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1

Joshua Anthony Vomo, Papireddypalli Sushma, Bukke Geethanjali, B Dhanush, and Kanala Somasekhar Reddy. "Swiss Dock 2025: Docking approaches comparison between attracting cavities and autodockvina." World Journal of Biology Pharmacy and Health Sciences 22, no. 2 (2025): 120–25. https://doi.org/10.30574/wjbphs.2025.22.2.0452.

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Molecular docking is a crucial computational tool in drug discovery enabling the prediction of ligand-target interactions and accelerating the screening of potential drug candidates. This study compares twowidely used docking algorithms AutodockVina and Attracting Cavities to evaluate their efficiency, accuracy and applicability in molecular docking studies. AutodockVina is known for its speed and computational efficiency making it suitable for high-throughput screening. In contrast, Attracting Cavities provides more accurate binding predictions particularly for covalent interactions but it re
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Mohammed, Z. M., Z. K. Haruna, Z. I. Abdullahi, et al. "In-silico comparative study of three (3) bioactive compounds from methanol extracts of Combretum micranthum leaf, and diazepam with Gabaa receptor molecule." Bayero Journal of Pure and Applied Sciences 12, no. 1 (2020): 235–41. http://dx.doi.org/10.4314/bajopas.v12i1.37s.

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Stress affects monoamine neurotransmitter in the central nervous system such as GABA (a major inhibitory neurotransmitter in the brain). GABAA receptor is hetero-oligomeric Cl-channel that is elective blocked by the alkaloid, bicuculline and modulated by steroids, barbiturates and benzodiazepines. The anticonvulsant activity of Diazepam may be mediated by enhancement of inhibition involving gamma-aminobutyric acid (GABA). Combretum micranthum is one of the maximum effective medicinal plants of therapeutic importance. Thus this study is to examine the effect of Combretum micranthum methanol lea
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Jagtap, Vaibhavkumar, Pooja Kakad, Jayprakash Suryawanshi, and Nitinchandra Patil. "Unlocking Novel Therapeutic Avenues: Drug Repurposing and Virtual Screening for Breast Cancer Targeting the Estrogen Receptor." INTERNATIONAL JOURNAL OF PHARMACEUTICAL QUALITY ASSURANCE 15, no. 02 (2024): 815–20. http://dx.doi.org/10.25258/ijpqa.15.2.42.

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This study explores the potential of drug repurposing for breast cancer therapy through virtual screening of Food and Drug Administration (FDA)-approved drugs against breast cancer-related targets. The estrogen receptor alpha ligand-binding domain, a key player in breast cancer progression, served as the primary target for virtual screening. Utilizing the DrugRep Virtual Screening Server and AutoDockVina, several compounds were identified with high binding affinities to the target protein. Notably, estradiol, benzhydrocodone, and ezetimibe emerged as top hits, showcasing diverse physicochemica
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Aliyah, Alma Nuril, Fauz Aulia El Maghfiroh та Fathia Faza Rahmadanita. "in Silico Prediction of Caesalpinia sappan L. Secondary Metabolites towards PPARγ". Proceeding Annual Symposium on Hajj and Umrah Medicine 1 (5 грудня 2022): 42. https://doi.org/10.18860/anshar.v1i0.2134.

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Chemotherapy can cause mitochondrial dysfunction and oxidative stress that induces Chemotherapy-induced Peripheral Neurotherapy (CIPN) condition. Inhibition of pro-inflammatory transcription factors by PPARγ agonist can be used to develop CIPN treatment. To find potential compounds from plants, this study conducted an in silico study of the secondary metabolites of Caesalpinia sappan L. In this study, we conducted a molecular docking study of 27 secondary metabolites of Caesalpinia sappan L. using an in silico approach targeting PPARγ (PDB ID: 2PRG) using AutoDockVina software. ADMET character
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Sousa, Glaydiane Alves de, Ivis Vinicius de Oliveira Martins, Vinícius Duarte Pimentel, and Joubert Aires Sousa. "Análise in silico da farmacodinâmica, farmacocinética e toxicidade de dois compostos isolados da Actinidia deliciosa para investigação do seu potencial anti-hiperlipêmico." Research, Society and Development 9, no. 7 (2020): e790974679. http://dx.doi.org/10.33448/rsd-v9i7.4679.

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A presente pesquisa visou avaliar in silico a farmacodinâmica, farmacocinética e toxicidade dos ácidos siríngico e ursólico isolados da Actinidia deliciosa e analisar o mecanismo que fundamente a sua atuação na redução do colesterol comparando-os com o fármaco sinvastatina. Foi utilizado o servidor online PreADME para a avaliação do perfil farmacocinético e toxicológico por meio da estrutura-atividade molecular e o software AutodockVina para o estudo da farmacodinâmica e potencial farmacológico das interações moleculares. Os dados ADME obtidos para os ácidos siríngico e ursólico foram semelhan
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6

Pham, Han Thi Ngoc, and Huong Thi Thu Phung. "Comparing the Performance of Molecular Docking Tools for HIV-1 Protease Inhibitors." Journal of Advanced Engineering and Computation 7, no. 2 (2023): 95. http://dx.doi.org/10.55579/jaec.202372.400.

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Human immunodeficiency virus (HIV) continues to pose a significant public health threat worldwide, disproportionately affecting marginalized and vulnerable populations despite advancements in prevention and treatment. One promising approach in the development of antiretroviral therapies is the inhibition of HIV-1 protease, a key enzyme in the virus life cycle. To this end, we evaluated 23 known inhibitors of HIV-1 protease using three docking methods - Autodock 4.2 (AD4), AutoDockVina (Vina), and a modified Vina (mVina)- and found that all three methods produced reasonable binding affinities fo
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Sharma, Abhishek Shankar, Salahuddin Salahuddin, Kavita Rana, et al. "Synthesis, anticonvulsant potential, and molecular docking studies of Schiff bases bearing 2', 6-dichloro-2,3'-biquinoline." INDIAN JOURNAL OF HETEROCYCLIC CHEMISTRY 35, no. 01 (2025): 119. https://doi.org/10.59467/ijhc.2025.35.119.

