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Journal articles on the topic 'Pharmacophore modelling'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Kaur, Paramjit, Vikas Sharma, and Vipin Kumar. "Pharmacophore Modelling and 3D-QSAR Studies on -Phenylpyrazinones as Corticotropin-Releasing Factor 1 Receptor Antagonists." International Journal of Medicinal Chemistry 2012 (May 31, 2012): 1–13. http://dx.doi.org/10.1155/2012/452325.

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Pharmacophore modelling-based virtual screening of compound is a ligand-based approach and is useful when the 3D structure of target is not available but a few known active compounds are known. Pharmacophore mapping studies were undertaken for a set of 50 N3-phenylpyrazinones possessing Corticotropin-releasing Factor 1 (CRF 1) antagonistic activity. Six point pharmacophores with two hydrogen bond acceptors, one hydrogen bond donor, two hydrophobic regions, and one aromatic ring as pharmacophoric features were developed. Amongst them the pharmacophore hypothesis AADHHR.47 yielded a statisticall

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Al-Sha'er, Mahmoud A., Rua'a A. Al-Aqtash та Mutasem O. Taha. "Discovery of New Phosphoinositide 3-kinase Delta (PI3Kδ) Inhibitors via Virtual Screening using Crystallography-derived Pharmacophore Modelling and QSAR Analysis". Medicinal Chemistry 15, № 6 (2019): 588–601. http://dx.doi.org/10.2174/1573406415666190222125333.

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<P>Background: PI3K&#948; is predominantly expressed in hematopoietic cells and participates in the activation of leukocytes. PI3K&#948; inhibition is a promising approach for treating inflammatory diseases and leukocyte malignancies. Accordingly, we decided to model PI3K&#948; binding. </P><P> Methods: Seventeen PI3K&#948; 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

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Singh, Avineesh, and Harish Rajak. "STRUCTURAL EXPLORATION AND PHARMACOPHORIC INVESTIGATION OF PYRAZOLE BASED ANALOGS AS NOVEL HISTONE DEACETYLASE 1 INHIBITOR USING COMBINATORIAL STUDIES." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 3 (2018): 90. http://dx.doi.org/10.22159/ijpps.2018v10i3.22735.

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Objective: Histone deacetylase inhibitors (HDACi) have four essential pharmacophores as cap group, connecting unit, a linker moiety and zinc binding group for their anticancer and histone deacetylase (HDAC) inhibition activity. On the basis of this fact, the objective of this research was to evaluate the exact role of pyrazole nucleus as connecting unit and its role in the development of newer HDACi.Methods: Ligand and structure-based computer-aided drug design strategies such as pharmacophore and atom based 3D QSAR modelling, molecular docking and energetic based pharmacophore mapping have be

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4

Langer, Thierry, and Rémy D. Hoffmann. "Pharmacophore modelling: applications in drug discovery." Expert Opinion on Drug Discovery 1, no. 3 (2006): 261–67. http://dx.doi.org/10.1517/17460441.1.3.261.

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Klenina, Olena. "In Silico Exploration of Molecular Mechanisms for Inhibiting Inflammatory Responses by 3Н-Thiazolo[4,5-b]pyridin-2-one Derivatives". Acta Chimica Slovenica 71, № 2 (2024): 264–87. http://dx.doi.org/10.17344/acsi.2024.8726.

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Combined in silico strategy for molecular mechanisms exploration of a series 3H-thiazolo[4,5-b]pyridin-2-ones exhibiting strong anti-exudative action through QSAR analysis, molecular docking and pharmacophore modelling is reported. GA-ML technique was used for QSAR models generation with 2D autocorrelation descriptors. One- and two-parameter regressions revealed that certain structural patterns or heteroatoms contribute mutually to the anti-exudative activity potentiation. Possible action mechanisms were discovered through flexible docking simulations with cyclooxygenase pathway enzymes (COX-1

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Witkowska, Ewa, Magda Godlewska, Jowita Osiejuk, et al. "Bifunctional Opioid/Melanocortin Peptidomimetics for Use in Neuropathic Pain: Variation in the Type and Length of the Linker Connecting the Two Pharmacophores." International Journal of Molecular Sciences 23, no. 2 (2022): 674. http://dx.doi.org/10.3390/ijms23020674.

