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Journal articles on the topic '3D QSAR pharmacophore'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Vaddavalli, Radha, Bagyanaryana Gaddam, and Pradeep Kumar Maddikara. "Discovery of Novel Inhibitors Against Resistant Streptococcus pneumoniae MurF Enzyme using Phamracophore Modeling and QSAR Analysis." International Journal of Drug Design and Discovery 2, no. 1 (2024): 403–12. https://doi.org/10.37285/ijddd.2.1.7.

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Main aim of the current study was to discover novel inhibitors against Streptococcus pneumoniae MurF enzyme using analogue based drug design. Pharmacophore mapping and 3D-QSAR analysis was performed on some previously synthesized and evaluated sulfonamide derivatives which are known to be potent inhibitors of penicillin resistant Streptococcus pneumoniae MurF receptor. 3D-QSAR study based on the principle of alignment of pharmacophoric features was performed on the same set of inhibitors using the PHASE module of Schrodinger suite. A five point pharmacophore, ADHRR, with one hydrogen bond acce

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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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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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Choudhari, Prafulla, Manish Bhatia, Sujit Desai, Santosh Kumbhar, and Swapnil Jadhav. "Structural Feature Identification of Amidinophenylurea Derivatives for Factor VIIa Inhibition." International Journal of Drug Design and Discovery 5, no. 1 (2025): 1264–68. https://doi.org/10.37285/ijddd.5.1.3.

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We describe the 3D QSAR and pharmacophore identification on 28 reported factor VIIa inhibitors. The QSAR and pharmacophore identification studies exhibited the significance of amidine group for factor VIIa inhibition.

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Shirbhate E., Divya, V. K. Patel, P. Patel, et al. "LEAD IDENTIFICATION OF HYDROXAMATE DERIVATIVE AS SELECTIVE HDAC2 INHIBITOR USING COMPUTATIONAL APPROACHES." INDIAN DRUGS 57, no. 07 (2020): 26–39. http://dx.doi.org/10.53879/id.57.07.12042.

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Histone deacetylase (HDAC) inhibitors have been established as a novel class of anticancer agents. The HDAC enzyme plays a vital role in gene transcription for regulation of cell proliferation, migration and apoptosis, immune pathways and angiogenesis. In this work, a series of 49 hydroxamate derivatives with available IC50 data were analyzed by computational method for the identification of leads. 3D-QSAR and pharmacophore modeling investigation were accomplished to identify the crucial pharmacophoric features and correlate 3D-chemical structure with HDAC inhibitory activity. The e-pharmacoph

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Gianibbi, Beatrice, Anna Visibelli, Giacomo Spinsanti, and Ottavia Spiga. "Three-Dimensional Quantitative Structure–Activity Relationship Study of Transient Receptor Potential Vanilloid 1 Channel Antagonists Reveals Potential for Drug Design Purposes." International Journal of Molecular Sciences 25, no. 14 (2024): 7951. http://dx.doi.org/10.3390/ijms25147951.

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Transient receptor potential vanilloid 1 (TRPV1) was reported to be a putative target for recovery from chronic pain, producing analgesic effects after its inhibition. A series of drug candidates were previously developed, without the ability to ameliorate the therapeutic outcome. Starting from previously designed compounds, derived from the hybridization of antagonist SB-705498 and partial agonist MDR-652, we performed a virtual screening on a pharmacophore model built by exploiting the Cryo-EM 3D structure of a nanomolar antagonist in complex with the human TRPV1 channel. The pharmacophore m

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Patel, Vijay K., and Harish Rajak. "Development of Structure Activity Correlation Model on Aroylindole Derivatives as Anticancer Agents." Letters in Drug Design & Discovery 15, no. 2 (2018): 143–53. http://dx.doi.org/10.2174/1570180814666170823161751.

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Background: Aroylindole derivatives, the structural analogs of Combretastatin A-4 has been found to possess potent growth inhibitory activity on several cancer cell lines due to its excellent antitumor and antivascular activities. The aim of present research work is to identify lead and establish structure activity correlation of trimethoxyaroylindole derivatives, using integrated ligand and structure based computational approaches. Materials and Methods: A correlation between structure and biological activity was established using computational approaches i.e., structure activity correlation

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Todkar, S. S., and A. H. Hoshmani. "DESIGN OF POTENTIAL CYCLOOXYGENASE INHIBITORS USING PHARMACOPHORE OPTIMIZATION BY MOLECULAR MODELING STUDIES." INDIAN DRUGS 52, no. 12 (2015): 16–22. http://dx.doi.org/10.53879/id.52.12.10154.

