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Journal articles on the topic 'Reverse docking'

Author: Grafiati

Published: 7 July 2024

Last updated: 31 July 2025

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1

Soto Zuluaga, Juan Pablo, Marcus Thiell, and Rosa Colomé Perales. "Reverse cross-docking." Omega 66 (January 2017): 48–57. http://dx.doi.org/10.1016/j.omega.2016.01.010.

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2

Listyani, Tiara Ajeng, and Rina Herowati. "Analisis Docking Molekuler Senyawa Derivat Phthalimide sebagai Inhibitor Non-Nukleosida HIV-1 Reverse Transcriptase." Jurnal Farmasi Indonesia 15, no. 2 (2018): 123–34. http://dx.doi.org/10.31001/jfi.v15i2.445.

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Senyawa derivat phthalimide dilaporkan sebagai kelas baru inhibitor nonnukleosida reverse transcriptase. Analisis docking molekuler senyawa derivat phthalimide terhadap enzim reverse transcriptase diperlukan untuk mengetahui afinitas dan pola interaksi antara senyawa di atas dengan enzim reverse transcriptase. Senyawa derivat phthalimide dioptimasi geometri menggunakan perangkat lunak VegaZZ selanjutnya dilakukan dengan cara preparasi target, preparasi ligan, validasi metode docking, dan analisis docking menggunakan PyRx-Python 0.8 - AutoDock Vina sehingga didapatkan interaksi ligan deng

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Seal, Abhik, Riju Aykkal, and Mriganka Ghosh Ghosh. "Docking study of HIV-1 reverse transcriptase with phytochemicals." Bioinformation 5, no. 10 (2011): 430–39. http://dx.doi.org/10.6026/97320630005430.

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4

Park, Kichul, and Art E. Cho. "Using reverse docking to identify potential targets for ginsenosides." Journal of Ginseng Research 41, no. 4 (2017): 534–39. http://dx.doi.org/10.1016/j.jgr.2016.10.005.

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5

DA SILVA, CARLOS H. T. P., IVONE CARVALHO, and CARLTON A. TAFT. "MOLECULAR DYNAMICS, DOCKING, DENSITY FUNCTIONAL, AND ADMET STUDIES OF HIV-1 REVERSE TRANSCRIPTASE INHIBITORS." Journal of Theoretical and Computational Chemistry 05, no. 03 (2006): 579–86. http://dx.doi.org/10.1142/s0219633606002441.

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Molecular dynamics, density functional with correlation, as well as docking studies of inhibitors of HIV-1 reverse transcriptase (RT) are reported. We propose in this work a novel potential HIV-1 RT inhibitor (RTI), which theoretically appears to bind in a similar mode as other nucleoside reverse transcriptase inhibitors, and in addition, it introduces a new hydrogen bond interaction with Trp229. Our novel RTI has high docking scores and the molecular dynamics studies, as well as the analysis of the ligand-receptor interactions in the active site and the ADMET properties suggest advantages and

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Wang, Yan, Aidong Wang, Jianhua Wang, Xiaoran Wu, Yijie Sun, and Yan Wu. "Me-Better Drug Design Based on Nevirapine and Mechanism of Molecular Interactions with Y188C Mutant HIV-1 Reverse Transcriptase." Molecules 27, no. 21 (2022): 7348. http://dx.doi.org/10.3390/molecules27217348.

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In this paper, the Y188C mutant HIV-1 reverse transcriptase (Y188CM-RT) target protein was constructed by homology modeling, and new ligands based on nevirapine (NVP) skeleton were designed by means of fragment growth. The binding activity of new ligands to Y188CM-RT was evaluated by structural analysis, ADMET prediction, molecular docking, energy calculation and molecular dynamics. Results show that 10 new ligands had good absorbability, and their binding energies to Y188CM-RT were significantly higher than those of wild-type HIV-1 reverse transcriptase(wt). The binding mode explained that fr

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Byler, Kendall, and William Setzer. "Protein Targets of Frankincense: A Reverse Docking Analysis of Terpenoids from Boswellia Oleo-Gum Resins." Medicines 5, no. 3 (2018): 96. http://dx.doi.org/10.3390/medicines5030096.