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In the present manuscript, a series of new 2',6-dichloro-N'-(substituted-benzylidene)-[2,3'-biquinoline]-4- carbohydrazides (6a-l; Schiff bases) has been synthesized by the reaction of 2',6-dichloro-[2,3']biquinolinyl-4-carboxylic acid hydrazide (5) with substituted benzaldehydes. All compounds have been screened for anticonvulsant potential by using the subcutaneous pentylenetetrazole model. From the entire series the compounds 6a, 6c, and 6e showed protection against convulsions at the dose concentration of 30 mg/kg body weight in correlation with conventional drug (phenytoin). The molecules
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Ritik R. Jamgade, Ritik R. Jamgade, Dr Dinesh R. Chaple Dr. Dinesh R. Chaple, Rida K. Saiyyad Rida K. Saiyyad, Prerna P. Bhange Prerna P. Bhange, Nandani K. Sonwane Nandani K. Sonwane, and Shivani P. Wadichar Shivani P. Wadichar. "Molecular Docking and ADME-Based Prioritization of 20 Quinazolinone Scaffolds for Anticonvulsant Potential." International Journal of Pharmaceutical Research and Applications 10, no. 3 (2025): 2046–63. https://doi.org/10.35629/4494-100320462063.

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Quinazolinone derivatives have attracted significant attention for their broad pharmacological potential, particularly in the treatment of central nervous system (CNS) disorders such as epilepsy. In the present study, a series of twenty novel quinazolinone derivatives were designed and evaluated for their potential anticonvulsant activity through molecular docking studies. The compounds were docked into the active site of the GABAAreceptor, a wellestablished target for antiepileptic drugs, using its crystallographic structure (PDB ID: 4COF). Molecular docking was carried out using AutoDockVina
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Alamri, Abdulhakeem S., Majid Alhomrani, Walaa F. Alsanie та ін. "Spectroscopic and Molecular Docking Analysis of π-Acceptor Complexes with the Drug Barbital". Applied Sciences 12, № 19 (2022): 10130. http://dx.doi.org/10.3390/app121910130.

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The drug barbital (Bar) has a strong sedative–hypnotic effect. The intermolecular charge transfer compounds associated with the chemical reactions between Bar and some π acceptors, such as 2,6-dibromoquinone-4-chloroimide (DBQ), tetracyanoquinodimethane (TCNQ), chloranil (CHL), and chloranilic acid (CLA), have been synthesized and isolated in solid state. The synthesized products have the molecular formulas (Bar–DBQ), (Bar–TCNQ), (Bar–CHL), and (Bar–CLA) with 1:1 stoichiometry based on Raman, IR, TG, 1H NMR, XRD, SEM, and UV-visible analysis techniques. Additionally, the comparative analysis o
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Annastasia ERAZUA, Ehimen, and Babatunde Benjamin ADELEKE. "DFT and Molecular Docking Investigation of Potential Anticancer Properties of Some Flavonoids." Journal of Pure and Applied Chemistry Research 8, no. 3 (2019): 225–31. http://dx.doi.org/10.21776/ub.jpacr.2019.008.03.485.

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There is a continuous need to discover and obtain more efficient drug-like molecule to suppress cancer in human being. Recently researchers are using molecular docking technique to improve the understanding of the interaction between drug and receptor, in other to obtain novel drugs for more efficient usage. Anticancer activities of some selected flavonoids were studied using quantum chemical method through Density Functional Theory (DFT) and molecular docking approach. These Flavoniods were docked against breast cancer cell line (3s7s) using Autodock tool, AutoDockVina as docking tools and Bi
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Evary, Yayu Mulsiani, Ayu Masyita, Arie Ariezandi Kurnianto, Rangga Meidianto Asri, and Yusnita Rifai. "Molecular Docking of Phytochemical Compounds of Momordica charantia as Potential Inhibitors against SARS-CoV-2." Infectious Disorders - Drug Targets 22, no. 3 (2022): 57–63. http://dx.doi.org/10.2174/1871526522666220113143358.

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Background: Coronavirus disease 2019 (COVID-19) has been recently declared as a global public health emergency, where the infection is caused by SARS-CoV-2. Nowadays, there is no specific treatment to cure this infection. The main protease (Mpro) of SARS-CoV-2 and SARS spike glycoprotein- human ACE2 complex have been recognized as suitable targets for treatment, including COVID-19 vaccines. Objective:: In our current study, we identified the potential of Momordica charantia as a prospective alternative and a choice in dietary food during a pandemic. Materials and Methods: A total of 16 bioacti
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Aarcha, Kurup, Nirmal Bosco J. Vasanth, and Rashmi Aarthi. "ANTIVIRAL PROPERTIES OF PHYTOCHEMICALS FROM TOMATO." INTERNATIONAL JOURNAL OF ENGINEERING SCIENCES & RESEARCH TECHNOLOGY 5, no. 3 (2016): 50–63. https://doi.org/10.5281/zenodo.46988.