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Based on the mechanism of neuropathic pain induction, a new type of bifunctional hybrid peptidomimetics was obtained for potential use in this type of pain. Hybrids consist of two types of pharmacophores that are connected by different types of linkers. The first pharmacophore is an opioid agonist, and the second pharmacophore is an antagonist of the pronociceptive system, i.e., an antagonist of the melanocortin-4 receptor. The results of tests in acute and neuropathic pain models of the obtained compounds have shown that the type of linker used to connect pharmacophores had an effect on antin

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Yunusa, Abdulmajeed, and Albashir Tahir. "A search for FDA approved drugs with multiple antiemetic targets: A computational-based drug repositioning study." Sokoto Journal of Medical Laboratory Science 10, no. 1 (2025): 210–18. https://doi.org/10.4314/sokjmls.v10i1.23.

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Emesis is a complex physiological response posing significant challenges in managing medical conditions such as gastroparesis, chemotherapy-induced nausea and vomiting (CINV), and post-operative nausea and vomiting (PONV). Antiemetic drugs are readily available; however, poor responses and adverse effects are still common, leading to non-compliance and exacerbation of existing health problems, thus underscoring the need for improved and innovative treatment strategies. This study aims to evaluate the potential of some selected FDA-approved drugs as multi-target antiemetic agents by assessing t

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Faya Castillo, Juan Enrique, Richard Junior Zapata Dongo, Paolo Alberto Wong Chero, and Stefany Fiorella Infante Varillas. "Mitoxantrone and abacavir: An ALK protein-targeted in silico proposal for the treatment of non-small cell lung cancer." PLOS ONE 19, no. 2 (2024): e0295966. http://dx.doi.org/10.1371/journal.pone.0295966.

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Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK+. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK+ NSCLC patients. However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an in silico approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling t

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Neale, Diana S., Philip E. Thompson, Paul J. White, David K. Chalmers, Elizabeth Yuriev, and David T. Manallack. "Binding Mode Prediction of PDE4 Inhibitors: A Comparison of Modelling Methods." Australian Journal of Chemistry 63, no. 3 (2010): 396. http://dx.doi.org/10.1071/ch09463.

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Molecular modelling is widely used in support of medicinal chemistry programs, with several theoretical approaches used in attempts to expedite drug discovery. In this study, three methods – molecular docking (Glide), shape similarity (ROCS), and pharmacophore modelling (Phase) – were evaluated for their ability to reproduce experimentally determined binding modes of 25 PDE4 inhibitors, identified by X-ray crystallography. Molecular docking was able to provide a good approximation (RMSD less than 2 Å) in 59% of cases, when considering the top binding pose. The pairwise comparisons, using molec

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Arba, Muhammad, and Jasriati Jasriati. "Structure-based Pharmacophore Modelling for identifying VEGFR2 Inhibitor." Research Journal of Pharmacy and Technology 13, no. 7 (2020): 3129. http://dx.doi.org/10.5958/0974-360x.2020.00553.3.

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T.H. Khan, M., Y. Wuxiuer, and I. Sylte. "Binding Modes and Pharmacophore Modelling of Thermolysin Inhibitors." Mini-Reviews in Medicinal Chemistry 12, no. 6 (2012): 515–33. http://dx.doi.org/10.2174/138955712800493799.

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12

Kohlbacher, Stefan Michael, Matthias Schmid, Thomas Seidel, and Thierry Langer. "Applications of the Novel Quantitative Pharmacophore Activity Relationship Method QPhAR in Virtual Screening and Lead-Optimisation." Pharmaceuticals 15, no. 9 (2022): 1122. http://dx.doi.org/10.3390/ph15091122.

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Pharmacophores are an established concept for the modelling of ligand–receptor interactions based on the abstract representations of stereoelectronic molecular features. They became widely popular as filters for the fast virtual screening of large compound libraries. A lot of effort has been put into the development of sophisticated algorithms and strategies to increase the computational efficiency of the screening process. However, hardly any focus has been put on the development of automated procedures that optimise pharmacophores towards higher discriminatory power, which still has to be do

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Tutone, Marco, Giulia Culletta, Luca Livecchi, and Anna M. Almerico. "A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings." Current Drug Discovery Technologies 17, no. 5 (2020): 740–47. http://dx.doi.org/10.2174/1570163816666190620113944.