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Recently discovery of relation between cyclooxygenase–2 (COX–2) inhibition and prevention of growth of cansar cells is a major area for research in medicinal chemistry, as it is free from side effects which are genetically shown by developed anticancer agents. In an attempt to develop potent and nontoxic COX–2 inhibitors, we have optimized the 1,5- diaryl pyrazole pharmacophore by using molecular modeling studies. In this paper we present results of 2D and 3D QSAR studies of a series of 22 molecules containing 1,5- diaryl pyrazole pharmacophore as selective COX–2 inhibitors. The 3D QSAR studie

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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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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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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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Desai, Sujit, Sachin Gadkari, Prafulla Choudhari, and Manish Bhatia. "3D QSAR, Pharmacophore Identification of 2-Methoxy Benzanilides and their Thioxo Analogues as Antimycobacterials." International Journal of Drug Design and Discovery 4, no. 3 (2025): 1153–57. https://doi.org/10.37285/ijddd.4.3.6.

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The three dimensional quantitative structure–activity relationship (3D-QSAR) and pharmacophore identification studies on 52 substituted 2- methoxy benzanilides and thioxo derivatives as antimycobacterials agents have been carried out. Multiple linear regressions (MLR) method was applied for QSAR model development considering training and test set approaches with various feature selection methods. Stepwise MLR method was applied to derive QSAR models which were further validated for statistical significance and predictive ability by internal and external validation. The results of pharmacophore

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13

Asgaonkar, K. D., S. M. Patil, T. S. Chitre, S. D. Wani, and M. T. Singh. "QSAR tool for optimization of nitrobenzamide pharmacophore for antitubercular activity." Bulletin of the Karaganda University. "Chemistry" series 105, no. 1 (2022): 60–68. http://dx.doi.org/10.31489/2022ch1/60-68.

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Tuberculosis (TB) is a leading cause of death worldwide from a single infectious agent, Mycobacterium tuberculosis (MTB), especially due to the development of resistant strains and its co-infections in HIV. Quantitative-structure activity relationship (QSAR) studies aid rapid drug discovery. In this work, 2D and 3D QSAR studies were carried out on a series of nitrobenzamide derivatives to design newer analogues for antitubercular activity. 2D QSAR was performed using MLR on a data set showing antitubercular activity. The 3D-QSAR studies were performed by kNN–MFA using simulated annealing varia

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Rai, Amit, Mohamed H. Aboumanei, Suraj P. Verma, Sachidanand Kumar, and Vinit Raj. "Molecular Docking, Pharmacophore, and 3D-QSAR Approach: Can Adenine Derivatives Exhibit Significant Inhibitor Towards Ebola Virus?" Open Medicinal Chemistry Journal 11, no. 1 (2017): 127–37. http://dx.doi.org/10.2174/1874104501711010127.

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Introduction: Ebola Virus Disease (EVD) is caused by Ebola virus, which is often accompanied by fatal hemorrhagic fever upon infection in humans. This virus has caused the majority of deaths in human. There are no proper vaccinations and medications available for EVD. It is pivoting the attraction of scientist to develop the potent vaccination or novel lead to inhibit Ebola virus. Methods & Materials: In the present study, we developed 3D-QSAR and the pharmacophoric model from the previous reported potent compounds for the Ebola virus. Results & Discussion: Results & Discussion: Th

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J.T, Patrisha, Madu Battu, Sriram D., and Yogeeswari P. "3D-QSAR Studies Combined with Virtual Screening to Identify Novel Inhibitors of N-Acetyl Glucosamine 1-Phosphate Uridyltransferase from Mycobacterium Tuberculosis." International Journal of Drug Design and Discovery 4, no. 3 (2025): 1134–48. https://doi.org/10.37285/ijddd.4.3.4.

