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Journal articles on the topic 'Pharmacophore groups'

Author: Grafiati

Published: 3 June 2025

Last updated: 19 July 2025

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1

Suprapto, Suprapto, and Yatim Lailun Nimah. "Molecules Absorption Prediction Using Support Vector, Adaboost, Random Forest and Decision Tree Classification." Journal of Biomedical Research & Environmental Sciences 3, no. 3 (2022): 277–82. http://dx.doi.org/10.37871/jbres1433.

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Classification is supervised machine learning applicable to predict chemicals based on their properties. The chemical properties are derived from its structural and functional groups. Many molecular descriptors have been developed, one of which, was pharmacophore. Pharmacophore is a quantitative measure of molecules in their application as a pharmaceutical ingredient. The training datasets were 59 molecules categorized on their adsorption properties. The classification was carried out to divide the training set into their adsorption class using their pharmacophores. The prediction of enolic cu

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Suprapto, S. Ni'mah YL. "Molecules Absorption Prediction Using Support Vector, Adaboost, Random Forest and Decision Tree Classification." J Biomed Res Environ Sci 3, no. 3 (2022): 277–82. https://doi.org/10.37871/jbres1433.

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Classification is supervised machine learning applicable to predict chemicals based on their properties. The chemical properties are derived from its structural and functional groups. Many molecular descriptors have been developed, one of which, was pharmacophore. Pharmacophore is a quantitative measure of molecules in their application as a pharmaceutical ingredient. The training datasets were 59 molecules categorized on their adsorption properties. The classification was carried out to divide the training set into their adsorption class using their pharmacophores. The prediction of enolic cu

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Wang, Ying, Hongwei Wang, Li Liang, and Chongyang Jia. "Effects of Computer Virtual Screening and Treatment Based on Pharmacophore BRD4-Targeted Small-Molecule Inhibitors on NSE and CA19-9 Levels in Patients with Liver Cancer." Journal of Biomedical Nanotechnology 19, no. 7 (2023): 1295–300. http://dx.doi.org/10.1166/jbn.2023.3620.

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Objective: Neuron-specific enolase (NSE) and carbohydrate antigen 19-9 (CA19-9) levels were compared before and after treatment with brd4-targeting small-molecule inhibitors based on pharmacophores and computer technology to investigate an efficient virtual screening method for bromodomain protein 4 (brd4)-targeted small-molecule inhibitors. The purpose of this research was to examine the efficacy of pharmacophore screening and BRD4 targeting by small-molecule inhibitors in the management of liver cancer. Methods: Subjects included 106 individuals with hepatocellular cancer who were hospitalis

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Pradhan, Joohee, and Sunita Panchawat. "Molecular Docking Studies and Pharmacophore Modeling of Some Insulin Mimetic Agents from Herbal Sources: A Rational Approach towards Designing of Orally Active Insulin Mimetic Agents." Current Traditional Medicine 6, no. 2 (2020): 121–33. http://dx.doi.org/10.2174/2215083805666191001220342.

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Background:: Many herbal drugs have been found to possess oral insulin mimetic property as evidenced from the literature. Although, to date there is no efficient, synthetic orally active insulin-mimetic drug available clinically. Computer-Aided Drug Design (CADD) may help in the development of such agents through Pharmacophore modeling. Objective:: The present work is aimed at the In-silico designing of Pharmacophore that defines the structural requirements of a molecule to possess oral insulin-mimetic properties. Methods:: A set of 16 orally active insulin-mimetic natural compounds available

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Gopiwad, Prachit. "Medicinal chemistry of catechol, a versatile pharmacophore." Current Trends in Pharmacy and Pharmaceutical Chemistry 6, no. 1 (2024): 7–11. http://dx.doi.org/10.18231/j.ctppc.2024.003.

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Catechol being a versatile pharmacophore, used in medicine as a molecular group in adjunction with other moieties and functional groups. The versatile pharmacophore has rendered several useful pharmaceuticals so far. The major medicines or the pharmaceutical drugs containing catechol moiety include levodopa, carbidopa, and several others. The FDA approved pharmaceutical preparations have been highlighted and reviewed in this paper.

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Mahajani, Nivedita S., and John D. Chisholm. "Promoter free allylation of trichloroacetimidates with allyltributylstannanes under thermal conditions to access the common 1,1′-diarylbutyl pharmacophore." Organic & Biomolecular Chemistry 16, no. 21 (2018): 4008–12. http://dx.doi.org/10.1039/c8ob00687c.