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Cyclin Dependent Kinases-2 (CDK2) are members of serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicate that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free ener

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Giordano, Deborah, Carmen Biancaniello, Maria Antonia Argenio, and Angelo Facchiano. "Drug Design by Pharmacophore and Virtual Screening Approach." Pharmaceuticals 15, no. 5 (2022): 646. http://dx.doi.org/10.3390/ph15050646.

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Computer-aided drug discovery techniques reduce the time and the costs needed to develop novel drugs. Their relevance becomes more and more evident with the needs due to health emergencies as well as to the diffusion of personalized medicine. Pharmacophore approaches represent one of the most interesting tools developed, by defining the molecular functional features needed for the binding of a molecule to a given receptor, and then directing the virtual screening of large collections of compounds for the selection of optimal candidates. Computational tools to create the pharmacophore model and

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15

Bandoy, DJ Darwin. "Pangenome guided pharmacophore modelling of enterohemorrhagic Escherichia coli sdiA." F1000Research 8 (January 9, 2019): 33. http://dx.doi.org/10.12688/f1000research.17620.1.

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Enterohemorrhagic Escherichia coli (EHEC) continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences are a potential resource for predictive modelling of the different regulatory mechanism of pathogens, particularly quorum sensing. We used a pangenome approach to determine EHEC genome clustering, determine the synonymous and nonsynonymous mutations across the EHEC sdiA and modelled the associated amino acid changes. Across the EHEC population, nonsynonymous variants are notably absent in ligand binding site for quorum sensing, indicat

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16

Ren, Ji-Xia, Rui-Tao Zhang, and Hui Zhang. "Identifying Novel ATX Inhibitors via Combinatory Virtual Screening Using Crystallography-Derived Pharmacophore Modelling, Docking Study, and QSAR Analysis." Molecules 25, no. 5 (2020): 1107. http://dx.doi.org/10.3390/molecules25051107.

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Autotaxin (ATX) is considered as an interesting drug target for the therapy of several diseases. The goal of the research was to detect new ATX inhibitors which have novel scaffolds by using virtual screening. First, based on two diverse receptor-ligand complexes, 14 pharmacophore models were developed, and the 14 models were verified through a big test database. Those pharmacophore models were utilized to accomplish virtual screening. Next, for the purpose of predicting the probable binding poses of compounds and then carrying out further virtual screening, docking-based virtual screening was

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Dhaval, V. Patel Mukesh Nandave Prashant S. Kharkar. "PHARMACOPHORE MODELLING FOR THE DISCOVERY OF SYSTEM XC- ANTIPORTER INHIBITORS." INDO AMERICAN JOURNAL OF PHARMACEUTICAL RESEARCH 07, no. 09 (2017): 532–36. https://doi.org/10.5281/zenodo.1036492.

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Cancer is one of the major disorders with increasing rates of morbidity and mortality. Recent drug discovery of anti cancer drug has identified several molecular targets and tried to achieve a goal of therapeutic effecative and safe molecule. Amongst these, system xc- antiporter is a novel promising target to control cancer progression. This antiporter is found to be over expressed in majority of cancer cells and functions by transporting amino acids, cystine and glutamate, in opposite directions. System xc- antiporter uptakes one molecule of cystine with the release of one molecule of glutama

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18

Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud E. S. Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling." Molecules 24, no. 17 (2019): 3125. http://dx.doi.org/10.3390/molecules24173125.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties availabl

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Bapusaheb Jare, Krushna, Miss Aaditee Gore, and Dr Megha T.Salve. "An overview on a Computer-Aided Drug Designby Pharmacophore modelling and Virtual screening approach." International Journal of Pharmaceutical Research and Applications 09, no. 06 (2024): 669–77. https://doi.org/10.35629/4494-0906669677.

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The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimize every step of the process in order to maximize the chances of success. As a result of the recent advancements in computer power and technology, computer-aid

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20

Chokshi, Avani B., Mahesh T. Chhabria, and Pritesh R. Desai. "Rational Discovery of Novel Squalene Synthase Inhibitors through Pharmacophore Modelling." Current Computer-Aided Drug Design 14, no. 3 (2018): 221–33. http://dx.doi.org/10.2174/1573409914666180507143024.