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Background: Frankincense, the oleo-gum resin of Boswellia trees, has been used in traditional medicine since ancient times. Frankincense has been used to treat wounds and skin infections, inflammatory diseases, dementia, and various other conditions. However, in many cases, the biomolecular targets for frankincense components are not well established. Methods: In this work, we have carried out a reverse docking study of Boswellia diterpenoids and triterpenoids with a library of 16034 potential druggable target proteins. Results: Boswellia diterpenoids showed selective docking to acetylcholines

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Resti, Lady Ichwana, Herman Mawengkang, and Elly Rosmaini. "Mathematical Model for Vehicle Routing and Scheduling with Forward and Reverse Logistics." Sinkron 8, no. 3 (2023): 1536–43. http://dx.doi.org/10.33395/sinkron.v8i3.12599.

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Companies usually use cross-docking to reduce logistics costs. The product delivery process from suppliers to retailers and vice versa is facilitated by crossdocking facilities. One of important problem in crossdocking is vehicle routes. In this work we discuss about cross-docking problem for vehicle routes which is brought into the form of an integration model. We also present the strategy to handle the forward and reverse logistics. From this strategy we have a NP-hard mathematical model as the result.

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Saleem, Mehmood, Mehar, et al. "Bioassay Directed Isolation, Biological Evaluation and in Silico Studies of New Isolates from Pteris cretica L." Antioxidants 8, no. 7 (2019): 231. http://dx.doi.org/10.3390/antiox8070231.

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Members of genus Pteris have their established role in the traditional herbal medicine system. In the pursuit to identify its biologically active constituents, the specie Pteris cretica L. (P. cretica) was selected for the bioassay-guided isolation. Two new maleates (F9 and CB18) were identified from the chloroform extract and the structures of the isolates were elucidated through their spectroscopic data. The putative targets, that potentially interact with both of these isolates, were identified through reverse docking by using in silico tools PharmMapper and ReverseScreen3D. On the basis of

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Ruswanto, Ruswanto, Richa Mardianingrum, Siswandono Siswandono, and Dini Kesuma. "Reverse Docking, Molecular Docking, Absorption, Distribution, and Toxicity Prediction of Artemisinin as an Anti-diabetic Candidate." Molekul 15, no. 2 (2020): 88. http://dx.doi.org/10.20884/1.jm.2020.15.2.579.

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Aldose reductase is an enzyme that catalyzes one of the steps in the sorbitol (polyol) pathway that is responsible for fructose formation from glucose. In diabetes, aldose reductase activity increases as the glucose concentration increases. The purpose of this research was to identify and develop the use of artemisinin as an anti-diabetic candidate through in silico studies, including reverse docking, receptor analysis, molecular docking, drug scan, absorption, and distributions and toxicity prediction of artemisinin. Based on the results, we conclude that artemisinin can be used as an anti-di

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11

Riza, Hafrizal, Andhi Fahrurroji, Arif Wicaksono, Ahmad Kharis Nugroho, and Sudibyo Martono. "DOCKING STUDY OF METHYL HESPERIDIN AS NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 3 (2018): 85. http://dx.doi.org/10.22159/ijpps.2018v10i3.22724.

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Objective: This study aims to analyze the methyl hesperidin physicochemical properties related to solubility and permeability, and the affinity of methyl hesperidin against reverse transcriptase HIV-1 activity as a competitive substrate.Methods: This research was conducted using the computerized method, ChemOffice 15.0, to predict ligand physicochemical properties related to solubility and permeability, and Autodock Vina with Autodock Tools program to analyze ligand-receptor affinity.Results: The analysis result of physicochemical properties of hesperidin and methyl hesperidin is respectively

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12

., T. B. Kakade. "Homology Modeling and Docking Studies on HIV Reverse Transcriptase Inhibitors." Journal of Current Pharma Research 3, no. 3 (2013): 965–82. http://dx.doi.org/10.33786/jcpr.2013.v03i03.010.

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13

Iksan, Muhamad, Frida M. Yusuf, Fitriani Fitriani B, and Wa Ode Al Zarliani. "Antipyretic Drug Candidates Through Reverse Docking Techniques Used In Science Learning." Jurnal Penelitian Pendidikan IPA 9, no. 8 (2023): 6398–405. http://dx.doi.org/10.29303/jppipa.v9i8.4863.