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Hepatitis D (hepatitis delta) is a disease caused by the hepatitis D virus (HDV), a small circular enveloped RNA virus. This is one of five known hepatitis viruses : A, B, C, D, and E. HDV is considered to be a sub viral because it can propagate only in the presence of the hepatitis B virus (HBV). Transmission of HDV can occur either via simultaneous infection with HBV or superimposed on chronic hepatitis B or hepatitis B carrier state. Auto Dock is molecular modelling simulation software. It is especially effective for Protein-ligand docking. Auto Dock 4 is available under the GNU General Pub
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13

Severina, Hanna I., Victoriya A. Georgiyants, Sergiy M. Kovalenko, Natalia V. Avdeeva, Artem I. Yarcev, and Svetlana N. Prohoda. "Molecular docking studies of N-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives as potential modulators of glutamate receptors." Research Results in Pharmacology 6, no. 1 (2020): 69–82. http://dx.doi.org/10.3897/rrpharmacology.6.52026.

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Introduction: The virtual target-oriented screening is a necessary stage of modern drug-design. In the present study, the affinity of pyridazine derivatives for the most promising antiparkinsonian biotargets – I–III groups of metabotropic and ionotropic NMDA-glutamate receptors – was evaluated. Materials and methods: Docking of the studied ligands to the active sites of biotargets – mGluR5, mGluR3, mGluR8, NMDA GluN2B – was performed using AutoDockVina. Base of the preparation of ligands and proteins – AutoDockTools-1.5.6. A Discovery Studio Visualizer 2017/R2 was used to visualize the interpr
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14

Wiraswati, Hesti L., Fida M. Warganegara, Akhmaloka Akhmaloka, and Muhamad A. Martoprawiro. "Molecular Docking Studies of ROS Agent from Quinone Family to Reductase Enzymes:Implication in Finding Anticancer Drug Candidate." Biomedical and Pharmacology Journal 14, no. 02 (2021): 681–89. http://dx.doi.org/10.13005/bpj/2170.

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Understanding the metabolism of cytotoxic compounds of quinone family is importance in cancer therapy because they have been successfully explored for their anti-tumor activity. Quinone which form radical semiquinone (by reductase enzymes) to generate Reactive Oxygen Species (ROS) is associated to be anticancer drug candidate. However, molecular mechanism of those compounds to reductase enzymes has not yet clearly understood.This study aimed to understand molecular interaction of quinones to oxidoreductase enzymes such as cytochrome P450 reductase or ubiquinone reductase (NQO1), or apoptosis i
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Bernal, Cristian. "Acoplamiento molecular de derivados de la 6-(piridin)-7H-indeno[2,1-c]quinolina como inhibidores de la Topoisomerasa 1 y PARP 1." BISTUA REVISTA DE LA FACULTAD DE CIENCIAS BASICAS 20, no. 2 (2022): 22–28. http://dx.doi.org/10.24054/bistua.v20i2.1434.

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Una variedad de compuestos derivados de la 7H-indeno[2,1-c]quinolina han sido reportados ya que poseen propiedades anticáncer significativas. Sin embargo, los modos de acción aún no están claramente definidos. Se seleccionaron treinta derivados 6-(pyridin)-7H-indeno[2,1-c]quinolínicos los cuales exhiben actividad anticáncer y fueron sometidos a cálculos de acoplamiento molecular usando AutodockVina. Para investigar preliminarmente las dianas moleculares potenciales y confirmar la prueba de actividad experimental para estos compuestos anticancerígenos, el acoplamiento se realizó utilizando dos
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Severina, Hanna I., Victoriya A. Georgiyants, Sergiy M. Kovalenko, Natalia V. Avdeeva, Artem I. Yarcev, and Svetlana N. Prohoda. "Molecular docking studies of N-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives as potential modulators of glutamate receptors." Research Results in Pharmacology 6, no. (1) (2020): 69–82. https://doi.org/10.3897/rrpharmacology.6.52026.

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Introduction: The virtual target-oriented screening is a necessary stage of modern drug-design. In the present study, the affinity of pyridazine derivatives for the most promising antiparkinsonian biotargets – I–III groups of metabotropic and ionotropic NMDA-glutamate receptors – was evaluated. Materials and methods: Docking of the studied ligands to the active sites of biotargets – mGluR5, mGluR3, mGluR8, NMDA GluN2B – was performed using AutoDockVina. Base of the preparation of ligands and proteins – AutoDockTools-1.5.6. A Discovery Studio Visualizer 2017/R2 was used to visualize the interpr
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Shamsara, Jamal. "Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases." International Journal of Medicinal Chemistry 2014 (December 25, 2014): 1–9. http://dx.doi.org/10.1155/2014/162150.

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Matrix metalloproteinases (MMPs) have distinctive roles in various physiological and pathological processes such as inflammatory diseases and cancer. This study explored the performance of eleven scoring functions (D-Score, G-Score, ChemScore, F-Score, PMF-Score, PoseScore, RankScore, DSX, and X-Score and scoring functions of AutoDock4.1 and AutoDockVina). Their performance was judged by calculation of their correlations to experimental binding affinities of 3D ligand-enzyme complexes of MMP family. Furthermore, they were evaluated for their ability in reranking virtual screening study results
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Melo, Danielly Silva de, José Arimatéa de Oliveira Nery Neto, Maisa de Sousa dos Santos, et al. "Isopropyl Gallate, a Gallic Acid Derivative: In Silico and In Vitro Investigation of Its Effects on Leishmania major." Pharmaceutics 14, no. 12 (2022): 2701. http://dx.doi.org/10.3390/pharmaceutics14122701.

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Isopropyl gallate (IPG) is a polyphenol obtained from alterations in the gallic acid molecule via acid catalysis with previously reported leishmanicidal and trypanocidal activities. The present study aims to evaluate in silico binding activity towards some targets for antileishmanial chemotherapy against Leishmania major species, and ADMET parameters for IPG, as well as in vitro antileishmanial and cytotoxic effects. Molecular docking was performed using AutoDockVina and BIOVIA Discovery Studio software, whereas in silico analysis used SwissADME, PreADMET and admetSAR software. In vitro antile
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Ahire, Eknath D., and Sanjay J. Kshirsagar. "Irinotecan's molecular mechanisms against cancer: a primary system biology and chemoinformatics approach for novel formulation development." Current Issues in Pharmacy and Medical Sciences 38, no. 1 (2025): 31–37. https://doi.org/10.12923/cipms-2025-0005.