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21

El Bakkali, Mustapha, Lhassane Ismaili, Isabelle Tomassoli, Laurence Nicod, Marc Pudlo, and Bernard Refouvelet. "Pharmacophore Modelling and Synthesis of Quinoline-3-Carbohydrazide as Antioxidants." International Journal of Medicinal Chemistry 2011 (March 28, 2011): 1–10. http://dx.doi.org/10.1155/2011/592879.

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From well-known antioxidants agents, we developed a first pharmacophore model containing four common chemical features: one aromatic ring and three hydrogen bond acceptors. This model served as a template in virtual screening of Maybridge and NCI databases that resulted in selection of sixteen compounds. The selected compounds showed a good antioxidant activity measured by three chemical tests: DPPH radical, OH∘ radical, and superoxide radical scavenging. New synthetic compounds with a good correlation with the model were prepared, and some of them presented a good antioxidant activity.

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22

Nazmiye Sabanc, Nazmiye Sabanc. "Pharmacophore Modelling and 4D QSAR Analysis of Some Indole Glyoxamide Derivatives as HIV-1 Binding Inhibitors." Journal of the chemical society of pakistan 44, no. 2 (2022): 160. http://dx.doi.org/10.52568/001000/jcsp/44.02.2022.

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The main aim of this study is to uncover the main pharmacophoric features of a series of indole glyoxamide derivatives which are known as HIV-1 attachment inhibitors and to estimate the biological activity to develop a 4D-QSAR model by using the EC-GA method. Conformational analysis and quantum mechanical calculations were accomplished by using the Hartree Fock method with the 3-21G basis set. Based on the data produced from the quantum chemical calculations, the electron conformational matrices of congruity (ECMC)s, as the 3D- arrangement of electronic and geometric properties, were generated

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23

Raphael, Vinod P., K. S. Shaju, T. K. Bindu, and A. Sini. "In silico investigations on the repurposing of antivirals for Covid-19 and pharmacophore modelling." Current Chemistry Letters 13, no. 1 (2024): 199–206. http://dx.doi.org/10.5267/j.ccl.2023.7.001.

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The pandemic COVID-19 has been spreading around the globe from December 2019 onwards and is considered the most infectious disease of this century. To date, there is no effective drug against SARS-CoV-2 discovered by pharmaceutical scientists, and the research is going rigorously all over the world. In this work, we examined the interaction of the already existing antivirals (Lopinavir, Atazanavir, and Remdesivir) with the structural proteins of SARS-CoV-2 using computational methods. Pharmacophore modeling of these drugs was conducted using molecular databases to determine the lead compounds

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Kathiravan, Muthu Kumaradoss. "Molecular modelling investigation on 4-aminoquinoline derivatives as potent anti-tubercular agents." Journal of medical pharmaceutical and allied sciences 11, no. 5 (2022): 5304–11. http://dx.doi.org/10.55522/jmpas.v11i5.4167.

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The emergency of new Mycobacterium tuberculosis strains leads to multi-drug resistant tuberculosis (MDR) and total drug resistant tuberculosis (TDR) indicating the urgency in the development of newer anti-tubercular agents to be effective against the resistance strains. In the present study pharmacophore modelling and atom-based 3D-QSAR of 4-Aminoquinoline derivatives was carried out to understand the key structural features responsible for anti-tb activity. Phase module of Schrödinger was used to generate a five-point Pharmacophore for 46 molecules belonging to 4-Aminoquinolines. The best sco

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Chagaleti, Bharath Kumar, Venkatesan Saravanan, Chitra Vellapandian, and Muthu K. Kathiravan. "Exploring cyclin-dependent kinase inhibitors: a comprehensive study in search of CDK-6 inhibitors using a pharmacophore modelling and dynamics approach." RSC Advances 13, no. 48 (2023): 33770–85. http://dx.doi.org/10.1039/d3ra05672d.

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26

Shy, Teng Woei, and Anand Gaurav. "Pharmacophore Modelling and Virtual Screening Studies for the Discovery of Potential Natural Products Based PDE1B Inhibitor Lead Compounds." Central Nervous System Agents in Medicinal Chemistry 21, no. 3 (2021): 195–204. http://dx.doi.org/10.2174/1871524922666211231115638.