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Red ginger (Zingiber officinale var. Rubrum) is a commonly used rhizome known for its fragrant and spicy taste. It contains gingerol and shogaol compounds that have antipyretic effects by inhibiting prostaglandin formation and stimulating the production of interleukin-10, an endogenous antipyretic. This study aimed to evaluate the potential of gingerol and shogaol compounds as antipyretic drug candidates through reverse docking techniques targeting interleukin-10 (IL-10). Ten natural compounds from red ginger were predicted for their potential as antipyretic drugs and docked with the IL-10 rec

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Savita, Mahendra Kumar, Neha Bora, Ruby Singh, and Prachi Srivastava. "Screening of camphene as a potential inhibitor targeting SARS-CoV-2 various structural and functional mutants: Through reverse docking approach." Environmental Health Engineering and Management 10, no. 2 (2023): 123–29. http://dx.doi.org/10.34172/ehem.2023.14.

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Background: SARS-CoV was first identified in 2003 but SARS-CoV-2, which gained its recognition again in 2019 as COVID-19, has been a crucial threat worldwide and has caused more death rates than the SARS-CoV but till now no confined treatments are available. The present study aimed to investigate the efficacy of camphene against various structural and functional mutants of SARS-CoV-2 using reverse docking protocol. Methods: To investigate the efficacy of camphene as a potential antiviral drug against COVID-19, against of all possible target proteins in SARS-CoV-2, which could lead to a new pla

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15

Tong, Jianbo, Shan Lei, Pei Zhan, Shangshang Qin, and Yang Wang. "QSAR and Docking Studies of DATA Analogues as HIV-1 Reverse Transcriptase Inhibitors." Letters in Drug Design & Discovery 16, no. 2 (2018): 153–59. http://dx.doi.org/10.2174/1570180815666180413152636.

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Background: Acquired Immunodeficiency Syndrome (AIDS) caused by Human Immunodeficiency Virus (HIV) has seriously threatened human health, so development of new, selective and safe non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) remains a high priority for medical research. Diaryltriazine (DATA) have been identified as a new class of potent nonnucleoside HIV-1 Reverse Transcriptase (RT) inhibitors. The study deals with Topomer CoMFA (Comparative Molecular Field Analysis) and molecular docking to explore the important features of DATA analogues for exerting potent HIV-1 RT inhibitors ac

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Darme, Pierre, Manuel Dauchez, Arnaud Renard, et al. "AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability." International Journal of Molecular Sciences 22, no. 14 (2021): 7489. http://dx.doi.org/10.3390/ijms22147489.

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Molecular docking is widely used in computed drug discovery and biological target identification, but getting fast results can be tedious and often requires supercomputing solutions. AMIDE stands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inverse docking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvement by using AutoDock-GPU and by pulling a total revision of programming workflow, leading to better performances, easier use, bug corrections, parallelization improvements and PC/HPC compatibility. In addition to inverse

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17

Kotadiya, Manisha, and Ravi Ajudia. "In-silico Docking and ADME Studies of Natural Phytoconstituents from Different Medicinal Plants as Potential HIV Reverse Transcriptase Inhibitors." INTERNATIONAL JOURNAL OF PHARMACEUTICAL QUALITY ASSURANCE 15, no. 01 (2024): 115–18. http://dx.doi.org/10.25258/ijpqa.15.1.18.

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Human immunodeficiency virus (HIV) is a serious global public health concern, having claimed more than 35 million lives to date. Human immunodeficiency virus-1 reverse transcriptase is an essential enzyme for viral replication. If the enzyme is blocked, viral replication may be dramatically reduced. Several human immunodeficiency virus medicines are available, though better effective treatments are always needed due to the drug confrontation and negative outcomes. According to prior research, several natural substances have a high affinity for the human immunodeficiency virus-1 reverse transcr

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Kharkar, Prashant S., Sona Warrier, and Ram S. Gaud. "Reverse docking: a powerful tool for drug repositioning and drug rescue." Future Medicinal Chemistry 6, no. 3 (2014): 333–42. http://dx.doi.org/10.4155/fmc.13.207.