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Cancer is the third most common type of cancer generally. It affects 6.1% of the entire world’s population and kills 9.2% of all people of both sexes. Even though people with colon cancer have a number of chemotherapies and surgeries to choose from, the disease often returns after the first treatment. AutoDockVina by PyRx 0.8v was used to do molecular docking. The admetSAR2.0 web server was employed for ADMET analysis. The MolSoft and ADVERPred tools were applied to predict the drug's potential for abuse and its potential for side effects. The anti-tumor effects of irinotecan may be aimed at t
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Shah, Yamini, and Kavish Shah. "Anti-viral herbal phytoconstituents of tulsi (Ocimum sanctum) against Covid-19." IP International Journal of Comprehensive and Advanced Pharmacology 7, no. 2 (2022): 77–80. http://dx.doi.org/10.18231/j.ijcaap.2022.014.

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A novel corona virus originated from Wuhan, China in 2019. Millions of people were affected due to this virus outbreak and quarantined for almost 2 years resulting in great loss in millions of lives in the world. This also resulted in a great impact in economy and health sector globally. After the outbreak the development of cure against SARS-CoV-2 is in full motion, less efforts have been spent on the prevention of rapidly spreading respiratory infectious agents. At present there is no effective treatment that could mitigate SARS-CoV-2. Available clinical intervention for covid-19 is only lim
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Martínez-Pérez, Raúl Balam, and Lorena Moreno-Vilet. "Molecular interaction of linear and branched fructans of different sizes with levansucrase and inulosucrase from Lactobacillus gasseri: modeling and computational analysis." Mexican journal of biotechnology 7, no. 4 (2022): 14–36. http://dx.doi.org/10.29267/mxjb.2022.7.4.14.

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Human beings consume probiotics and prebiotics because of the health benefits they provide. Lactobacillus gasseri is a probiotic microorganism native to humans which produces glycolytic enzymes directed at the hydrolysis of soluble fibers as prebiotic fructans. In this work, levansucrase (LevG) and inulosucrase (InuGB) from L. gasseri were used to predict the ability of L. gasseri to interact with linear and branched fructans prebiotics (inulin and agavins). AlphaFold and SWISS-MODEL were the servers used for tertiary structure prediction of LevG and InuGB, and fructans with different degrees
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Rahmatullah, Mohammed. "Can Javanicins be Potential Inhibitors of SARS-Cov-2 C-3 like Protease? An Evaluation through Molecular Docking Studies." Journal of Natural & Ayurvedic Medicine 4, no. 2 (2020): 1–5. http://dx.doi.org/10.23880/jonam-16000250.

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Objectives: Corona virus SARS-CoV-2, otherwise known as COVID-19 has created a pandemic from which any respite seems far away. Since its outbreak in late December in 2019, till as of June 9, 2020 the virus has infected 7,237,929 people throughout practically every country of the world and caused deaths of 409,630 persons. Thus far, despite the best efforts of scientists, any vaccine or drug against COVID-19 is yet to be discovered. The objective of the present study was to evaluate through molecular docking studies a number of quassinoid compounds (javanicins) present in the plant Picrasma jav
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Kulabas, Necla, Fahrettin Bugra Kilic, and Sevil Senkardes. "Investigations of Some Chlorocresol Hydrazones Against Tyrosinase Enzyme by Molecular Docking Method: In Silico Study." Pharmedicine Journal 2, no. 1 (2025): 16–23. https://doi.org/10.62482/pmj.23.

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Introduction: Tyrosinase, found in various organisms, including plants and mammals, and is responsible for pigmentation as well as the undesirable browning of fruits and vegetables, is a multi-copper enzyme involved in the synthesis of melanin in human. As it is known, melanin provides protection against harmful ultraviolet radiation, which can lead to serious conditions like skin cancers. However, excessive melanin accumulation could result in hyperpigmented spots, creating aesthetic concerns. Tyrosinase inhibitors could potentially lead to the development of novel skin-whitening agents, anti
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Ishola, Ahmed A., and Kayode E. Adewole. "In Silico Screening Reveals Histone Deacetylase 7 and ERK1/2 as Potential Targets for Artemisinin Dimer and Artemisinin Dimer Hemisuccinate." Current Drug Discovery Technologies 17, no. 5 (2020): 725–34. http://dx.doi.org/10.2174/1570163816666190705164756.

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Background: Recent studies have observed overexpression of histone deacetylase 7 (HDAC7) and overactivity of extracellular signal-regulated kinases 1/2 (ERK1/2) in many tumors; therefore, pharmacological interventions to inhibit overexpression of HDAC7 and overactivity of ERK1/2 in cancerous cells holds great promise in cancer treatment. The promising anticancer properties of artemisinin and artemisinin-derivatives (ARTs) have been validated by various experimental reports, including advanced pre-clinical trials. Objective: Our aim in this in silico study is to identify additional inhibitors o
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Nurhan, Ahmad Dzulfikri, Maria Apriliani Gani, Aniek Setiya Budiatin, Siswandono Siswodihardjo, and Junaidi Khotib. "Molecular docking studies of Nigella sativa L and Curcuma xanthorrhiza Roxb secondary metabolites against histamine N-methyltransferase with their ADMET prediction." Journal of Basic and Clinical Physiology and Pharmacology 32, no. 4 (2021): 795–802. http://dx.doi.org/10.1515/jbcpp-2020-0425.