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The emergence of drug resistant tuberculosis poses a serious concern globally and researchers are in rigorous search for new drugs to fight against the disease. Recently, the bacterial GlmU protein (N-acetylglucosamine-1-phosphate uridyltransferase), involved in peptidoglycan, lipopolysaccharide and techoic acid synthesis, has been identified to be crucial for cell wall synthesis and survival of bacteria. The absence of this enzyme in humans makes it an important and attractive target to develop drugs for the treatment of this lethal disease. In the present study, pharmacophore mapping studies

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Sharma, Vidushi, Hirdesh Kumar, and Sharad Wakode. "Pharmacophore generation and atom based 3D-QSAR of quinoline derivatives as selective phosphodiesterase 4B inhibitors." RSC Advances 6, no. 79 (2016): 75805–19. http://dx.doi.org/10.1039/c6ra11210b.

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Reported PDE4B inhibitors were used to design QSAR based pharmacophore model. Using developed pharmacophore model, virtual screening was performed followed by cross-docking to identify novel PDE4B specific inhibitors.

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Ambre, Premlata K., Raghuvir R. S. Pissurlenkar, Evans C. Coutinho, and Radhakrishnan P. Iyer. "Identification of new checkpoint kinase-1 (Chk1) inhibitors by docking, 3D-QSAR, and pharmacophore-modeling methods." Canadian Journal of Chemistry 90, no. 8 (2012): 675–92. http://dx.doi.org/10.1139/v2012-047.

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Inhibition of checkpoint kinase-1 (Chk1) by small molecules is of great therapeutic interest in the field of oncology and for understanding cell-cycle regulations. This paper presents a model with elements from docking, pharmacophore mapping, the 3D-QSAR approaches CoMFA, CoMSIA and CoRIA, and virtual screening to identify novel hits against Chk1. Docking, 3D-QSAR (CoRIA, CoMFA and CoMSIA), and pharmacophore studies delineate crucial site points on the Chk1 inhibitors, which can be modified to improve activity. The docking analysis showed residues in the proximity of the ligands that are invol

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Asakawa, Naoyuki, Seiichi Kobayashi, Junichi Goto, and Noriaki Hirayama. "AutoGPA: An Automated 3D-QSAR Method Based on Pharmacophore Alignment and Grid Potential Analysis." International Journal of Medicinal Chemistry 2012 (November 26, 2012): 1–9. http://dx.doi.org/10.1155/2012/498931.

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3D-QSAR approach has been widely applied and proven to be useful in the case where no reliable crystal structure of the complex between a biologically active molecule and the receptor is available. At the same time, however, it also has highlighted the sensitivity of this approach. The main requirement of the traditional 3D-QSAR method is that molecules should be correctly overlaid in what is assumed to be the bioactive conformation. Identifying an active conformation of a flexible molecule is technically difficult. It has been a bottleneck in the application of the 3D-QSAR method. We have dev

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Raut, K. G., S. N. Kothawade, V. V. Pande, V. S. Wagh, S. S. Bole, and R. B. Sumbe. "In-silico Design of Potent Anti-tubercular Agents containing Isatinylthiosemicarbazone Pharmacophore." International Journal of Pharmaceutical Sciences and Drug Research 15, no. 06 (2023): 730–41. http://dx.doi.org/10.25004/ijpsdr.2023.150606.

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A recent study reveals that Isatinylthiosemicarbazone analogues inhibit mycobacterial growth by inhibiting the isocitrate lyase (ICL). Hence two-dimensional (2D), three-dimensional (3D), and group QSAR (GQSAR) studies were performed to reduce the amount of pharmacophore needed to make effective ICL inhibitors. New chemical entities (NCEs) were created based on the findings of all QSAR studies. It was discovered that QSAR models produced noticeably positive statistical findings. i.e. (r2 > 0.7), cross-validation (q2 > 0.6), and external validation (pred_r2 > 0.6), indicating high predi

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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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Anant, Arjun, Kamalpreet Kaur, and Vivek Asati. "Discovery of Novel Antimalarial Drugs Based on Thiosemicarbazone Derivatives: An In Silico Approach." Current Signal Transduction Therapy 17, no. 1 (2022): 59–74. http://dx.doi.org/10.2174/1574362416666211015120514.

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Background: Thiosemicarbazones belong to the group of semicarbazides, which contains a sulfur atom instead of an oxygen atom. Several studies have shown that they are effective against extracellular protozoans like Trichomonas vaginalis, Plasmodium falciparum, Trypanosoma cruzi, and other parasites. Objective: The current research involves pharmacophore model design, 3-D-QSAR, virtual screening, and docking studies, all of which are evaluated using various parameters. Methods: The present study was performed by Schrodinger software. A total of 40 ligands were selected for the development of 3D

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Polamreddy, Prasanthi, Vinita Vishwakarma, and Manoj Kumar Mahto. "COMBINATORIAL PHARMACOPHORE MODELING AND ATOM BASED 3D QSAR STUDIES OF BENZOTHIADIAZINES AS HCV-NS5B INHIBITORS." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 3 (2018): 43. http://dx.doi.org/10.22159/ijpps.2018v10i3.23734.