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19

Kawsar, Sarkar Mohammad Abe, Mohammed Anowar Hosen, Tasneem Sultana Chowdhury, Kazi Masud Rana, Yuki Fujii, and Yasuhiro Ozeki. "Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase." Revista de Chimie 72, no. 3 (2021): 159–78. http://dx.doi.org/10.37358/rc.21.3.8446.

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In recent, millions of people are living with the human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. HIV-1 reverse transcriptase (RT) is one of the main viral targets for HIV-1 inhibition. Pyrimidine nucleoside derivative, 3′-azido-3′-deoxythymidine (AZT) is a highly active nucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). In this work, hydroxyl (-OH) groups of cytidine structure were modified with different aliphatic and aromatic groups to get 5´-O-acyl- and 2´,3´-di-O-acyl derivatives and then employed f

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20

Ganguly, Swastika, and Geeta Yadav. "Molecular Docking Studies of Novel Benzimidazole Analogs as HIV-1-RT Inhibitors with Broad Spectrum Chemotherapeutic Properties." International Journal of Drug Design and Discovery 4, no. 4 (2025): 1193–213. https://doi.org/10.37285/ijddd.4.4.5.

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The urgent need for novel HIV-1-RT inhibitors with broad spectrum chemotherapeutic properties has provided an impetus for understanding the structural requisites of HIV-1-RT inhibitors at the molecular level. Toward this objective, binding mode analysis of 113 benzimidazole analogs was performed. First, molecular docking studies were performed on novel benzimidazoles by Glide program in the active site of four different enzymes namely HIV-1 reverse transcriptase (PDB code 1RT2), peptide deformylase (PDB code 1G2A), Mycobacterium tuberculosis-CYP51 (PDB code 1EA1) and Candida albicans (CACYP51)

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21

Earlia, Nanda, Muslem, Rivansyah Suhendra, et al. "GC/MS Analysis of Fatty Acids on Pliek U Oil and Its Pharmacological Study by Molecular Docking to Filaggrin as a Drug Candidate in Atopic Dermatitis Treatment." Scientific World Journal 2019 (November 3, 2019): 1–7. http://dx.doi.org/10.1155/2019/8605743.

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Analysis of fatty acid contents and pharmacological properties of Pliek U oil was performed. Fatty acids were analyzed by gas chromatography-mass spectrometry (GC-MS), and pharmacological properties based on its potential on filament-aggregating protein (filaggrin) were studied with bioinformatics approach by the reverse docking technique using palmitic acid as a control compound. Two Pliek U extracts, namely, Pliek U oil (PUO) and ethanolic Pliek U oil extract (EPUOE), were prepared. The GC-MS results revealed that lauric acid, myristic acid, palmitic acid, and oleic acid are the predominant

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22

Aldholmi, Mohammed, Rizwan Ahmad, Mohammad Habeeb Shaikh, Ayad Mohammed Salem, Maher Alqurashi, and Mansour Alturki. "Anti-Infective Activity of Momordica charantia Extract with Molecular Docking of Its Triterpenoid Glycosides." Antibiotics 13, no. 6 (2024): 544. http://dx.doi.org/10.3390/antibiotics13060544.

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Momordica charantia, commonly known as bitter melon, is a fruiting plant that has been used for several diseases including infectious diseases. In this study, we report the antibacterial, antifungal, and antiviral activity of different bitter melon fruit parts originating from India and Saudi Arabia. The in vitro experiments are supported by the molecular docking of karavilosides to verify their role in the bioactivity. The antimicrobial assays revealed activity against Candida albicans, Escherichia coli, and Staphylococcus aureus. The extracts exhibited the potent inhibition of HIV-I reverse

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Li, Yan-Chi, Yu-Meng Xiong, Ze-Ping Long, et al. "ML210 Antagonizes ABCB1- Not ABCG2-Mediated Multidrug Resistance in Colorectal Cancer." Biomedicines 13, no. 5 (2025): 1245. https://doi.org/10.3390/biomedicines13051245.