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Fernandes, Adriana de Oliveira, Valéria Vieira Moura Paixão, Yria Jaine Andrade Santos, et al. "Identification of Pharmacophore Groups with Antimalarial Potential in Flavonoids by QSAR-Based Virtual Screening." Drugs and Drug Candidates 4, no. 3 (2025): 33. https://doi.org/10.3390/ddc4030033.

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Background/Objectives: Severe malaria, mainly caused by Plasmodium falciparum, remains a significant therapeutic challenge due to increasing drug resistance and adverse effects. Flavonoids, known for their wide range of bioactivities, offer a promising route for antimalarial drug discovery. The aim of this study was to elucidate key structural features associated with antimalarial activity in flavonoids and to develop accurate, interpretable predictive models. Methods: Curated databases of flavonoid structures and their activity against P. falciparum strains and enzymes were constructed. Molec

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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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Zhang, Yan Ling, Yuan Ming Wang, and Yan Jiang Qiao. "Sub-Pharmacophore Generation of JNK3 Inhibitors." Applied Mechanics and Materials 444-445 (October 2013): 1756–60. http://dx.doi.org/10.4028/www.scientific.net/amm.444-445.1756.

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The structure-based pharmacophore (SBP) model is consisted by the complementarity of the chemical features and space of the interaction between the ligand and receptor. The SBP models always have a high specificity which can only represent the specific class of the ligand. To simplify the models, sub-pharmacophore was then proposed in present study, and was expected to have and only have the most important or the common chemical features which play the major role in the interaction of ligand and receptor. Sub-pharmacophore should contain 4-6 features, the higher specificity with more features,

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10

Sousa, Rui, Narayana Subbiah Hari Narayana Moorthy, Pedro Alexandrino Fernandes, Maria Joao Ramos, and Natércia Fernandes Brás. "Binding Mode Prediction and Identification of New Lead Compounds from Natural Products as 3-OST Enzyme Inhibitors." Letters in Drug Design & Discovery 17, no. 9 (2020): 1186–96. http://dx.doi.org/10.2174/1570180817666200313105944.

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Background and Introduction: The availability of antiviral medicines for the treatment of viral diseases is limited, hence the discovery of novel bioactive molecules is required. The present investigation has been carried out to develop novel 3-O-sulfotransferase enzyme inhibitors to treat viral diseases. Method: Virtual screening study (QSAR, docking and pharmacophore analysis) and binding mode analysis have been performed on a dataset collected from the literature (synthetic and natural compounds). Results: The docking studies showed that Glu184, His186, Lys215 and Lys368 residues establishe

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Mudarisova, Roza Khanifovna, Alina Failovna Sagitova, and Ol'ga Sergeyevna Kukovinets. "COMPLEXATION OF APPLE PECTIN, MODIFIED TO PHARMACOPHORE, WITH THE CATIONS MANGANESE (II) IN AQUEOUS SOLUTIONS." chemistry of plant raw material, no. 1 (March 5, 2020): 25–32. http://dx.doi.org/10.14258/jcprm.2020015161.

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Complex formation in systems containing manganese (II), natural pectin and/or pectin modified by organic pharmacophores (nicotine, salicylic, 5-aminosalicylic, anthranilic acids) was studied by spectral (UV-, IR-, NMR 13C spectroscopy), potentiometric and viscometric methods. Method isomolar series and the molar relationship defined by the molar composition and the range of stability of metal complexes: pectin + nicotinic acid > pectin + acid 5-aminosalicylic > pectin + anthranilic acid > pectin + salicylic acid > native pectin. It is shown that the stability constant of metal comp

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Tsirogianni, Artemis, Georgia G. Kournoutou, Anthony Bougas, Eleni Poulou-Sidiropoulou, George Dinos, and Constantinos M. Athanassopoulos. "New Chloramphenicol Derivatives with a Modified Dichloroacetyl Tail as Potential Antimicrobial Agents." Antibiotics 10, no. 4 (2021): 394. http://dx.doi.org/10.3390/antibiotics10040394.