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Objective: The objective of the current study was to elucidate the 3D pharmacophoric features of benzothiadiazine derivatives that are crucial for inhibiting Hepatitis C virus (HCV) Non-structural protein 5B (NS5B) and quantifying the features by building an atom based 3D quantitative structure-activity relationship (3D QSAR) model.Methods: Generation of QSAR model was carried out using PHASE 3.3.Results: A five-point pharmacophore model with two hydrogen bond acceptors, one negative ionization potential and two aromatic rings (AANRR) was found to be common among a maximum number of benzothiad

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Jagdale, Deepali M., and Ramaa C. S. "QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP ANALYSIS OF NOVEL PYRAZOLINE DERIVATIVES USING K NEAREST NEIGHBOUR MOLECULAR FIELD ANALYSIS METHOD." International Journal of Pharmacy and Pharmaceutical Sciences 9, no. 12 (2017): 87. http://dx.doi.org/10.22159/ijpps.2017v9i12.19401.

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Objective: Malonyl CoA decarboxylase (MCD) enzyme plays important role in fatty acid and glucose oxidation. Inhibition of MCD might turn to a novel approach to treat ischemia. The main objective of this research article was to develop a novel pharmacophore for enhanced activity.Methods: Three-dimensional quantitative structure-activity relationships (3D-QSAR) was performed for pyrazoline derivatives as MCD inhibitors using VLife MDS 4.6 software. The QSAR model was developed using the stepwise 3D-QSAR kNN-MFA method.Results: The statistical results generated from kNN-MFA method indicated the s

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Choudhari, Prafulla, Manish Bhatia, Sujit Desai, and Santosh Kumbhar. "3D QSAR, Pharmacophore Identification of 5-Azaindole Derivatives as Factor VIIa Inhibitors." International Journal of Drug Design and Discovery 5, no. 1 (2025): 1285–88. https://doi.org/10.37285/ijddd.5.1.6.

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The current manuscript deals with the three-dimensional quantitative structure-activity relationship (3D-QSAR) and pharmacophore identification studies on 33 substituted azaindole derivatives as factor VIIa inhibitors.

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Mendez, Nixon, and Md Afroz Alam. "Structural Features of Quercetin Derivatives by Using Pharmaco-phore Modeling Approach." Open Pharmaceutical Sciences Journal 3, no. 1 (2016): 79–98. http://dx.doi.org/10.2174/1874844901603010079.

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Background:Quercetin which is a natural occurring flavonoid, exert a direct pro-apoptotic effect on tumor cells by blocking the growth of several cancer cell lines at different phases of the cell cycle. Quercetin derivatives have attracted considerable attention for their cytotoxity against human cancer cell lines. In this study the derivatives of Quercetin were used for docking followed by pharmacophore modeling for studying the 3D features and configurations responsible for biological activity of structurally diverse compounds.Objective:To develop a model which depicts the crucial structural

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Rogić, Sanja, and Žarko Gagić. "3D-QSAR-based pharmacophore determination and design of novel DPP-4 inhibitors." Scripta Medica 53, no. 4 (2022): 271–79. http://dx.doi.org/10.5937/scriptamed53-40866.

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Background/Aim: Therapy of diabetes mellitus type 2 includes drugs that act as inhibitors of dipeptidyl peptidase 4 (DPP-4) enzyme. Several DPP-4 inhibitors are marketed today and although they have favourable safety profile and tolerability, they show moderate activity in controlling glycaemia. The 3D quantitative structure-activity relationship (3D-QSAR) methodology was employed in order to find pharmacophore responsible for good DPP-4 inhibitory activity and designed new compounds with enhanced activity. Methods: For 3D-QSAR model development, 48 compounds structurally related to sitaglipti

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Borota, Ana, Sorin Avram, Ramona Curpan, et al. "In silico studies on smoothened human receptor and its antagonists in search of anticancer effects." Journal of the Serbian Chemical Society 85, no. 3 (2020): 335–46. http://dx.doi.org/10.2298/jsc190403085b.