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Abstract Objectives Histamine N-methyltransferase (HNMT) is an enzyme that plays a crucial role in the inactivation of histamine in central nervous system, kidneys and bronchi. Inhibition of HNMT is known to have a potential role in treating attention-deficit hyperactivity disorder, memory impairment, mental illness and neurodegenerative illnesses. Therefore, to find potential compounds that could be developed as novel HNMT inhibitors, this study conducted an in silico study of the secondary metabolites of Nigella sativa L and Curcuma xanthorrhiza Roxb. Methods In this study, we conducted a mo
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Szefler, Beata, and Przemysław Czeleń. "Docking of Polyethylenimines Derivatives on Cube Rhombellane Functionalized Homeomorphs." Symmetry 11, no. 8 (2019): 1048. http://dx.doi.org/10.3390/sym11081048.

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Nowadays, in the world of science, an important goal is to create new nanostructures that may act as potential drug carriers. Among different, real or hypothetical, polymeric networks, rhombellanes are very promising and, therefore, attempts were made to deposit polyethylenimines as possible nano-drug complexes on the cube rhombellane homeomorphs surface. For the search of ligand–fullerene interactions, was used AutoDockVina software. As a reference structure, the fullerene C60 was used. After the docking procedure, the ligands–fullerenes interactions were tested. The important factor determin
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Bhaskarawilaputraka, Igustingurah Raka, Azminah Azminah, Linda Erlina, Rezi Riadhi Syahdi, and Arry Yanuar. "VIRTUAL SCREENING OF INDONESIAN HERBAL DATABASE FOR DNA METHYLTRANSFERASE INHIBITORS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 17 (2017): 153. http://dx.doi.org/10.22159/ajpcr.2017.v10s5.23120.

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Objective: DNA hypermethylation is an abnormal epigenetic process catalyzed by DNA methyltransferase 1 (DNMT1). It is also one of the factors that cause non-communicable diseases such as cancer, diabetes, and other metabolic diseases. DNA hypermethylation can be reversed by suppressing DNMT1 activity using a DNMT inhibitor. This study was conducted to seek out inhibitor candidates among natural products.Methods: The search for potential inhibitors was conducted through a virtual screening of the Indonesian Herbal Database using AutoDockVina as docking software. Twenty-five compounds known for
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Asati, Vivek, Piyush Ghode, Shalini Bajaj, Sanmati K. Jain, and Sanjay K. Bharti. "3D-QSAR and Molecular Docking Studies on Oxadiazole Substituted Benzimidazole Derivatives: Validation of Experimental Inhibitory Potencies Towards COX-2." Current Computer-Aided Drug Design 15, no. 4 (2019): 277–93. http://dx.doi.org/10.2174/1573409914666181003153249.

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Background: In past few decades, computational chemistry has seen significant advancements in design and development of novel therapeutics. Benzimidazole derivatives showed promising anti-inflammatory activity through the inhibition of COX-2 enzyme. Objective: The structural features necessary for COX-2 inhibitory activity for a series of oxadiazole substituted benzimidazoles were explored through 3D-QSAR, combinatorial library generation (Combi Lab) and molecular docking. Methods: 3D-QSAR (using kNN-MFA (SW-FB) and PLSR (GA) methods) and Combi Lab studies were performed by using VLife MDS Mol
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Sharma, Rakesh Kumar, and Ankita Singh Chakotiya. "Phytoconstituents of Zingiber officinale Targeting Host viral Protein Interaction at Entry Point of SARS CoV 2 A Molecular Docking Study." Defence Life Science Journal 5, no. 4 (2020): 268–77. http://dx.doi.org/10.14429/dlsj.5.15718.

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Current COVID 19 outbreak is a critical issue in safeguarding public health worldwide. The lack of prophylactic drugs, vaccine and effective antiviral and other supporting therapies has prompted researchers to look for promising leads against the virus. Metabolic pathways and biochemicals involved in pathophysiology of SARS-CoV-2 can be targeted to find out effective inhibitor molecules acting at the entry point of infection. SARS-CoV-2 uses their Spike protein to dock at ACE2 and the serine protease, TMPRSS2 of host cell for Spike protein priming to get entry into the host cell. In the presen
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Dr., Dinesh Kawade* Shikha Shahu Shriya Bagh Yashika Bhattad Sejal Kshirsagar. "In-Silico Study of Zingiber Officinale for Its Anti-Diabetic Activity." International Journal of Pharmaceutical Sciences 3, no. 4 (2025): 2767–89. https://doi.org/10.5281/zenodo.15268380.

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Today, diabetes is recognized as a prevalent and major disease condition worldwide. According to recent WHO studies, approximately 422 million people globally suffer from diabetes, with the majority residing in low- and middle-income countries, and diabetes directly causes 1.5 million deaths annually. The use of computational techniques in the drug discovery and development process is increasingly being implemented and appreciated. Terms such as computer-aided drug design (CADD) are commonly applied in this area. In-silico virtual screening, or high-throughput virtual screening (HTVS), has eme
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Sirari, Priyanka. "A Computational Approach to Predict the Molecular Drug Targets Against Candida glabrata." Bioscience Biotechnology Research Communications 14, no. 4 (2021): 1946–55. http://dx.doi.org/10.21786/bbrc/14.4.84.

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Non- albicans Candida (NAC) species are responsible for 35-65% of all candidaemias in the general population and are associated with a high rate of morbidity and mortality (about 15% to 35%). The availability of few commercially used antifungal drugs against candidiasis and rapid emergences of antibiotic resistance among NAC species has significantly contributed to their increased global outbreak. Green tea is known for its multi-beneficial effects including antimicrobial potential against Candida. The present study investigated the molecular drug targets of green tea phytocompounds against in
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Ibrahim, Mutiat B., Adeola T. Kola-Mustapha, Niyi S. Adelakun, and Neil A. Koorbanally. "Phytoconstituents from Markhamia tomentosa Bind To HPV Oncoprotein with Apoptogenic Potential: A Molecular Modeling Approach." Annals of Science and Technology 6, no. 2 (2021): 28–46. http://dx.doi.org/10.2478/ast-2021-0008.