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To combat the dangerously increasing pathogenic resistance to antibiotics, we developed new pharmacophores by chemically modifying a known antibiotic, which remains to this day the most familiar and productive way for novel antibiotic development. We used as a starting material the chloramphenicol base, which is the free amine group counterpart of the known chloramphenicol molecule antibiotic upon removal of its dichloroacetyl tail. To this free amine group, we tethered alpha- and beta-amino acids, mainly glycine, lysine, histidine, ornithine and/or beta-alanine. Furthermore, we introduced add

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Baldini, Lorenzo, Elena Lenci, Francesca Bianchini, and Andrea Trabocchi. "Identification of a Common Pharmacophore for Binding to MMP2 and RGD Integrin: Towards a Multitarget Approach to Inhibit Cancer Angiogenesis and Metastasis." Molecules 27, no. 4 (2022): 1249. http://dx.doi.org/10.3390/molecules27041249.

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During tumor angiogenesis different growth factors, cytokines and other molecules interact closely with each other to facilitate tumor cell invasion and metastatic diffusion. The most intensively studied as molecular targets in anti-angiogenic therapies are vascular endothelial growth factor (VEGF) and related receptors, integrin receptors and matrix metalloproteinases (MMPs). Considering the poor efficacy of cancer angiogenesis monotherapies, we reasoned combining the inhibition of αvβ3 and MMP2 as a multitarget approach to deliver a synergistic blockade of tumor cell migration, invasion and

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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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Lin, Yang, Heyanhao Zhang, Tong Niu, Mei-Lin Tang, and Jun Chang. "Discovery of Novel Indoleamine 2,3-Dioxygenase 1 (IDO1) and Histone Deacetylase 1 (HDAC1) Dual Inhibitors Derived from the Natural Product Saprorthoquinone." Molecules 25, no. 19 (2020): 4494. http://dx.doi.org/10.3390/molecules25194494.

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The discovery of IDO1 and HDAC1 dual inhibitors may provide a novel strategy for cancer treatment by taking advantages of both immunotherapeutic and epigenetic drugs. In this paper, saprorthoquinone (1) and 13 of its analogues from Salvia prionitis Hance were investigated for their SAR against IDO1, the results demonstrated the ortho-quinone was a key pharmacophore. Then a series of IDO1 and HDAC dual inhibitors connected by appropriate linkers were designed, synthesized, and evaluated from the hit compound saprorthoquinone (1). Among them, compound 33d showed balanced activity against both ID

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Ujiantari, Navista Sri Octa, and Cintya Nurul Apsari. "Pharmacophore mapping of Angiotensin Converting Enzymes (ACEs): Insight to Binding Site of ACE1 and ACE2." Biology, Medicine, & Natural Product Chemistry 13, no. 2 (2024): 337–41. http://dx.doi.org/10.14421/biomedich.2024.132.337-341.

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Angiotensin Converting Enzymes (ACEs) are carboxypeptidase enzymes involved in the renin-angiotensin system (RAS), which catalyze angiotensin I by cleavage of the peptide bond. ACE1 has been known as a target for antihypertensive drugs. Another homolog of ACE1, ACE2 has been popular since 2020 because this enzyme is responsible for the SARS-COV2 infection in the human body. Interestingly, it was found that ACE1 inhibitors did not inhibit ACE2. Hence, this study aims to elucidate the pharmacophore of ACE1 and ACE2 in order to understand the mechanism of these different inhibitions. Pharmacophor

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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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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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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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Sánchez-Álvarez, Axel A., Marco A. Velasco-Velázquez та Luis Cordova-Bahena. "In Silico Identification of 2,4-Diaminopyrimidine-Based Compounds as Potential CK1ε Inhibitors". Pharmaceuticals 18, № 5 (2025): 741. https://doi.org/10.3390/ph18050741.

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Background: Casein kinase 1 epsilon (CK1ε) plays a critical role in cancer progression by activating oncogenic signaling pathways, making it a target for cancer therapy. However, no inhibitors are currently available for clinical use, highlighting the need for novel therapeutic candidates. Methods: This study aimed to identify potential CK1ε inhibitors. To achieve this, a modified version of a previously reported pharmacophore model was applied to an ultra-large database of over 100 million compounds for virtual screening. Hits were filtered based on drug-likeness and pH-dependent pharmacophor

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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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Zhuravlova, Maryna, Nataliya Obernikhina, Stepan Pilyo, Maryna Kachaeva, Oleksiy Kachkovsky, and Volodymyr Brovarets. "In silico binding affinity studies of phenyl-substituted 1,3-oxazoles with protein molecules." Ukr. Bioorg. Acta 2020, Vol. 15, N1 15, no. 1 (2020): 12–19. http://dx.doi.org/10.15407/bioorganica2020.01.012.