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Aim: The aim of the present study was to apply pharmacophore based virtual screening to a natural product database to identify potential PDE1B inhibitor lead compounds for neurodegenerative and neuropsychiatric disorders. Background: Neurodegenerative and neuropsychiatric disorders are a major health burden globally. The existing therapies do not provide optimal relief and are associated with substantial adverse effects. This has resulted in a huge unmet medical need for newer and more effective therapies for these disorders. Phosphodiesterase (PDEs) enzymes have been identified as potential t

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27

Sairam, Kalapatapu, Roop Khar, Rama Mukherjee, and Swatantra Jain. "Three Dimensional Pharmacophore Modelling of Monoamine oxidase-A (MAO-A) inhibitors." International Journal of Molecular Sciences 8, no. 9 (2007): 894–919. http://dx.doi.org/10.3390/i8090894.

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28

Parihar, R. T. "AcylAminoBenzothiazole Series as Inhibitors of Trypanosoma Cruzi : A Pharmacophore Modelling Approach." International Journal for Research in Applied Science and Engineering Technology 7, no. 12 (2019): 1053–55. http://dx.doi.org/10.22214/ijraset.2019.12164.

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Caporuscio, F., and A. Tafi. "Pharmacophore Modelling: A Forty Year Old Approach and its Modern Synergies." Current Medicinal Chemistry 18, no. 17 (2011): 2543–53. http://dx.doi.org/10.2174/092986711795933669.

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Behera, D. K., P. M. Behera, L. Acharya, and A. Dixit. "Pharmacophore modelling, virtual screening and molecular docking studies on PLD1 inhibitors." SAR and QSAR in Environmental Research 28, no. 12 (2017): 991–1009. http://dx.doi.org/10.1080/1062936x.2017.1393774.

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31

Kansal, Neha, Om Silakari, and Muttineni Ravikumar. "Three dimensional pharmacophore modelling for c-Kit receptor tyrosine kinase inhibitors." European Journal of Medicinal Chemistry 45, no. 1 (2010): 393–404. http://dx.doi.org/10.1016/j.ejmech.2009.09.013.

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Vittorio, Serena, Rosaria Gitto, Ilenia Adornato, Emilio Russo, and Laura De Luca. "In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules." Molecules 26, no. 4 (2021): 1103. http://dx.doi.org/10.3390/molecules26041103.

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Computer aided drug-design methods proved to be powerful tools for the identification of new therapeutic agents. We employed a structure-based workflow to identify new inhibitors targeting mTOR kinase at rapamycin binding site. By combining molecular dynamics (MD) simulation and pharmacophore modelling, a simplified structure-based pharmacophore hypothesis was built starting from the FKBP12-rapamycin-FRB ternary complex retrieved from RCSB Protein Data Bank (PDB code 1FAP). Then, the obtained model was used as filter to screen the ZINC biogenic compounds library, containing molecules derived f

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33

Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase Through Target-Focused Modelling." Proceedings 22, no. 1 (2019): 103. http://dx.doi.org/10.3390/proceedings2019022103.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the Nedd4-1 E3 Ubiquitin ligase is an enzyme that may be targeted either covalently, or non-covalently, there are few studies that demonstrate effective inhibitors of the enzyme. In this work, we aimed to identify covalent inhibitors of Nedd4-1. This task however, proved to be challenging due to the limited available electrophilic moieties in virtual libraries. We therefore opted to divide an existing covalent Nedd4-1 inhibitor in two parts: A non-covalent binding part and a pre-

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Kawade, V. S., S. S. Kumbhar, P. B. Choudhari, and M. S. Bhatia. "3D QSAR and Pharmacophore Modelling of some Pyrimidine Analogs as CDK4 Inhibitors." Asian Journal of Research in Chemistry 8, no. 4 (2015): 231. http://dx.doi.org/10.5958/0974-4150.2015.00040.1.

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Moaddel, R., S. Ravichandran, F. Bighi, R. Yamaguchi, and I. W. Wainer. "Pharmacophore modelling of stereoselective binding to the human organic cation transporter (hOCT1)." British Journal of Pharmacology 151, no. 8 (2007): 1305–14. http://dx.doi.org/10.1038/sj.bjp.0707341.

