 and Virtual Screening Based on it for Novel Inhibitors." Molecular Informatics 30, no. 6-7 (2011): 579–92. http://dx.doi.org/10.1002/minf.201000178.

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Lin, Hsuan-Yu, Yih Ho, and Hsuan-Liang Liu. "Structure-Based Pharmacophore Modeling to Discover Novel CCR5 Inhibitors for HIV-1/Cancers Therapy." Journal of Biomedical Science and Engineering 12, no. 01 (2019): 10–30. http://dx.doi.org/10.4236/jbise.2019.121002.

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Elumalai, Pavadai, Hsuan-Liang Liu, Zheng-Li Zhou, et al. "Ligand and Structure-Based Pharmacophore Modeling for the Discovery of Potential Human HNMT Inhibitors." Letters in Drug Design & Discovery 9, no. 1 (2012): 17–29. http://dx.doi.org/10.2174/157018012798192955.

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Thangapandian, Sundarapandian, Shalini John, Sugunadevi Sakkiah, and Keun Woo Lee. "Ligand and structure based pharmacophore modeling to facilitate novel histone deacetylase 8 inhibitor design." European Journal of Medicinal Chemistry 45, no. 10 (2010): 4409–17. http://dx.doi.org/10.1016/j.ejmech.2010.06.024.

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Putri, Isma Aulia, Dian Ayu Estiningtyas, Nadira Butsaina Idelia, et al. "Potential Bioactive Compounds in Java Cardamom Fruit (Amomum compactum) As Candidate COX-2 Targeted Anti-Inflammatory Agents: In Silico Study." Jurnal Ilmu Farmasi dan Farmasi Klinik 21, no. 2 (2024): 198–208. https://doi.org/10.31942/jiffk.v21i2.11340.

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Inflammation is the defense mechanism of the body against harmful stimuli, such as pathogens, damaged cells, toxic compounds, or irradiation. Javanese cardamom (Amomum compactum) has pharmacological activity that has potential as an anti-inflammatory based on in vitro tests. This study aims to assess the physico-chemical characteristics of bioactive compounds contained in Java cardamom and molecular interactions on cyclooxygenase-2 (COX-2) as a target of inflammatory processes through a computational study. This study used molecular docking and pharmacophore modeling with structure-based drug

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Le, Minh-Tri, Viet-Nham Hoang, Dac-Nhan Nguyen, et al. "Structure-Based Discovery of ABCG2 Inhibitors: A Homology Protein-Based Pharmacophore Modeling and Molecular Docking Approach." Molecules 26, no. 11 (2021): 3115. http://dx.doi.org/10.3390/molecules26113115.

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ABCG2 is an ABC membrane protein reverse transport pump, which removes toxic substances such as medicines out of cells. As a result, drug bioavailability is an unexpected change and negatively influences the ADMET (absorption, distribution, metabolism, excretion, and toxicity), leading to multi-drug resistance (MDR). Currently, in spite of promising studies, screening for ABCG2 inhibitors showed modest results. The aim of this study was to search for small molecules that could inhibit the ABCG2 pump. We first used the WISS MODEL automatic server to build up ABCG2 homology protein from 655 amin

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Kumar, Vinay, and Achintya Saha. "Chemometric Modeling of Structurally Diverse Carbamates for the Inhibition of Acetylcholinesterase (AChE) Enzyme in Alzheimer's Disease." International Journal of Quantitative Structure-Property Relationships 5, no. 3 (2020): 6–60. http://dx.doi.org/10.4018/ijqspr.2020070102.

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In this research, we have developed two-dimensional quantitative structure-activity relationship (2D-QSAR) and group-based QSAR (GQSAR) models employing a dataset of 78 carbamate derivatives (acetylcholinesterase enzyme inhibitors). The developed models were validated using various stringent validation parameters. From the insights obtained from the developed 2D-QSAR and GQSAR models, we have found that the structural features appearing in the models are responsible for the enhancement of the inhibitory activity against the AChE enzyme. Furthermore, we have performed the pharmacophore modeling

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He, Yusu, Ludi Jiang, Zhen Yang, Yanjiang Qiao, and Yanling Zhang. "A combination of pharmacophore modeling, molecular docking, and virtual screening for P2Y12 receptor antagonists from Chinese herbs." Canadian Journal of Chemistry 93, no. 3 (2015): 311–16. http://dx.doi.org/10.1139/cjc-2014-0429.

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P2Y12, a member of the G-protein-coupled receptors, is associated with abnormal platelet aggregation, a condition that contributes to thrombus formation. As receptor antagonists are effective solutions for anti-thrombus, the P2Y12 receptor is a popular drug target. After the recent resolution of the P2Y12 receptor’s crystal structure, pharmacophore modeling and docking were combined to discover potential natural antagonists. Various approaches were used for the validation of the pharmacophore models and the optimization of docking algorithms. Hypo18, which was generated by 24 known antagonists

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Tuffaha, Ghada Omar, Ma'mon M. Hatmal, and Mutasem O. Taha. "Discovery of new JNK3 inhibitory chemotypes via QSAR-Guided selection of docking-based pharmacophores and comparison with other structure-based pharmacophore modeling methods." Journal of Molecular Graphics and Modelling 91 (September 2019): 30–51. http://dx.doi.org/10.1016/j.jmgm.2019.05.015.

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