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The new model approach of interaction between the pharmacophores with bio-molecules, fragment-to-fragment, is presented. It is a new step of the molecular modeling and takes correctly into consideration not only the spatial complementarity of the interacted molecules but also the contribution of the stacking π-π-electron interaction and hydrogen bonds. As an example, the correct analysis of the interaction of the biological active phenyl-substituted 1,3-oxazoles with protein fragments is performed. It was shown that the length and energy of the hydrogen bond uniquely depend on the chemical con

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Sharma, Kalicharan, Apeksha Srivastava, Pooja Tiwari, et al. "3D QSAR Based Virtual Screening of Pyrido[1,2-a] Benzimidazoles as Potent Antimalarial Agents." Letters in Drug Design & Discovery 16, no. 3 (2019): 301–12. http://dx.doi.org/10.2174/1570180815666180502115147.

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Background: Development of novel antimalarial agents has been one of the sought areas in medicinal chemistry. In this study the same was done by virtual screening of in-house database on developed QSAR model. </P><P> Methods: A six point pharmacophore model was generated (AADHRR.56) from 41 compounds using PHASE module of Schrodinger software and used for pharmacophore based search. Docking studies of the obtained hits were performed using GLIDE. Most promising hit was synthesized & biologically evaluated for antimalarial activity. </P><P> Result: The best generated

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Singh, Karanveer, Manish Sinha, Shruti Kuletha, et al. "Synthesis, Antitubercular Activity, Molecular Modeling and Docking Studies of Novel Thiazolidin-4-One Linked Dinitrobenzamide Derivatives." Current Bioactive Compounds 16, no. 1 (2020): 64–71. http://dx.doi.org/10.2174/1573407214666180720150009.

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Background: Tuberculosis is a catastrophe sprawled across the world. The World Health Organization Global Tuberculosis Report 2017 inferred that there were an estimated 10.4 million people suffered from tuberculosis including 490000 Multidrug-Resistant TB (MDR-TB) cases. Several new lead molecules like dinitrobenzamide derivatives were found to be highly active against multidrugresistant strains of M. tuberculosis. To further explore the pharmacophoric space around the dinitobenzamide moiety, a series of compounds have been synthesized by linking it with the thiazolidin- 4-one. The presented w

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Islamova, Liliya N., Valentina P. Gubskaya, Guzel M. Fazleeva, et al. "Synthesis of derivatives of fullerenes C 60 and C 70 containing pharmacophore groups." Mendeleev Communications 27, no. 2 (2017): 204–6. http://dx.doi.org/10.1016/j.mencom.2017.03.033.

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Luk'yanenko, N. G., A. V. Bogatskii, T. A. Voronina, et al. "Macroheterocyclic compounds. XXIII. Antihypoxic and antiamnestic properties of azacrown ethers with pharmacophore groups." Pharmaceutical Chemistry Journal 19, no. 6 (1985): 403–5. http://dx.doi.org/10.1007/bf00766946.

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Aroso, Rafael T., Rita C. Guedes, and Mariette M. Pereira. "Synthesis of Computationally Designed 2,5(6)-Benzimidazole Derivatives via Pd-Catalyzed Reactions for Potential E. coli DNA Gyrase B Inhibition." Molecules 26, no. 5 (2021): 1326. http://dx.doi.org/10.3390/molecules26051326.

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A pharmacophore model for inhibitors of Escherichia coli’s DNA Gyrase B was developed, using computer-aided drug design. Subsequently, docking studies showed that 2,5(6)-substituted benzimidazole derivatives are promising molecules, as they possess key hydrogen bond donor/acceptor groups for an efficient interaction with this bacterial target. Furthermore, 5(6)-bromo-2-(2-nitrophenyl)-1H-benzimidazole, selected as a core molecule, was prepared on a multi-gram scale through condensation of 4-bromo-1,2-diaminobenzene with 2-nitrobenzaldehyde using a sustainable approach. The challenging function

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Barbosa, Bárbara Lima Fonseca, Tulio Resende Freitas, Michell de Oliveira Almeida, et al. "Virtual Screening of Adenylate Kinase 3 Inhibitors Employing Pharmacophoric Model, Molecular Docking, and Molecular Dynamics Simulations as Potential Therapeutic Target in Chronic Lymphocytic Leukemia." Future Pharmacology 1, no. 1 (2021): 60–79. http://dx.doi.org/10.3390/futurepharmacol1010006.