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Rampogu, S., C. Park, M. Son, et al. "Modulation of aromatase by natural compounds—A pharmacophore guided molecular modelling simulations." South African Journal of Botany 120 (January 2019): 230–40. http://dx.doi.org/10.1016/j.sajb.2018.06.019.

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Mahrous, Rahma, Hoda Fathy, Rasha Abu EL-Khair, Abdallah Omar, and Reham Ibrahim. "Molecular docking and pharmacophore modelling; A bridged explanation with emphasis on validation." Journal of Advanced Pharmaceutical Sciences 1, no. 1 (2024): 138–52. http://dx.doi.org/10.21608/japs.2024.253925.1007.

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38

Toplak, Žan, Louise Antonia Hendrickx, Špela Gubič, et al. "3D Pharmacophore-Based Discovery of Novel KV10.1 Inhibitors with Antiproliferative Activity." Cancers 13, no. 6 (2021): 1244. http://dx.doi.org/10.3390/cancers13061244.

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(1) Background: The voltage-gated potassium channel KV10.1 (Eag1) is considered a near- universal tumour marker and represents a promising new target for the discovery of novel anticancer drugs. (2) Methods: We utilized the ligand-based drug discovery methodology using 3D pharmacophore modelling and medicinal chemistry approaches to prepare a novel structural class of KV10.1 inhibitors. Whole-cell patch clamp experiments were used to investigate potency, selectivity, kinetics and mode of inhibition. Anticancer activity was determined using 2D and 3D cell-based models. (3) Results: The virtual

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Cui, Zhijie, Hong Kang, Kailin Tang, Qi Liu, Zhiwei Cao, and Ruixin Zhu. "Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation." BioMed Research International 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/657159.

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The issue of herb-drug interactions has been widely reported. Herbal ingredients can activate nuclear receptors and further induce the gene expression alteration of drug-metabolizing enzyme and/or transporter. Therefore, the herb-drug interaction will happen when the herbs and drugs are coadministered. This kind of interaction is called inductive herb-drug interactions. Pregnane X Receptor (PXR) and drug-metabolizing target genes are involved in most of inductive herb-drug interactions. To predict this kind of herb-drug interaction, the protocol could be simplified to only screen agonists of P

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Alzain, Abdulrahim A., Mohammed A. Almogaddam, Alaa A. Makki, et al. "Screening Enamine Fragments Library in the Quest for Novel SOS2 Inhibitors: Pharmacophore Modelling, Molecular Docking, MMGBSA Calculations, and MD Simulation." Journal of Pharmacy and Bioallied Sciences 17, Suppl 2 (2025): S1894—S1899. https://doi.org/10.4103/jpbs.jpbs_534_25.

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ABSTRACT Introduction: The son of sevenless (SOS) proteins are rat sarcoma virus nucleotide exchange factors that act as regulatory switches of the rat sarcoma virus (RAS) system through the conversion of the inactive guanosine diphosphate (GDP) bound RAS to the GTP-bound active form, thereby modulating numerous biological events. SOSs contribute in disease incidence and progression in numerous cancers. Currently, SOSs inhibiting strategies deemed a substantial interest in the fight against cancer. Materials and methods: To date, there are various SOS1 inhibitors in the clinical trials, howeve

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Wang, Jian, Maocai Yan, Dongmei Zhao, Yu Sha, Feng Li, and Maosheng Cheng. "Pharmacophore identification of PAK4 inhibitors." Molecular Simulation 36, no. 1 (2010): 53–57. http://dx.doi.org/10.1080/08927020903096098.

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Kumar, Sivakumar Prasanth, and Prakash Chandra Jha. "Multi-level structure-based pharmacophore modelling of caspase-3-non-peptide complexes: Extracting essential pharmacophore features and its application to virtual screening." Chemico-Biological Interactions 254 (July 2016): 207–20. http://dx.doi.org/10.1016/j.cbi.2016.06.011.

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Rampogu, Shailima, Doneti Ravinder, Smita Pawar, and Keun Lee. "Natural Compound Modulates the Cervical Cancer Microenvironment—A Pharmacophore Guided Molecular Modelling Approaches." Journal of Clinical Medicine 7, no. 12 (2018): 551. http://dx.doi.org/10.3390/jcm7120551.