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Abstract Markhamia tomentosa crude extract and fractions exhibited potent growth inhibitory effects capable to induce apoptosis in cervical (HeLa) cancer cell line via in vitro model. Presently, interaction of M. tomentosa phytoconstituents with molecular drug targets to exert its anticancer property is evaluated via in silico study. Identified phytoconstituents from M. tomentosa were retrieved from PubChem database and docked in active sites of HPV 16 E6, caspase -3 and caspase -8 targets using AutoDockVina from PyRx software. Screening for druglikeness; and absorption, distribution, metaboli
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33

Sujatha, S., and R. Rajini. "In-Silico Enactment of Musa paradisiaca (L.) Exudate Against the Urotlithiatic Disease by Docking Study." Indian Journal Of Science And Technology 17, no. 28 (2024): 2889–96. http://dx.doi.org/10.17485/ijst/v17i28.1899.

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Objectives: Urolithiasis is a condition that occurs when the stones exit the renal pelvis and move onto the remainder of the urinary collecting system. Musa paradisiaca (L.) is a plant with high nutritive value and has been used for the treatment of various diseases including urolithiasis. The objective of the present study was designed to detect the receptor-ligand binding energy and interaction through a molecular docking from the bio-active compounds in an exudates of M. paradisiaca pseudo stem on urolithiatic causative protein named as glycolate oxidase receptor (PDB ID: 2RDU). Methods: In
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34

Lu, Yun, Haopeng Luan, Cong Peng, et al. "Application of network pharmacology and dock of molecules on the exploration of the mechanism of frankincense-myrrh for lumbar intervertebral disc degeneration: A review." Medicine 103, no. 29 (2024): e38953. http://dx.doi.org/10.1097/md.0000000000038953.

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To investigate the efficacy of Frankincense-Myrrh in lumbar Intervertebral degenerative diseases (LIDD). The active components of frankincense-myrrh was retrieved with a unique system pharmacology platform for Traditional Chinese Medicine Systems Pharmacology (TCMSP). The LIDD-related target genes were screened with DisGeNET and Genecards databases. Then, STRING & Cytoscape were used for analyzing the Protein-Protein Interaction network. DAVID was used for analyzing Gene Ontology (GO) & Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Finally, molecules of AutoDockVina and Py
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35

Wu, Fengzhen, Jing Liu, Zhengtong Cao, et al. "Molecular Mechanism of the Saposhnikovia divaricata–Angelica dahurica Herb Pair in Migraine Therapy Based on Network Pharmacology and Molecular Docking." Evidence-Based Complementary and Alternative Medicine 2022 (November 26, 2022): 1–12. http://dx.doi.org/10.1155/2022/1994575.

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Objective. This work studied the molecular mechanism of the Saposhnikovia divaricata–Angelica dahurica herb pair (SAHP) in migraine treatment. Methods. The active ingredients of drugs were screened, and potential targets were predicted by the Traditional Chinese Medicine Systems Pharmacology (TCMSP), TCMID, ETCM, and other databases. Migraine-related targets were obtained by harnessing the GeneCards, DrugBank, OMIM, TTD, and other databases. The protein-protein interaction (PPI) network was constructed with STRING software by performing a Venn analysis with bioinformatics. Gene Ontology (GO) f
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Xu, Mengru, Wenwen Zhang, Sheng Xu, et al. "Elucidation of the mechanism of Zhenbao pills for the treatment of spinal cord injury by network pharmacology and molecular docking: A review." Medicine 103, no. 7 (2024): e36970. http://dx.doi.org/10.1097/md.0000000000036970.

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To explore the mechanism of the Zhenbao pill (ZBP) in treating spinal cord injury (SCI). The TCMSP Database, HERB Database and literature search were used to screen the effective ingredients and targets of ZBP; SCI-related genes were searched in GeneCards, OMIM, PharmGkb, TTD and DrugBank databases; the potential targets of ZBP for treating SCI were predicted and Venn diagrams were drawn, and the “herb-ingredient-target” network was constructed by Cytoscape software. The PPI network was constructed by STRING software, and the core targets were screened by cytoNCA plug-in; GO enrichment and KEG
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Pentu, Narendra, Ajitha Azhakesan, and Pasupuleti Kishore Kumar. "Insilico molecular docking and ADME/T studies of flavonol compounds against selected proteins involved in inflammation mechanism." Journal of Applied Pharmaceutical Research 13, no. 1 (2025): 95–111. https://doi.org/10.69857/joapr.v13i1.706.

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Background: Using computational tools in drug discovery advanced the research in identifying new drug candidates for the benefit of the pharmaceutical industry and assessing the safety and pharmacokinetic profiles of phytochemicals. Understanding the inflammatory mechanism is not possible, but inflammatory signal transduction by cytokines can be mitigated by using the flavonoid class of drugs like flavonols. Methodology: A molecular docking study of flavonol compounds with proteins linked with inflammation was carried out using the AutodockVina program. SwissADME and pkCSM modules were used to
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38

Emmanuel Chuks Oranu, IC Uzochukwu, Ebere Ifejirika Ezeonyi, et al. "Binding affinities and molecular dynamics simulations of selected approved drugs and Mucuna pruriens phytoconstituents with Escherichia coli Shiga toxin." GSC Biological and Pharmaceutical Sciences 30, no. 2 (2025): 029–35. https://doi.org/10.30574/gscbps.2025.30.2.0038.