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Objectives: ABCB1-mediated multidrug resistance (MDR) compromises chemotherapy efficacy in colorectal cancer (CRC). Despite decades of research, no selective ABCB1 inhibitor has achieved clinical success. This study investigates ML210 as a novel ABCB1-specific inhibitor to reverse ABCB1-driven MDR. Methods: Cytotoxicity assays (MTT) were performed on ABCB1-overexpressing HCT-8/V and ABCG2-overexpressing S1-M1-80 CRC cells. Drug accumulation (doxorubicin/mitoxantrone) was quantified via flow cytometry, and cell cycle effects were analyzed using propidium iodide staining. Molecular docking utili

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Chandra, Priyanka, Swastika Ganguly, and Soikata Karmakar. "Comparative Studies of Various NNRTIs in the Active Site of Different HIV-1RT Receptors." Chemistry Proceedings 3, no. 1 (2020): 33. http://dx.doi.org/10.3390/ecsoc-24-08313.

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HIV is one of the most deadly viruses known to humans and causes a disease, known as Acquired Immunodeficiency Syndrome (or, AIDS). There are only a handful of drugs which are totally effective against the virus. This is due to the enzyme reverse transcriptase present within the virus. Due to various mutations in the enzyme, the virus becomes unresponsive towards the drugs. In the present study, docking studies of the standard non-nucleoside reverse transcriptase inhibitors were performed in the non-nucleoside inhibitory binding pocket of reverse transcriptase enzymes of wild type and the resi

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Tshering, Kipchu, and Mir Misbahuddin. "In silico prediction of telomerase reverse transcriptase inhibitors using modified retinol for the treatment of arsenical cancer." Bangabandhu Sheikh Mujib Medical University Journal 9, no. 3 (2016): 164. http://dx.doi.org/10.3329/bsmmuj.v9i3.29650.

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<p align="left">Retinol molecule was modified to predict the inhibitors of telomerase reverse transcriptase for the treatment of arsenical cancer through <em>in silico</em> study. Telomerase activity is expressed in the cancerous conditions which can be the target for anticancer activity by inhibiting telomerase reverse transcriptase enzyme. The inhibitors were predicted through molecular docking of modified retinol with telomerase reverse transcriptase. Taking into account of low binding energy and high binding affinity two new compounds, compound number 606 and compound num

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26

Harriman, D. Joseph, and Ghislain Deslongchamps. "Reverse-docking as a computational tool for the study of asymmetric organocatalysis." Journal of Computer-Aided Molecular Design 18, no. 5 (2004): 303–8. http://dx.doi.org/10.1023/b:jcam.0000047813.47656.36.

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Zhang, Haiping, Jianbo Pan, Xuli Wu, Ai-Ren Zuo, Yanjie Wei, and Zhi-Liang Ji. "Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach." ACS Omega 4, no. 6 (2019): 9710–19. http://dx.doi.org/10.1021/acsomega.9b00020.

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Harriman, D. Joseph, and Ghislain Deslongchamps. "Reverse-docking study of the TADDOL-catalyzed asymmetric hetero-Diels–Alder reaction." Journal of Molecular Modeling 12, no. 6 (2006): 793–97. http://dx.doi.org/10.1007/s00894-006-0097-z.

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29

Lee, Aeri, Kyoungyeul Lee, and Dongsup Kim. "Using reverse docking for target identification and its applications for drug discovery." Expert Opinion on Drug Discovery 11, no. 7 (2016): 707–15. http://dx.doi.org/10.1080/17460441.2016.1190706.

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30

Sanober, MD, and Estari Mamidala. "Pharmacophore Generation and Structure-Based Strategies For Nnrti Development Against HIV-1 Rt." Advances in Applied Biological Research 1, no. 1 (2024): 7–13. https://doi.org/10.48165/aabr.2024.1.02.

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The development of Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) is critical in combating HIV-1 due to the virus’s high mutation rate and resistance to current therapies. This study aims to identify potential NNRTIs through pharmacophore generation and structure-based drug design, focusing on the interaction of candidate molecules with HIV-1 Reverse Transcriptase (RT). Using molecular docking, three ligands, ZINC000002416705, ZINC000002416703, and ZINC000014171386, were analyzed for their binding affinity, inhibition constants, and interactions with key active site residues. The nee

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K., Sony Jacob, and Swastika Ganguly. "A BATTLE AGAINST AIDS: NEW PYRAZOLE KEY TO AN OLDER LOCK-REVERSE TRANSCRIPTASE." International Journal of Pharmacy and Pharmaceutical Sciences 8, no. 11 (2016): 75. http://dx.doi.org/10.22159/ijpps.2016v8i11.12634.