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Cervical cancer is regarded as one of the major burdens noticed in women next to breast cancer. Although, human papilloma viruses (HPVs) are regarded as the principal causative agents, they require certain other factors such as oestrogen hormone to induce cervical cancer. Aromatase is an enzyme that converts androgens into oestrogens and hindering this enzyme could subsequently hamper the formation of oestrogen thereby alleviating the disease. Accordingly, in the current investigation, a structure based pharmacophore was generated considering two proteins bearing the Protein Data Bank (PDB) co

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Deng, Xiao-Qiang, Hui-Yuan Wang, Ying-Lan Zhao, et al. "Pharmacophore Modelling and Virtual Screening for Identification of New Aurora-A Kinase Inhibitors." Chemical Biology & Drug Design 71, no. 6 (2008): 533–39. http://dx.doi.org/10.1111/j.1747-0285.2008.00663.x.

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Karkola, Sampo, Sari Alho-Richmond та Kristiina Wahala. "Pharmacophore modelling of 17β-HSD1 enzyme based on active inhibitors and enzyme structure". Molecular and Cellular Endocrinology 301, № 1-2 (2009): 225–28. http://dx.doi.org/10.1016/j.mce.2008.08.030.

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Sorich, Michael J., Paul A. Smith, Ross A. McKinnon, and John O. Miners. "Pharmacophore and quantitative structure activity relationship modelling of UDP-glucuronosyltransferase 1A1 (UGT1A1) substrates." Pharmacogenetics 12, no. 8 (2002): 635–45. http://dx.doi.org/10.1097/00008571-200211000-00008.

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Vijayalakshmi, Periyasamy, Chandrabose Selvaraj, Raja Mohmed Beema Shafreen, Sanjeev Kumar Singh, Shunmugiah Karutha Pandian, and Pitchai Daisy. "Ligand-based pharmacophore modelling and screening of DNA minor groove binders targetingStaphylococcus aureus." Journal of Molecular Recognition 27, no. 7 (2014): 429–37. http://dx.doi.org/10.1002/jmr.2363.

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Mishra, Shweta, Rashmi Dahima та Rajesh Sharma. "Design of Some Benzimidazoles as Target for α-Glucosidase Inhibitors". Journal of Drug Delivery and Therapeutics 10, № 2-s (2020): 198–208. http://dx.doi.org/10.22270/jddt.v10i2-s.4017.

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Diabetes mellitus is rising globally touching more than 180 million people worldwide. This is prevailing mostly in type 2 diabetes and according to WHO report the incidence is likely to be more than doubled by 2030. α-Glucosidase inhibitors work by reducing the amount of glucose that the intestines absorb from food. In this work, forty-five benzimidazole analogues were studied using 3D QSAR, HQSAR, pharmacophore mapping and based on their results 60 compounds were designed. The results show that the best Comparative Molecular Field Analysis (CoMFA) model has q2 = 0.742 and r2 = 0.973, and the

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Rampogu, Shailima, Gihwan Lee, Ayoung Baek, et al. "Discovery of Non-Peptidic Compounds against Chagas Disease Applying Pharmacophore Guided Molecular Modelling Approaches." Molecules 23, no. 12 (2018): 3054. http://dx.doi.org/10.3390/molecules23123054.

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Chagas disease is one of the primary causes of heart diseases accounting to 50,000 lives annually and is listed as the neglected tropical disease. Because the currently available therapies have greater toxic effects with higher resistance, there is a dire need to develop new drugs to combat the disease. In this pursuit, the 3D QSAR ligand-pharmacophore (pharm 1) and receptor-based pharmacophore (pharm 2) search was initiated to retrieve the candidate compounds from universal natural compounds database. The validated models were allowed to map the universal natural compounds database. The obtai

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Zhang, Xiangyu, Hailun Jiang, Wei Li, Jian Wang, and Maosheng Cheng. "Computational Insight into Protein Tyrosine Phosphatase 1B Inhibition: A Case Study of the Combined Ligand- and Structure-Based Approach." Computational and Mathematical Methods in Medicine 2017 (2017): 1–13. http://dx.doi.org/10.1155/2017/4245613.

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Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. Firstly, the pharmacophore model of PTP1B inhibitors was built based on the common feature of sixteen compounds. It was found that the pharmacophore model consisted of five chemical features: one aromatic ring (R) region, two hydrophobic (H) groups, and two hydrogen bond acceptors (A). To further elucidate

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