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Adenylate kinase 3 (AK3) is an enzyme located in the mitochondrial matrix involved in purine homeostasis. This protein has been considered a potential therapeutic target in chronic lymphocytic leukemia (CLL), because the silencing of the AK3 gene has inhibited cell growth in CLL in vitro models. This study aimed to design potential AK3 inhibitors by applying molecular modeling techniques. Through the mapping of AK3 binding sites, essential interaction fields for pharmacophore design were identified. Online libraries were virtually screened by using a pharmacophore model, and 6891 compounds exh

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Narayana Moorthy, N. S. Hari, Sergio F. Sousa, Maria J. Ramos, and Pedro A. Fernandes. "In Silico–Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects." Journal of Biomolecular Screening 16, no. 9 (2011): 1037–46. http://dx.doi.org/10.1177/1087057111414899.

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In the present investigation, the authors have performed an in silico–based analysis on a series of arylthiophene derivatives for the determination of their structural features responsible for farnesyltransferase (FTase) inhibitory activity, hERG blocking activity, and toxicity by quantitative structure–activity relationship and pharmacophore analysis techniques. The statistically significant models derived through multiple linear regression analysis were validated by different validation methods. The applicability of the descriptors contributed in the selected models show that the polar and p

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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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Gelmboldt, V. O., I. V. Lytvynchuk, I. O. Shyshkin, L. N. Ognichenko, and V. E. Kuz’min. "Prognosis of biological activity and lipophilicity of some pyridine derivatives as components of anti-caries agents." Farmatsevtychnyi zhurnal, no. 2 (May 7, 2020): 79–85. http://dx.doi.org/10.32352/0367-3057.2.20.08.

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In recent years, a high carioprophylactic efficacy of ammonium hexafluorosilicates with biologically active cations has been discovered (АHBC). In the case of using AHBC, there is a potential possibility of enhancing the anticaries effect of the fluorine-containing anion as a result of the contribution of the effects of cations, for example, anti-inflammatory effects. The purpose of the work is a virtual analysis of the biological activity and lipophilicity of pyridine derivatives containing pharmacophores associated with anti-inflammatory activity (AIA), as possible candidates for the synthes

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Galli, Ubaldina, Gian Cesare Tron, Beatrice Purghè, Giorgio Grosa, and Silvio Aprile. "Metabolic Fate of the Isocyanide Moiety: Are Isocyanides Pharmacophore Groups Neglected by Medicinal Chemists?" Chemical Research in Toxicology 33, no. 4 (2020): 955–66. http://dx.doi.org/10.1021/acs.chemrestox.9b00504.

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Masand, Vijay H., Sami A. Al-Hussain, Mithilesh M. Rathore, et al. "Pharmacophore Synergism in Diverse Scaffold Clinches in Aurora Kinase B." International Journal of Molecular Sciences 23, no. 23 (2022): 14527. http://dx.doi.org/10.3390/ijms232314527.

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Aurora kinase B (AKB) is a crucial signaling kinase with an important role in cell division. Therefore, inhibition of AKB is an attractive approach to the treatment of cancer. In the present work, extensive quantitative structure–activity relationships (QSAR) analysis has been performed using a set of 561 structurally diverse aurora kinase B inhibitors. The Organization for Economic Cooperation and Development (OECD) guidelines were used to develop a QSAR model that has high statistical performance (R2tr = 0.815, Q2LMO = 0.808, R2ex = 0.814, CCCex = 0.899). The seven-variable-based newly devel

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Torrens, Francisco, and Gloria Castellano. "Structure-Activity Relationships of Cytotoxic Lactones as Inhibitors and Mechanisms of Action." Current Drug Discovery Technologies 17, no. 2 (2020): 166–82. http://dx.doi.org/10.2174/1570163816666190101113434.

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Background: Some lactones prevent protein Myb-dependent gene expression. Objective: The object is to calculate inhibitors of Myb-brought genetic manifestation. Methods: Linear quantitative structure–potency relations result expanded, among sesquiterpene lactones of a variety of macrocycles (pseudoguaianolides, guaianolides, eudesmanolides and germacranolides), to establish which part of the molecule constitutes their pharmacophore, and predict their inhibitory potency on Myb-reliant genetic manifestation, which may result helpful as leads for antileukaemic therapies with a new mechanism of act

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Sharma, Simant, Arijit Basu, and R. K. Agrawal. "Pharmacophore Modeling and Docking Studies on Some Nonpeptide-Based Caspase-3 Inhibitors." BioMed Research International 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/306081.