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Shiga toxin (Stx)–producing Escherichia coli (STEC), also known as “verocytotoxin- producing E. coli” is a major food and waterborne pathogen of zoonotic origin. STEC infection is involved in several life-threatening disease conditions that includes diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome. We determined the binding affinities of selected approved drugs and Mucuna pruriens phytoconstituents to shiga toxin and ricin receptors (a toxin similar in structure to shiga toxin) by molecular docking simulations. The 3D crystal structures of Stx1, Stx2 and ricin receptor were obtaine
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39

Ding, Shanshan, Weihao Wang, Xujiao Song, and Hao Ma. "Based on Network Pharmacology and Molecular Docking to Explore the Underlying Mechanism of Huangqi Gegen Decoction for Treating Diabetic Nephropathy." Evidence-Based Complementary and Alternative Medicine 2021 (May 6, 2021): 1–14. http://dx.doi.org/10.1155/2021/9928282.

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Background. Huangqi Gegen decoction (HGD), a Chinese herb formula, has been widely used to treat diabetic nephropathy in China, while the pharmacological mechanisms are still unclear. Therefore, the present study aims to explore the underlying mechanism of HGD for treating diabetic nephropathy (DN). Materials and Methods. Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), UniProt, and SwissTargetPrediction databases were used to search the active ingredients and potential targets of HGD. In addition, multiple disease-related databases were used to collect DN-related targets. C
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40

Mondal, Milon, Cristina Quispe, Chandan Sarkar, et al. "Analgesic and Anti-Inflammatory Potential of Essential Oil of Eucalyptus camaldulensis Leaf: In Vivo and in Silico Studies." Natural Product Communications 16, no. 4 (2021): 1934578X2110076. http://dx.doi.org/10.1177/1934578x211007634.

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The objective of our present study is to scrutinize the analgesic and anti-inflammatory potentials of essential oil of Eucalyptus camaldulensis leaf using different in vivo assay models at doses of 100, 200, and 400 mg/kg body weight. Twenty chemical compounds, which were isolated from the leaves essential oil of E. camaldulensis, were docked using AutodockVina against cyclooxygenase 2, tumor necrosis factor-α, and interleukin-1β convertase to elucidate the analgesic and anti-inflammatory activity. The essential oil of E. camaldulensis exhibited noteworthy analgesic activities in the writhing
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41

Reddy, PurraBuchi, M. B. Madhusudana Reddy, Ramakrishna Reddy, Santosh S. Chhajed, and Pramodkumar P. Gupta. "Computational modelling and analysis of Pyrimidine analogues as EGFR inhibitor in search of anticancer agents." Biomedicine 41, no. 1 (2021): 130–38. http://dx.doi.org/10.51248/.v41i1.548.

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Introduction and Aim:Epidermal Growth Factor Receptor tyrosine kinase is a well-known and widely studied cancer therapeutic target protein. Based on the reported anticancer activity of pyrimidines, a series of 13 compounds are designed. In the present studythe EGFR kinase domain is targeted with the designed 13 compounds.
 Materials and Methods:With missing residue in the kinase domain of EGFR crystallized structure, the domain is modelled using homology modelling, evaluated, energy-based optimization is carried out using OPLS in Gromacs. The default bindingsite was considered from the kn
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42

Abdusalam, Ashraf A. A., and Gazala M. Ben-Hander. "Identification of Potential Natural Bioactive Compounds from Glycyrrhiza glabra as Sars-CoV-2 Main Protease (MPRO) Inhibitors: In-Silico Approach." Al-Mukhtar Journal of Sciences 37, no. 2 (2022): 150–61. http://dx.doi.org/10.54172/mjsc.v37i2.679.

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The SARS-CoV-2 virus caused the COVID-19 pandemic declared in early 2020, generating a global health emergency. So far, no approved drugs or vaccines are available. Therefore, there is an urgent need to explore and develop effective new therapeutics against SARS-CoV-2. In addition, the main protease (Mpro) of the SARS-CoV-2 virus is considered essential in the virus replication propagation and considered a drug discovery target. Consequently, plant-derived compounds are an important and valuable source for novel drugs. This study reports molecular docking-based virtual screening (VS) of 20 com
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43

Oh, Ki-Kwang, Md Adnan, and Dong-Ha Cho. "Network Pharmacology-Based Study to Uncover Potential Pharmacological Mechanisms of Korean Thistle (Cirsium japonicum var. maackii (Maxim.) Matsum.) Flower against Cancer." Molecules 26, no. 19 (2021): 5904. http://dx.doi.org/10.3390/molecules26195904.

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Cirsium japonicum var. maackii (Maxim.) Matsum. or Korean thistle flower is a herbal plant used to treat tumors in Korean folk remedies, but its essential bioactives and pharmacological mechanisms against cancer have remained unexplored. This study identified the main compounds(s) and mechanism(s) of the C. maackii flower against cancer via network pharmacology. The bioactives from the C. maackii flower were revealed by gas chromatography-mass spectrum (GC-MS), and SwissADME evaluated their physicochemical properties. Next, target(s) associated with the obtained bioactives or cancer-related ta
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44

Ryabzeva, T. V., D. A. Makarevich, E. M. Ermola, V. P. Golubovich, and V. V. Kirkovskiy. "Molecular design and virtual docking of oligopeptides for binding and elimination interleukin-6 from blood plasma." Proceedings of the National Academy of Sciences of Belarus, Biological Series 64, no. 3 (2019): 350–58. http://dx.doi.org/10.29235/1029-8940-2019-64-3-350-358.