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Objective: The reason for the failure of most of the anti-HIV drugs are their poor pharmacokinetics, the poor risk to benefit ratio and the drug resistance. With the objective of developing newer pyrazole scaffolds for effective treatment of HIV, binding mode analysis of designing ligands with the HIV-1RT protein and prediction of key ADME and toxicity parameters of the compounds was in an area of interest.Methods: In this study, molecular docking studies and ADME-T studies were carried out in designing of some novel pyrazole analogs. The protein (PDB ID: 1RT2) was prepared using the Protein P

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Nugraha, Rivo YB, Icha FD Faratisha, Kana Mardhiyyah, et al. "Antimalarial Properties of Isoquinoline Derivative from Streptomyces hygroscopicus subsp. Hygroscopicus: An In Silico Approach." BioMed Research International 2020 (January 9, 2020): 1–15. http://dx.doi.org/10.1155/2020/6135696.

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Malaria is one of the life-threatening diseases in the world. The spread of resistance to antimalarial drugs is a major challenge, and resistance to artemisinin has been reported in the Southeast Asian region. In the previous study, the active compound of Streptomyces hygroscopicus subsp. Hygroscopicus (S. hygroscopicus), eponemycin, has been shown to have antimalarial effects. To further analyze the effects of other active compounds on the Plasmodium parasite, identifying and analyzing the effectiveness of compounds contained in S. hygroscopicus through instrumentation of liquid chromatograph

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Tien, Nguyen Truong, and Bui Tho Thanh. "Predicting binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase using molecular docking." Science and Technology Development Journal - Natural Sciences 2, no. 1 (2019): 53–58. http://dx.doi.org/10.32508/stdjns.v2i1.674.

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The HIV/AIDS epidemic has become one of the most dangerous causes leading to millions of deaths around the world a year. To date, there have not had effective anti-HIV drugs in the treatment of HIV/AIDS because of emerging drug-resistant HIV mutants. In this work, potential non-nucleoside reverse transcriptase inhibitors (NNRTIs) were studied by means of molecular docking. The Diversity “drug-like” database from the National Cancer Institute, is composed of 1.420 compounds, was performed docking into the NNRTI binding pocket of HIV-1 reverse transcriptase crystal structure (1fk9) by using Auto

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Wang, Junmei, Xinshan Kang, Irwin D. Kuntz, and Peter A. Kollman. "Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM−PB/SA." Journal of Medicinal Chemistry 48, no. 7 (2005): 2432–44. http://dx.doi.org/10.1021/jm049606e.

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Tu, Nhat Quang, Clémence Richetta, Federica Putzu, et al. "Identification of HIV-1 Reverse Transcriptase-Associated Ribonuclease H Inhibitors Based on 2-Hydroxy-1,4-naphthoquinone Mannich Bases." Molecules 30, no. 3 (2025): 495. https://doi.org/10.3390/molecules30030495.

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There is a strong demand for new and efficient antiviral compounds. A series of 2-hydroxy-1,4-naphthoquinone Mannich bases were screened for their HIV-1-RNase H inhibitory activity. An HIV-1-RNase H assay was used to study the RNase H inhibition by the test compounds. Docking of active derivatives into the active site of the enzyme was carried out. Compounds 1e and 2k showed distinctly higher HIV-1-RNase H inhibitory activity (IC50 = 2.8–3.1 µM) than the known inhibitors RDS1759 and compound 13. The binding mode and possible interactions of 1e and 2k with the HIV-1-RNase H active site were det

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Khan, Mahmood-ul-Hassan, Shahid Hameed, Muhammad Farman, Najim A. Al-Masoudi, and Helen Stoeckli-Evans. "Synthesis, anti-HIV activity and molecular modeling study of 3-aryl-6-adamantylmethyl-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives." Zeitschrift für Naturforschung B 70, no. 8 (2015): 609–16. http://dx.doi.org/10.1515/znb-2015-0032.

