Artykuły w czasopismach: „Reverse docking”

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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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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 dengan target, energi bebas pengikatan, ikatan hidrogen, dan pola interaksi. Pola interaksi dilihat dari tiga puluh tiga senyawa derivat phthalimide dengan enzim reverse transcriptase menunjukkan ikatan hidrogen dengan asam amino Lys101 dimana interaksi tersebut mirip dengan interaksi senyawa TIBO R 86183 yang merupakan ligan asli protein target.

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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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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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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 specificities for this potential RTI.

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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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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 fragment growth contributed to larger ligands, leading to improved suitability at the docking pocket. In the way of fragment growth, the larger side chain with extensive contact at terminal is obviously better than substituted benzene ring. The enhancement of docking activity is mainly due to the new fragments such as alkyl chains and rings with amino groups at NVP terminal, resulting in a large increase in hydrophobic bonding and the new addition of hydrogen bonding or salt bonding. This study is expected to provide reference for the research on non-nucleoside reverse transcriptase inhibitors resistance and AIDS treatment.

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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 acetylcholinesterase, several bacterial target proteins, and HIV-1 reverse transcriptase. Boswellia triterpenoids targeted the cancer-relevant proteins (poly(ADP-ribose) polymerase-1, tankyrase, and folate receptor β), inflammation-relevant proteins (phospholipase A2, epoxide hydrolase, and fibroblast collagenase), and the diabetes target 11β-hydroxysteroid dehydrogenase. Conclusions: The preferential docking of Boswellia terpenoids is consistent with the traditional uses and the established biological activities of frankincense.

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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-diabetic candidate through inhibition of aldose reductase

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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 300,27 g/Mol, 1,78, and 314,29 g/Mol, 2,04. The docking result shows that the binding energy of hesperidin, methyl hesperidin and zidovudine with receptor are respectively-8,0,-8,8 and-9,3 kcal/Mol. The type of interactions between receptor and hesperidin is van der Waals and phi-phi staked, methyl hesperidin are van der Waals, hydrogen bond, phi-sigma, and phi-phi stacked, and zidovudine is an attractive charge, hydrogen bond, and phi-sigma.Conclusion: Methyl hesperidin has good solubility and permeability, and has affinity with the receptor, a substrate of reverse transcriptase HIV-1.

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., 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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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 reverse docking results, both isolates were screened for their antioxidant, acetylcholinesterase (AChE) inhibition, α-glucosidase (GluE) inhibition and antibacterial activities. Both isolates depicted moderate potential for the selected activities. Furthermore, docking studies of both isolates were also studied to investigate the binding mode with respective targets followed by molecular dynamics simulations and binding free energies. Thereby, the current study embodies the poly-pharmacological potential of P. cretica.

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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 receptor protein using various computer programs. The molecular docking results showed that (6)-shogaol had four amino acid bond residues that were the same as the ibuprofen control compound, indicating its potential as an antipyretic drug candidate. Furthermore, (6)-shogaol had the same binding affinity as the control compound and was safe for oral consumption based on pharmacokinetic and toxicity tests using Lipinski's Rule, Toxtree, and admet-T. These findings suggest that (6)-shogaol is a promising antipyretic drug candidate compared to other compounds. In conclusion, this study identified the potential of (6)-shogaol as an antipyretic drug candidate through reverse docking techniques targeting interleukin-10. Red ginger could provide a natural alternative for antipyretic drugs, and further research is recommended to explore the role of gingerol and shogaol compounds in targeting other proteins

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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 activity. Methods: In this work, 40 DATA analogues were studied using a combination of molecular modeling techniques including Three-Dimensional Quantitative Structure–Activity Relationship (3D-QSAR), molecular docking, and Topomer CoMFA were used to build 3D-QSAR models. Results: The results show that the Topomer CoMFA analysis has the cross-validation q2 = 0.800, SDCV = 0.45, the non-cross-validated r2 = 0.958, SD = 0.21, and the correlation coefficient of external validation Q2 ext = 0.965 showed that the model is reasonable and credible, and has a good predictive ability. Then binding mode pattern of the compounds to the binding site of enzyme was confirmed and the mechanism of drug and acceptor was studied by docking studies, the results showed that the drug and GLU138, LYS101, THR139 sites have an obvious function, these researches have provided an useful information for designing more effective HIV-1IN inhibitors. Conclusion: A series of 40 DATAs analogues was subjected to a 3D-QSAR study. Using Topomer CoMFA 3D-QSAR method built model, and the model has shown a good predictive and statistical validation. Substituent with low electronic density in the R5 and R3 positions and substituent with high electronic density in the R2 and C2 positions will increase the biological activity, small substituent on R4 positions and naphthyloxy as the spacer group C6 substituent hydrophobic will increase biological activity. This effect is supported by Topomer CoMFA contour map and docking results of HIV-1RT inhibition active site, the results of the 3D-QSAR and docking analyses have provided a guide for the synthesis of new putative inhibitors for HIV-1RT to improved inhibitory activity.