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Binding of interleukin-6 (IL-6) is the perspective target for the anti-inflammatory therapy in many pathological conditions (sepsis, autoimmune pathology, allergic diseases). The aim of this work was to develop and study the binding IL-6 oligopeptides. To achieve the goal, were set and successfully solved the following tasks: studying three-dimensional models of molecular structures of IL-6 incombination with the R-IL-6 and gp130, prediction and virtual synthesis low molecular weight oligopeptides; evaluating the free energy of IL-6 binding for identity the most effective oligopeptide; studyin
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45

S, Sreekumar. "In silico screening and identification of leads against multi-targets of type II diabetes in Plectranthus vettiveroides." Journal of medical pharmaceutical and allied sciences 11, no. 5 (2022): 5268–82. http://dx.doi.org/10.55522/jmpas.v11i5.3957.

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Generally, phytochemicals have activity on multi-targets and such molecules have been used as effective drugs against the diseases caused by multi-factorial causation like diabetes mellitus (DM). Plectranthus vettiveroides (Jacob) N.P. Singh & B.D. Sharma has been used as a polychrest against various diseases including type II diabetes in tradition system of medicine. The present investigation aimed to validate anti-diabetic property of the root derived essential oil of P. vettiveroides and identification of leads with activity on six targets of DM through in silico method. A total of 78 p
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M, Rahmatullah. "In Silico Studies on Binding of Vernonia Amygdalina Phytochemicals to Main Protease (Mpro) of SARS-CoV-2." Journal of Natural & Ayurvedic Medicine 5, no. 3 (2021): 1–8. http://dx.doi.org/10.23880/jonam-16000318.

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Objectives: The corona virus SARS-CoV-2 emerged in late December 2019 and since then has created a global pandemic, which shows no signs of abating as of this date. As of July 9 2021, the virus has been responsible throughout the world for 186,357,958 infections and 4.026,907 deaths. Any drugs against this virus remains to be discovered. Several vaccines have been approved by the World Health Organization but administering the vaccines have been difficult because of production shortages and distribution anomalies between rich and poor nations. Towards finding a new and affordable antiviral dru
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Emmanuel Chuks Oranu, Esther Oluchukwu Eze, Adanna Ijeawele, et al. "Validation of the binding affinities and stabilities of ivermectin and moxidectin against Sars-CoV-2 receptors using molecular docking and molecular dynamics simulation." GSC Biological and Pharmaceutical Sciences 26, no. 1 (2024): 303–14. http://dx.doi.org/10.30574/gscbps.2024.26.1.0030.

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Corona-viruses (CoVs), a large family of single-stranded RNA viruses, can infect animals and also humans, causing respiratory, gastrointestinal, hepatic, and neurologic disease. As the largest known RNA viruses, they are further divided into four genera: alpha-coronavirus, beta- corona- virus, gamma-corona virus and delta-coronavirus. SARS-CoV-2 belong to genus betacoronavirus. The viral genome of SARS-CoV-2 codes 4 major structural proteins: the nucleocapsid (N) protein, the transmembrane (M) protein, the envelope (E) protein, and the spike (S) protein. It also encodes 16 nonstructural protei
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48

Amelia, Marsha A., Dini Kesuma, Aguslina Kirtishanti, I. Gede A. Sumartha, and Maria Claudya. "Molecular docking, synthesis, and in vitro activity testing of chalcone derivatives from Boesenbergia rotunda (L.) Mansf. against MCF-7 breast cancer cells." Journal of Pharmacy & Pharmacognosy Research 13, s1 (2025): S129—S139. https://doi.org/10.56499/jppres24.2220_13.s1.129.

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Context: The chalcone derivative compounds (bis-2-chlorobenzyloxychalcone and bis-3-chlorobenzyloxychalcone) synthesized from pinostrobin, which is found in Boesenbergia rotunda (L.) Mansf., which has cytotoxic activity relative to the estrogen receptor alpha. Aims: To determine the anticancer activity of chalcone derivative compounds synthesized from B. rotunda as an in silico and in vitro breast cancer candidate. Methods: An in silico test was performed to predict the cytotoxic activity using AutoDockVina and the synthesis of chalcone and derivatives from pinostrobin compounds contained in B
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Emmanuel, Chuks Oranu, Oluchukwu Eze Esther, Ijeawele Adanna, et al. "Validation of the binding affinities and stabilities of ivermectin and moxidectin against Sars-CoV-2 receptors using molecular docking and molecular dynamics simulation." GSC Biological and Pharmaceutical Sciences 26, no. 1 (2024): 303–14. https://doi.org/10.5281/zenodo.10969665.

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Corona-viruses (CoVs), a large family of single-stranded RNA viruses, can infect animals and also humans, causing respiratory, gastrointestinal, hepatic, and neurologic disease. As the largest known RNA viruses, they are further divided into four genera: alpha-coronavirus, beta- corona- virus, gamma-corona virus and delta-coronavirus. SARS-CoV-2 belong to genus betacoronavirus. The viral genome of SARS-CoV-2 codes 4 major structural proteins: the nucleocapsid (N) protein, the transmembrane (M) protein, the envelope (E) protein, and the spike (S) protein. It also encodes 16 nonstructural protei
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50

S, Sujatha, and Rajini R. "In-Silico Enactment of Musa paradisiaca (L.) Exudate Against the Urotlithiatic Disease by Docking Study." Indian Journal of Science and Technology 17, no. 28 (2024): 2889–96. https://doi.org/10.17485/IJST/v17i28.1899.

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Abstract <strong>Objectives:</strong>&nbsp;Urolithiasis is a condition that occurs when the stones exit the renal pelvis and move onto the remainder of the urinary collecting system. Musa paradisiaca (L.) is a plant with high nutritive value and has been used for the treatment of various diseases including urolithiasis. The objective of the present study was designed to detect the receptor-ligand binding energy and interaction through a molecular docking from the bio-active compounds in an exudates of M. paradisiaca pseudo stem on urolithiatic causative protein named as glycolate oxidase recep
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