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Neurodegenerative disorders are major consequences of excessive apoptosis caused by a proteolytic enzyme known as caspase-3. Therefore, caspase-3 inhibition has become a validated therapeutic approach for neurodegenerative disorders. We performed pharmacophore modeling on some synthetic derivatives of caspase-3 inhibitors (pyrrolo[3,4-c]quinoline-1,3-diones) using PHASE 3.0. This resulted in the common pharmacophore hypothesis AAHRR.6 which might be responsible for the biological activity: two aromatic rings (R) mainly in the quinoline nucleus, one hydrophobic (H) group (CH3), and two acceptor

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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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Viana, Jéssika O., Marcus T. Scotti, and Luciana Scotti. "Computer-aided Drug Design Investigations for Benzothiazinone Derivatives Against Tuberculosis." Combinatorial Chemistry & High Throughput Screening 23, no. 1 (2020): 66–82. http://dx.doi.org/10.2174/1386207323666200117102316.

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Background: Tuberculosis (Mycobacterium tuberculosis) is an infectious bacterial disease with the highest levels of mortality worldwide, presenting numerous cases of resistance. In silico studies, which elaborate chemical and biological models in computational tools and make it possible to interpret molecular characteristics, are among the methods used in the search for new drugs. Objective: In this perspective, our aim was to use QSAR and molecular modeling to propose possible pharmacophores from benzothiazinone derivatives. Methods: In this study, a set of 69 benzothiazinone derivatives, tog

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AHMED, SHIEK S. S. J., A. AHAMEETHUNISA, and WINKINS SANTOSH. "QSAR AND PHARMACOPHORE MODELING OF 4-ARYLTHIENO [3, 2-d] PYRIMIDINE DERIVATIVES AGAINST ADENOSINE RECEPTOR OF PARKINSON'S DISEASE." Journal of Theoretical and Computational Chemistry 09, no. 06 (2010): 975–91. http://dx.doi.org/10.1142/s0219633610006146.

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A series of 47, 4-arylthieno[3, 2-d] pyrimidine derivatives was subjected to quantitative structure-antiparkinson activity relationships (QSAR) studies to evaluate the antagonist activity towards both adenosine A1 and adenosine A2A targets in Parkinson's drug discovery. QSAR models were derived with the aid of genetic function approximation (GFA) technique using descriptors to make connections between structural parameters and antiparkinson's activity followed by ADMET analysis and pharmacophore model generation. QSAR model was assessed using a test set of 12 compounds for A1 (r2 pred = 0.961)

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Ignatovich, Zh V. "Synthesis of chimeric amides of 2-arilaminopyrimidine series." Proceedings of the National Academy of Sciences of Belarus, Chemical Series 56, no. 2 (2020): 166–80. http://dx.doi.org/10.29235/1561-8331-2020-56-2-38-166-180.

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Methodological approaches to the synthesis of 2-arylpyrimidine amides with predicted antitumor activity using the design of chimeric molecules by combining pharmacophore fragments of known antitumor drugs are considered. The results of the synthesis of chimeric amides containing, along with the 2-amino-pyrimidine fragment, fragments of other nitrogen and oxygen-containing heterocycles (piperazine, morpholine, isoxazole, etc.), aromatic cycles (benzene, methylnitroaniline, phenylenediamine) and functional (methyl-, amino-, carboxy-, etc.) groups in different positions of the molecule, are prese

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Catalán, Mabel, Ivonne Olmedo, Jennifer Faúndez, and José A. Jara. "Medicinal Chemistry Targeting Mitochondria: From New Vehicles and Pharmacophore Groups to Old Drugs with Mitochondrial Activity." International Journal of Molecular Sciences 21, no. 22 (2020): 8684. http://dx.doi.org/10.3390/ijms21228684.

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Interest in tumor cell mitochondria as a pharmacological target has been rekindled in recent years. This attention is due in part to new publications documenting heterogenous characteristics of solid tumors, including anoxic and hypoxic zones that foster cellular populations with differentiating metabolic characteristics. These populations include tumor-initiating or cancer stem cells, which have a strong capacity to adapt to reduced oxygen availability, switching rapidly between glycolysis and oxidative phosphorylation as sources of energy and metabolites. Additionally, this cell subpopulatio

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Xiaoping, Zhao, Yu Ting, Zhu Yu, Viktar Lemiasheuski, and Wang Hui. "Research Potato Extract as a Multifunctional Drug Carrier." BIO Web of Conferences 179 (2025): 01021. https://doi.org/10.1051/bioconf/202517901021.