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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 platform for drug discovery. Reverse pharmacology (Reverse docking) approach was performed, which involved docking of camphene and 20 structural and non-structural proteins (NSPs) of SARS-CoV-2 performed using maestro 12.8 of Schrödinger. Results: The results were evaluated since the minimum binding energy obtained after docking and camphene was effective against most of the proteins responsible for SARS-CoV-2, but camphene showed greater efficacy against the main protease (protease 9), which is main functional protein of SARS-CoV-2. Hence, the study proves that camphene can be a good drug candidate for different mutants of SARS-CoV-2. Conclusion: Protease 9, which is the main functional protein of SARS-CoV-2, expressed the best binding affinity with camphene having the minimum binding energy (-5.616). Hence, it is concluded that camphene could be the drug contender against protease 9 as it is a more potent target in SARS-CoV-2. This could be a major finding, as camphene is related to camphor, which is already very beneficial against many respiratory problems.

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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 docking, AMIDE is now an optimized tool capable of high throughput inverse screening. For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing Unit), while version 1 required 300 cores to reach the same execution time. Moreover, we have shown an exponential acceleration of the computation time as a function of the number of GPUs used, allowing a significant reduction of the duration of the inverse docking process on large datasets.

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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 transcriptase enzyme. Flavonoid glycosides are some of these chemicals. This work aimed to get more ideas about phytocompounds with human immunodeficiency virus-1 reverse transcriptase inhibitory effects utilising docking. From the results, the most suggested phytocompounds, those with the highest negative free energy to make complex were menthoside, morindin and sesaminol glucosides. This was due to the interactions of all three phytocompounds with key amino acid residues: Leu 100, Val 179, Tyr 318, Tyr 188, Val 106, Lys 101, Gly 190, His 235. Flavonoid glycoside (Menthoside) showed lowest binding energy with a docking score -10.6 kcal/mol.

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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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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 for molecular modeling, molecular docking, biological prediction, and pharmacological studies. Herein, we relate the optimization of cytidine and its acylated analogues applying density functional theory (DFT) with B3LYP/3-21G level theory to explore their thermochemical and molecular electrostatic potential (MEP) properties. Prediction of activity spectra for substances (PASS) indicated promising antiviral, anti-carcinogenic, and antifungal functionality of these cytidine esters compared to the antibacterial activities. To support this observation, their cytotoxic prediction and molecular docking studies have been performed against HIV-1 reverse transcriptase (RT) (PDB: 3V4I). Most of the molecules studied out here could bind near the crucial catalytic binding site, Tyr181, Ile94, Ile382, Lys374, Val381, Val90, and Tyr34 of the HIV-1 reverse transcriptase (RT), and the molecules were surrounded by other active site residues like Gln332, Trp406, Asn265, Gly93, His96, Pro95, and Thr165. Finally, these novel molecules were analyzed for their pharmacokinetic properties which expressed that the combination of in silico ADMET prediction, toxicity prediction, and drug-likeness had shown a promising result. The study discusses the performance of molecular docking to suggest the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1.

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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 fatty acids, with lauric acid being the abundant one in all Pliek U oil extracts. The reverse docking technique results showed that oleic acid had the most stable interaction to filaggrin with the lowest binding affinity (−6.1 kcal/mol). Oleic acid and palmitic acid have one same side binding to filaggrin on amino acid LEU D75. These findings indicated that oleic acid has the best potential to be used as a drug candidate in atopic dermatitis treatment.

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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 transcriptase, with an IC50 of 0.125 mg/mL observed for the pith extract originating from Saudi Arabia and the standard drug doxorubicin. The molecular docking of karavilosides exhibited a significant affinity to reverse transcriptase comparable to Rilpivirine and higher than that of doxorubicin. These outcomes encourage the precious bioactive components of the seed and pith of the Saudi bitter melon fruits to be further studied for isolation and structure elucidation.

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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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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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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 resistant strains of HIV-1RT virus with PDB IDs 1RT2, 1KLM, 3BGR, and 1JLB, respectively, by using Autodock version 4.5.6. A comparison of different compounds docked into the active site of various HIV-1RT strains was carried out. The obtained results indicate that most of the compounds docked into the active site of the different receptors, such as 1RT2, 1KLM, 3BGR, and 1JLB, with good docking scores, are comparable to that of the internal standard (TNK 651) of the wild type strain of HIV-1 virus. A comparison was made based on the binding modes of the compounds in the active site of all the four receptors.

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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 Preparation Wizard (Schrodinger Glide 5.0). ADME parameters calculated by QikProp 3.0v and toxicity of designed analogs checked by using two different online software’s namely Lazar and protox.Results: Most of the designed pyrazole analogs have good oral absorption as well as good binding affinity towards HIV-1 reverse transcriptase.Conclusion: Finally total 5 analogs (SGS-2, 3, 12, 13 and 14) from the 14 designed leads were found to be best on the basis of molecular docking and ADME-T studies.