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Lately, the cancers related with abnormal hedgehog (Hh) signalling pathway are targeted by smoothened (SMO) receptor inhibitors that are rapidly developing. Still, the problems of known inhibitors such as severe side effects, weak potency against solid tumors or even the acquired resistance need to be overcome by developing new suitable inhibitors. To explore the structural requirements of antagonists needed for SMO receptor inhibition, pharmacophore mapping, 3D-QSAR models, database screening and docking studies were performed. The best selected pharmacophore hypothesis based on which statist

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Mali, Suraj N., and Hemchandra K. Chaudhari. "Computational Studies on Imidazo[1,2-a] Pyridine-3-Carboxamide Analogues as Antimycobacterial Agents: Common Pharmacophore Generation, Atom-based 3D-QSAR, Molecular dynamics Simulation, QikProp, Molecular Docking and Prime MMGBSA Approaches." Open Pharmaceutical Sciences Journal 5, no. 1 (2018): 12–23. http://dx.doi.org/10.2174/1874844901805010012.

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Background: IMB-1402, Q203 and ND09759 analogs were found to have strong efficiency against Multi-drug-resistant tuberculosis (MDR-TB)/Extensively drug-resistant tuberculosis (XDR-TB) strains. Objectives: To know the structural necessities for imidazo[1,2-a]pyridine-3-carboxamide analogues, we intended to develop the ligand-based pharmacophore, Quantitative structure–activity relationship models(3D-QSAR model). We also performed Molecular docking, molecular simulation and Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA) studies. Methods: All the studies like Common pharm

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Terzioglu, Nalan, and Hans-Dieter Höltje. "Receptor-Based 3D QSAR Analysis of Serotonin 5-HT1D Receptor Agonists." Collection of Czechoslovak Chemical Communications 70, no. 9 (2005): 1482–92. http://dx.doi.org/10.1135/cccc20051482.

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A three-dimensional quantitative structure-activity relationship study (3D QSAR) has been successfully applied to explain the binding affinities for the serotonin 5-HT1D receptor of a triptan series. The paper describes the development of a receptor-based 3D QSAR model of some known agonists and recently developed triptans on the 5-HT1D serotonergic receptor, showing a significant correlation between predicted and experimentally measured binding affinity (pIC50). The pIC50 values of these agonists are in the range from 5.40 to 9.50. The ligand alignment obtained from dynamic simulations was ta

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Samad, Abdul, Moawiah M. Naffaa, Mohammed Afroz Bakht, Manav Malhotra, and Majid A. Ganaie. "Target Based Designing of Anthracenone Derivatives as Tubulin Polymerization Inhibiting Agents: 3D QSAR and Docking Approach." International Journal of Medicinal Chemistry 2014 (April 17, 2014): 1–15. http://dx.doi.org/10.1155/2014/658016.

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Novel anthracenone derivatives were designed through in silico studies including 3D QSAR, pharmacophore mapping, and molecular docking approaches. Tubulin protein was explored for the residues imperative for activity by analyzing the binding pattern of colchicine and selected compounds of anthracenone derivatives in the active domain. The docking methodology applied in the study was first validated by comparative evaluation of the predicted and experimental inhibitory activity. Furthermore, the essential features responsible for the activity were established by carrying out pharmacophore mappi

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Hess, Jessica, Li Zheng, and Binghui Shen. "Abstract 6996: Integrating high-throughput screening with ligand-based pharmacophore modeling and virtual screening strategies to optimize exonuclease 1 inhibitor design." Cancer Research 85, no. 8_Supplement_1 (2025): 6996. https://doi.org/10.1158/1538-7445.am2025-6996.

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Abstract Pharmacophores are the specific steric and electronic features of a small molecule that are necessary to ensure interaction with a specific biological target and to trigger or block its biological response. Three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophore modeling is a computational approach that utilizes data collected from in vitro experiments and molecular docking to map the shared features of known actives, producing a template that can be used to optimize the physical and chemical properties of lead compounds. Our goal is to generate a 3D-QSA

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Hess, Jessica D., Li Zheng, and Binghui Shen. "Abstract A004: Integrating high-throughput screening with ligand-based pharmacophore modeling and virtual screening strategies to optimize exonuclease 1 inhibitor design." Clinical Cancer Research 31, no. 13_Supplement (2025): A004. https://doi.org/10.1158/1557-3265.aimachine-a004.