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This study constructs a Drug-Component-Target-Disease regulatory network based on the structural and efficacy similarities among drugs, combined with the molecular interactions in the body and Disease- Related genes. By using network pharmacology, it deeply analyzes the chemical composition and structure of potato extract, accurately identifies the pharmacophore groups and action mechanisms, comprehensively evaluates the anti - cancer targeting efficacy, and focuses on exploring the roles of α - solanine, Quercetin, and chlorogenic acid in drug encapsulation, tumor - targeted delivery, and ind

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Dashyan, Shushanik, Eugene Babaev, Ervand Paronikyan, Armen Ayvazyan, Ruzanna Paronikyan, and Lernik Hunanyan. "Evaluation of Neurotropic Activity and Molecular Docking Study of New Derivatives of pyrano[4″,3″:4′,5′]pyrido[3′,2′:4,5]thieno[3,2-d]pyrimidines on the Basis of pyrano[3,4-c]pyridines." Molecules 27, no. 11 (2022): 3380. http://dx.doi.org/10.3390/molecules27113380.

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Background: Heterocyclic compounds and their fused analogs, which contain pharmacophore fragments such as pyridine, thiophene and pyrimidine rings, are of great interest due to their broad spectrum of biological activity. Chemical compounds containing two or more pharmacophore groups due to additional interactions with active receptor centers usually enhance biological activity and can even lead to a new type of activity. The search for new effective neurotropic drugs in the series of derivatives of heterocycles containing pharmacophore groups in organic, bioorganic and medical chemistry is a

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Paronikyan, Ervand G., Shushanik Sh Dashyan, Suren S. Mamyan, et al. "Synthesis and Psychotropic Properties of Novel Condensed Triazines for Drug Discovery." Pharmaceuticals 17, no. 7 (2024): 829. http://dx.doi.org/10.3390/ph17070829.

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The exploration of heterocyclic compounds and their fused analogs, featuring key pharmacophore fragments like pyridine, thiophene, pyrimidine, and triazine rings, is pivotal in medicinal chemistry. These compounds possess a wide array of biological activities, making them an intriguing area of study. The quest for new neurotropic drugs among derivatives of these heterocycles with pharmacophore groups remains a significant research challenge. The aim of this research work was to develop a synthesis method for new heterocyclic compounds, evaluate their neurotropic and neuroprotective activities,

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Hawthorne, M. Frederick, and Alexei Pushechnikov. "Polyhedral borane derivatives: Unique and versatile structural motifs." Pure and Applied Chemistry 84, no. 11 (2012): 2279–88. http://dx.doi.org/10.1351/pac-con-12-02-11.

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Compounds with polyhedral borane moieties have demonstrated numerous unique properties for a variety of applications, including nanoelectronics, drug delivery vehicles, and live cell imaging. Polyhedral boranes are good pharmacophore analogs of carbocycles because polyhedral boranes are inherently insensitive to many undesirable enzymatic metabolic transformations typical for a majority of aromatic compounds. The defined shape, low molecular volume, and high 3D symmetry of the surface are useful for the application of the polyhedral borane scaffolds as universal and convenient spacers for the

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S. Megantara, I. Musfiroh, and D. Lestari. "In-silico STUDY OF DITERPENOID LACTONES FROM Andrographis paniculate TO INTERLEUKIN-6 (IL-6) PROTEIN TARGET." RASAYAN Journal of Chemistry 15, no. 03 (2022): 2004–9. http://dx.doi.org/10.31788/rjc.2022.1536999.

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Interleukin-6 (IL-6) is a type of cytokine that is most often produced when there is inflammation of the respiratory system. Andrographolide, a diterpenoid lactone has been shown to inhibit the amount of IL-6 by binding to IL-6 receptors on human cells. This research was conducted to determine the other potential of diterpenoid lactones from Andrographis paniculate in inhibiting IL-6 with a computational chemistry approach method. The hexameric human IL-6 complex (1P9M) crystal structure was downloaded from the Protein Data Bank. The test compounds were built using MarvinSketch of ChemAxon and

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Zhang, Zuolong, Xin He, Dazhi Long, Gang Luo, and Shengbo Chen. "Enhancing generalizability and performance in drug–target interaction identification by integrating pharmacophore and pre-trained models." Bioinformatics 40, Supplement_1 (2024): i539—i547. http://dx.doi.org/10.1093/bioinformatics/btae240.