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AbstractA series of novel 3-aryl-6-adamantylmethyl-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazoles 6a–l were synthesized by a simple method with the aim of developing novel HIV non-nucleoside reverse transcriptase inhibitors. All the synthesized compounds were structurally confirmed by spectral analyses. The structure of 6a was unambiguously verified by X-ray structure determination. The synthesized compounds were evaluated for their anti-HIV activity and four analogs displayed moderate inhibitory activity with EC50 values ranging from 10.10 to 12.40 μg mL–1. Molecular docking of 6g with HIV-1 rever

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Konyar, Dilan, and Muhammed Tılahun Muhammed. "MOLECULAR DOCKING AND MOLECULAR DYNAMICS SIMULATIONS INHIBITION AGAINST OF HUMAN TELOMERASE BY NUCLEOSIDE AND NON-NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS (NRTIs/NNRTIs)." Ankara Universitesi Eczacilik Fakultesi Dergisi 48, no. 2 (2024): 18. http://dx.doi.org/10.33483/jfpau.1444259.

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Objective: This study investigated the anticancer effects of nucleoside and non-nucleoside reverse transcriptase inhibitors drugs by computational methods. The study aimed to evaluate the binding capacity of these drugs on the telomerase essential N-terminal (TEN) domain of telomerase reverse transcriptase (TERT). Molecular docking was used to assess the drugs' binding potential to the TEN domain. The stability of the protein-drug combination obtained from the docking method was assessed using molecular dynamics (MD) modeling. Material and Method: The TEN domain of TERT's crystal structure was

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Pitta, Eleni, Evangelia Tsolaki, Athina Geronikaki, et al. "4-Thiazolidinone derivatives as potent antimicrobial agents: microwave-assisted synthesis, biological evaluation and docking studies." MedChemComm 6, no. 2 (2015): 319–26. http://dx.doi.org/10.1039/c4md00399c.

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Alharbi, Ahmed. "Molecular docking based design of Inhibitors for viral Non-Nucleosidase as potential anti-retroviral agents." Bioinformation 16, no. 10 (2020): 736–41. http://dx.doi.org/10.6026/97320630016736.

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Reverse Transcriptase (RT) inhibitors are highly promising agents for use as an effective anti-retroviral therapy (HAART) which is typically a combination of three or four antiretroviral drugs. We used direct drug design approach to discover new chemical entities for the target protein. The validated template of the protein targeting reverse transcriptase PDB ID 1JKH was extracted for three sites hydrophobic, steric, and electronic parameters explain the interactions at the active site by the inhibitors. We used the Zinc library of compounds to explore the possible leads for HAART through RT i

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Tarasova, Olga, Vladimir Poroikov, and Alexander Veselovsky. "Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review." Molecules 23, no. 5 (2018): 1233. http://dx.doi.org/10.3390/molecules23051233.

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Fan, Shengjun, Qiang Geng, Zhenyu Pan, et al. "Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach." BMC Systems Biology 6, no. 1 (2012): 152. http://dx.doi.org/10.1186/1752-0509-6-152.

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Billones, Junie. "Reverse docking study unravels the potential Mycobacterium tuberculosis enzyme targets of Agelasine F." Oriental Journal of Chemistry 32, no. 2 (2016): 851–58. http://dx.doi.org/10.13005/ojc/320210.

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Joseph Harriman, D., Glen F. Deleavey, Andreas Lambropoulos, and Ghislain Deslongchamps. "Reverse-docking study of the organocatalyzed asymmetric Strecker hydrocyanation of aldimines and ketimines." Tetrahedron 63, no. 52 (2007): 13032–38. http://dx.doi.org/10.1016/j.tet.2007.10.009.

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Ragno, Rino, Simona Frasca, Fabrizio Manetti, Antonella Brizzi, and Silvio Massa. "HIV-Reverse Transcriptase Inhibition: Inclusion of Ligand-Induced Fit by Cross-Docking Studies." Journal of Medicinal Chemistry 48, no. 1 (2005): 200–212. http://dx.doi.org/10.1021/jm0493921.

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Kheirkhah, Amirsaman, and Saeid Rezaei. "Using cross-docking operations in a reverse logistics network design: a new approach." Production Engineering 10, no. 2 (2015): 175–84. http://dx.doi.org/10.1007/s11740-015-0646-3.