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Abstract Pharmacophores are the specific steric and electronic features of a small molecule that are necessary to ensure interaction with a specific biological target and to trigger or block its biological response. Three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophore modeling is a computational approach that utilizes data collected from in vitro experiments and molecular docking to map the shared features of known actives, producing a template that can be used to optimize the physical and chemical properties of lead compounds. Our goal is to generate a 3D-QSA

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Kishore, Deb Pran, Ajay Rana, Upendra Kumar Jain, and P. Mallikarjuna Rao. "Pharmacophore-Based 3D-QSAR Studies of Aromatase Inhibitors." Asian Journal of Chemistry 25, no. 18 (2013): 10588–94. http://dx.doi.org/10.14233/ajchem.2013.16288.

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Chung, Jae Yoon, F. A. Pasha, Seung Joo Cho, Misun Won, Jung Joon Lee, and Kyeong Lee. "Pharmacophore-based 3D-QSAR of HIF-1 inhibitors." Archives of Pharmacal Research 32, no. 3 (2009): 317–23. http://dx.doi.org/10.1007/s12272-009-1301-3.

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Sharma, Mayank Kumar, Prashant R. Murumkar, Guanglin Kuang, Yun Tang, and Mange Ram Yadav. "Identifying the structural features and diversifying the chemical domain of peripherally acting CB1 receptor antagonists using molecular modeling techniques." RSC Advances 6, no. 2 (2016): 1466–83. http://dx.doi.org/10.1039/c5ra20612j.

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A four featured pharmacophore and predictive 3D-QSAR models were developed which were used for virtual screening of the Asinex database to get chemically diverse hits of peripherally active CB1 receptor antagonists.

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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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Mitra, Indrani, Achintya Saha, and Kunal Roy. "Quantification of contributions of different molecular fragments for antioxidant activity of coumarin derivatives based on QSAR analyses." Canadian Journal of Chemistry 91, no. 6 (2013): 428–41. http://dx.doi.org/10.1139/cjc-2012-0527.

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Attempts have been made in the present work using in silico techniques for identification of essential structural features imparting antioxidant potential to naturally available coumarin molecules and their synthetic derivatives. Four different types of modeling tools have been employed for the qualitative and quantitative assessment of the molecular fragments constituting the biological pharmacophore. The descriptor-based quantitative structure–activity relationship (QSAR) and group-based QSAR (G-QSAR) models provide a quantitative estimation of the substituent requirements and the chemical n

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Sharma, Aastha, Nitish Banga, Rakesh Kumar Marwaha, and Balasubramanian Narasimhan. "Identification of novel potential benzimidazole derivatives by pharmacophore generation, 3D-QSAR, virtual screening, molecular docking and ADME/ TOX analysis against breast cancer as targeted estrogen alpha receptor." Journal of Applied Pharmaceutical Research 13, no. 2 (2025): 149–63. https://doi.org/10.69857/joapr.v13i2.951.

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Background: The estrogen alpha receptor (ERα) is critical in breast carcinogenesis. Although selective estrogen receptor modulators like tamoxifen are clinically used, their adverse effects highlight the need for safer alternatives. The study uses computational methods to identify potential ERα inhibitors within a benzimidazole scaffold. Methodology: This study employed computational approaches, including pharmacophore generation, 3D-QSAR, virtual screening, molecular docking, and in silico ADME/Tox analysis. The best pharmacophore model (DDRRR_1) identified two hydrogen donors and three aroma

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Choudhari, Prafulla Balkrishna, Onkar Sunil Pawar, and Sachin Gadkari. "3D QSAR and Pharmacophore Identification of Heteroarylpiperazine-Substituted l-Prolylthiazolidines as Dipeptidyl Peptidase-4 Inhibitors." International Journal of Drug Design and Discovery 4, no. 3 (2025): 1149–52. https://doi.org/10.37285/ijddd.4.3.5.

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This research article focuses on 3D QSAR, pharmacophore identification of heteroarylpiperazine-substituted l-prolylthiazolidines as dipeptidyl peptidase-4 inhibitors to identifly the structural requirement for DPP-4 inhibition for the development of novel potent DPP4 inhibitors.