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Abstract Motivation In drug discovery, it is crucial to assess the drug–target binding affinity (DTA). Although molecular docking is widely used, computational efficiency limits its application in large-scale virtual screening. Deep learning-based methods learn virtual scoring functions from labeled datasets and can quickly predict affinity. However, there are three limitations. First, existing methods only consider the atom-bond graph or one-dimensional sequence representations of compounds, ignoring the information about functional groups (pharmacophores) with specific biological activities.

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Turan, Nazlı, Ümide Demir Özkay, Nafiz Öncü Can, and Özgür Devrim Can. "Investigating the Antidepressant-like Effects of some Benzimidazolepiperidine Derivatives by In-Vivo Experimental Methods." Letters in Drug Design & Discovery 16, no. 3 (2019): 341–46. http://dx.doi.org/10.2174/1570180815666181004103112.

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Background: Benzimidazole and piperidine rings are important pharmacophore groups for drug design studies. </P><P> Objective: In this study, we aimed to investigate the antidepressant-like activity of some 2-(4- substituted-phenyl)-1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazole derivatives. </P><P> Methods: Tail-suspension Test (TST) and Modified Forced Swimming Tests (MFST) were used to assess antidepressant-like activities of the test compounds. Moreover, locomotor activity performances of the animals were evaluated by an activity cage device. </P><P> Result

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Tuleuov, B. I., M. Kozhanova, B. S. Temirgaziyev та ін. "Studying the Specific (Adaptogenic and Anabolic) Activity of the Supramolecular Complex of 20-Hydroxyecdysone Triacetate with β-Cyclodextrin". Open Access Macedonian Journal of Medical Sciences 12, № 2 (2024): 356–61. http://dx.doi.org/10.3889/oamjms.2024.11906.

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BACKGROUND: A supramolecular complex of ecdysterone triacetate with β-cyclodextrin (β-CD) was synthesized to obtain new potentially bioactive substances and study the effect of bulky pharmacophore-functional groups on the preservation of the specific activity of 20-hydroxyecdysone. The adaptogenic and anabolic activities of the resulting water-soluble inclusion complex were studied. It was established that with the introduction of 3 acyl-pharmacophore groups in the form of encapsulated and hydrophilic supramolecular forms to experimental animals at a dose of 10 mg/kg, the studied complex has a

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Musfiroh, Ida, Rahmana E. Kartasasmita, Slamet Ibrahim, Muchtaridi Muchtaridi, Syahrul Hidayat, and Nur Kusaira Khairul Ikram. "Stability Analysis of the Asiatic Acid-COX-2 Complex Using 100 ns Molecular Dynamic Simulations and Its Selectivity against COX-2 as a Potential Anti-Inflammatory Candidate." Molecules 28, no. 9 (2023): 3762. http://dx.doi.org/10.3390/molecules28093762.

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Asiatic acid, a triterpenoid compound, has been shown to have anti-inflammatory activity through the inhibition of the formation of cyclooxygenase-2 (COX-2) in vitro and in vivo. This study was conducted to determine the binding stability and the inhibitory potential of asiatic acid as an anti-inflammatory candidate. The study involved in vitro testing utilizing a colorimetric kit as well as in silico testing for the pharmacophore modeling and molecular dynamic (MD) simulation of asiatic acid against COX-2 (PDB ID: 3NT1). The MD simulations showed a stable binding of asiatic acid to COX-2 and

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Wang, Ying, and Dachuan Liu. "An Important Potential Anti-Epileptic/Anticonvulsant Active Group: A Review of 1,2,4-Triazole Groups and Their Action." Drug Research 72, no. 03 (2021): 131–38. http://dx.doi.org/10.1055/a-1670-6992.

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AbstractEpilepsy is one of the most common encountered neurological disorders. Many individuals continue to have seizures despite medical and surgical treatments, suggesting new antiepileptic/anticonvulsant drugs are required. Triazole compounds are widely used in pharmaceuticals and have gained significant importance in medicinal chemistry. This article is an attempt to systematically review the research of triazole derivatives in the design and development of anticonvulsant agents during the past two decades through extensive literature research. The results show that triazole occupy a disti

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