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Chandra, Priyanka, Swastika Swastika, and Manik Ghosh. "In Silico Studies of Piperazinyl-4-Nitroimidazole Derivatives in the Non-Nucleoside Inhibitory Binding Pocket of Human Immunodeficiency Virus-1-Reverse Transcriptase Enzyme." INDIAN JOURNAL OF HETEROCYCLIC CHEMISTRY 33, no. 03 (2023): 293. http://dx.doi.org/10.59467/ijhc.2023.33.293.

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Human immunodeficiency virus-1 (HIV-1) reverse transcriptase enzyme catalyzes the conversion of viral RNA to DNA. This viral DNA infects a healthy host body, it leads to the production of viral DNA in higher concentrations and leads to a disease called acquired immunodeficiency syndrome; which is a very fatal disease and leads to the development of several other diseases. Therefore, the development of effective inhibitors is required to execute the therapeutic effects against this disease. In this context, in the present study, the docking studies of compounds showing HIV-1 inhibition were per

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Gong, Chang, Zihao Liu, Qun Lin, et al. "Anti-PITPNM3 small molecular compounds reverse breast cancer metastasis by targeting PITPNM3." Journal of Clinical Oncology 39, no. 15_suppl (2021): e15005-e15005. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15005.

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e15005 Background: Recent studies highlight the fundamental roles of PITPNM3 in breast cancer metastasis. PITPNM3 is identified as the functional receptor of CCL18 and promotes breast cancer cell invasion and metastasis by binding with CCL18. Since anti-CCL18 neutralized antibodies shows medium binding affinity which restricts their clinical application, small molecular inhibitors targeting PITPNM3 are needed to be further investigated. Therefore, we identified several first in class small molecular inhibitors potentially targeting PITPNM3 and can inhibit breast cancer metastasis conducted by

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Rasyadan Taufiq Probojati, Ahmad Affan Ali Murtadlo, Md. Emdad Ullah, Sin War Naw, and Dora Dayu Rahma Turista. "Molecular Docking Study of HIV-1 Antiretroviral Candidate via Reverse Transcriptase Inhibitor from Zingiber officinale var. Roscoe." SAINSTEK International Journal on Applied Science, Advanced Technology and Informatics 1, no. 01 (2022): 26–31. http://dx.doi.org/10.24036/sainstek/vol1-iss01/6.

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HIV-1 is a member of the Retrovirus and the virus causes AIDS in humans. AIDS affects the dynamics of the immune system leading to fatal opportunistic infections. Reverse transcriptase plays an important role as a functional enzyme in the viral replication process, the enzyme works to carry out the transcription process of ssRNA into cDNA and then initiates the viral integration process of the genome into the nucleus. Currently many use of HIV-1 NNRTIs, the nevirapine type, with a molecular mechanism that can bind to the active site of the HIV-1 reverse transcriptase enzyme to inhibit its acti

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Krishnamoorthy, Praveen K. P., Sekar Subasree, Udhayachandran Arthi, Mohammad Mobashir, Chirag Gowda, and Prasanna D. Revanasiddappa. "T-cell Epitope-based Vaccine Design for Nipah Virus by Reverse Vaccinology Approach." Combinatorial Chemistry & High Throughput Screening 23, no. 8 (2020): 788–96. http://dx.doi.org/10.2174/1386207323666200427114343.

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Aim and Objective: Nipah virus (NiV) is a zoonotic virus of the paramyxovirus family that sporadically breaks out from livestock and spreads in humans through breathing resulting in an indication of encephalitis syndrome. In the current study, T cell epitopes with the NiV W protein antigens were predicted. Materials and Methods: Modelling of unavailable 3D structure of W protein followed by docking studies of respective Human MHC - class I and MHC - class II alleles predicted was carried out for the highest binding rates. In the computational analysis, epitopes were assessed for immunogenicity

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Wang, Yueping, Jie Chang, Jiangyuan Wang, et al. "3D-QSAR Studies of S-DABO Derivatives as Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors." Letters in Drug Design & Discovery 16, no. 8 (2019): 868–81. http://dx.doi.org/10.2174/1570180815666180810112321.

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Background: S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside reverse transcriptase inhibitors have received considerable attention during the last decade due to their high potency against HIV-1. Methods: In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2) was used t

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