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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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Bak, A., V. Kozik, A. Smolinski, and J. Jampilek. "Multidimensional (3D/4D-QSAR) probability-guided pharmacophore mapping: investigation of activity profile for a series of drug absorption promoters." RSC Advances 6, no. 80 (2016): 76183–205. http://dx.doi.org/10.1039/c6ra15820j.

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A hybrid approach that combines 3D and 4D-QSAR methods based on grid and neural paradigms with automated IVE-PLS procedure was examined to identify the pharmacophore pattern for cholic acid derivatives as potential drug absorption promoters.

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Nagamani, Selvaraman, Chandrasekhar Kesavan, and Karthikeyan Muthusamy. "Atom-based and Pharmacophore-based 3D – QSAR Studies on Vitamin D Receptor (VDR)." Combinatorial Chemistry & High Throughput Screening 21, no. 5 (2018): 329–43. http://dx.doi.org/10.2174/1386207321666180607101720.

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Aim and Objective: Vitamin D3 (1,25(OH)2D3) is a biologically active metabolite and plays a wide variety of regulatory functions in human systems. Currently, several Vitamin D analogues have been synthesized and tested against VDR (Vitamin D Receptor). Electrostatic potential methods are greatly influence the structure-based drug discovery. In this study, ab inito (DFT, HF, LMP2) and semi-empirical (RM1, AM1, PM3, MNDO, MNDO/d) charges were examined on the basis of their concert in predicting the docking pose using Induced Fit Docking (IFD) and binding free energy calculations against the VDR.

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Sharma, Mukesh C., D. V. Kohli, and Smita Sharma. "Molecular Modeling Studies of Substituted 2,4,5-Trisubstituted Triazolinones Aryl and Nonaryl Derivatives as Angiotensin II AT1Receptor Antagonists." Journal of Chemistry 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/427181.

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The development of new therapies to treat hypertension and cardiovascular diseases. A series of 2,4,5-trisubstituted triazolinones aryl and nonaryl derivatives were subjected toGroup-based QSAR,k-nearest neighbourmolecular field analysis, and pharmacophore mapping. Multiple linear regression (MLR) methodology coupled with feature selection method namely simulated annealing, was applied to derive Group based QSAR models which were further validated for statistical significance and predictive ability by internal and external validation. The best physicochemical descriptors, namely, R1chiV1, R2T_

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Noonan, Theresa, Katrin Denzinger, Valerij Talagayev, et al. "Mind the Gap—Deciphering GPCR Pharmacology Using 3D Pharmacophores and Artificial Intelligence." Pharmaceuticals 15, no. 11 (2022): 1304. http://dx.doi.org/10.3390/ph15111304.

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G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. Three-dimensional pharmacophore models are powerful computational tools in in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, the discovery of biased and allosteric ligands,

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Totrov, Maxim. "Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR." Chemical Biology & Drug Design 71, no. 1 (2007): 15–27. http://dx.doi.org/10.1111/j.1747-0285.2007.00605.x.

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Liang, Liu, Wang Ren-Xiao, Lai Lu-Hua, and Li Chong-Xi. "3D-QSAR and Pharmacophore Modeling of Growth Hormone Secretagogues." Acta Physico-Chimica Sinica 13, no. 12 (1997): 1090–96. http://dx.doi.org/10.3866/pku.whxb19971207.

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Huang, Dandan, Xiaoyun Zhu, Chunlei Tang, et al. "3D QSAR Pharmacophore Modeling for c-Met Kinase Inhibitors." Medicinal Chemistry 8, no. 6 (2012): 1117–25. http://dx.doi.org/10.2174/157340612804075142.

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Huang, Dandan, Xiaoyun Zhu, Chunlei Tang, et al. "3D QSAR Pharmacophore Modeling for c-Met Kinase Inhibitors." Medicinal Chemistry 8, no. 6 (2012): 1117–25. http://dx.doi.org/10.2174/1573406411208061117.

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Neaz, M. M., F. A. Pasha, M. Muddassar, et al. "Pharmacophore based 3D-QSAR study of VEGFR-2 inhibitors." Medicinal Chemistry Research 18, no. 2 (2008): 127–42. http://dx.doi.org/10.1007/s00044-008-9113-4.

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Nagarajan, Shanthi, Asif Ahmed, Hyunah Choo та ін. "3D QSAR pharmacophore model based on diverse IKKβ inhibitors". Journal of Molecular Modeling 17, № 2 (2010): 209–18. http://dx.doi.org/10.1007/s00894-010-0714-8.

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