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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 number 609 were predicted as the inhibitors of telomerase reverse transcriptase for the treatment of arsenical cancer. The prediction of these two compounds was further supported by drug-likeness test through Administration, Distribution, Metabolism, Excretion and Toxicity evaluation. The compounds were also compared with some of the known inhibitors of telomerase reverse transcriptase. </p>

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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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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 chromatography/mass spectrometry (LC/MS) and in silico studies were very useful. This study aimed at identifying other derivative compounds from S. hygroscopicus and screening the antimalarial activity of the compound by assessing the binding affinity, pharmacokinetic profile, and bond interaction. The derivative compounds were identified using LC/MS. Protein targets for derivative compounds were found through literature studies, and the results of identification of compounds and protein targets were reconstructed into three-dimensional models. Prediction of pharmacokinetic profiles was carried out using Swiss ADME. Screening of protein targets for the derivative compound was carried out using the reverse molecular docking method. Analyzing bond interaction was done by LigPlot. One compound from S. hygroscopicus, i.e., 6,7-dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione, was successfully identified using LC/MS. This compound was an isoquinoline derivative compound. Through literature studies with inclusion criteria, thirteen protein targets were obtained for reverse molecular docking. This isoquinoline derivative had the potential to bind to each protein target. The pharmacokinetic profile showed that this compound had the drug-likeness criteria. Conclusion. 6,7-Dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione has antimalarial activity as shown by reverse molecular docking studies and pharmacokinetic profiles. The best inhibitory ability of compounds based on bond affinity is with adenylosuccinate synthetase.

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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 Autodock version 4.2.6. Pharmacokinetic properties (absorption, distribution, metabolism and excretion (ADME)) and toxicity of potential inhibitors within the body were predicted by the PreADMET version 2.0. The obtained results point out that the compound, coded 2518, was discovered as a potential inhibitor that has good human intestinal absorption, weakly bound to plasma proteins as well as is negative to mutagenicity and carcinogenicity. This rational inhibitor would be further studied in order to contribute informations finding new anti-HIV drugs.

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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 reverse transcriptase was studied to rationalize some structure-activity relationships (SARs).

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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 obtained from the Protein Data Bank (PDB). The crystal structure identified by the PDB code 2B2A has a resolution of 2.2 Å. The molecular docking was performed using AutoDock Vina. The complexes were visualized using Biovia Discovery Studio. The MD simulation was conducted using GROMACS 2020 as indicated. An MD simulation was conducted for 200 ns on both the complexes and the free protein. The RMSD (root mean square deviation) of the protein and the molecules in relation to the protein, RMSF (root mean square fluctuation), and Rg (radius of gyration) were shown via Qt Grace. Result and Discussion: Doravirine, Etravirine, Rilpivirine showed higher binding affinity to the TEN domain compared to the reference TERT inhibitor, BIBR1532, based on the docking investigation. The MD simulation analysis showed that the protein-Doravirine complex had the highest stability in remaining within the protein's binding pocket. On the contrary, the protein-Rilpivirine complex decreased stability, potentially causing the ligand to not stay within the binding site. Doravirine was found to inhibit the TEN domain in the computational study. Therefore, the design and synthesis of novel doravirin derivatives is being considered because of the potential anticancer activity of doravirin in inhibiting the TEN domain of TERT.

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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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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 inhibition. We report 12 new chemical entities with possible activity against the targeted viral protein. These leads will provide new therapeutic means in antiretroviral therapy.

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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 PITPNM3 activation. Methods: We performed computer-assisted drug design by constructing PITPNM3 homology model, characterizing potential binding pockets and docking preselected high diversity structured small molecule compounds into the static PITPNM3 model. Top 100 small molecules in silico scores were selected and screened through basic experiments. After screening, the anti-metastasis effects of selected compounds were tested through transwell migration and invasion assay. Immunofluorescence and qPCR were applied to confirm the expression of vimentin and CDH1. Western blot were used to clarify the inhibition effects of selected compounds on PITPNM3 signaling pathways. Results: By using homology remodeling, we successfully constructed the PITPNM3(680-920aa) protein model. The PITPNM3(680-920aa) domain is responsible for interacting with PYK2 and phosphorylating PYK2. The phosphorylation of PYK2 conducted by PITPNM3 signaling pathway will lead to metastasis and epithelial-mesenchymal transition (EMT) of breast cancer cells. We then characterized the potential binding pockets of this static model and a druggable site was founded. More than 50K molecules with high diversity were docked into this druggable site and scored through their docking performance. Finally, top 100 scored small molecules were selected. In addition, through 1 rounds of toxicity screening, 1 round of transwell migration assay screening and 1 round of transwell invasion assay screening, 4 small molecules with higher bioactivity is identified and 1 compound with the highest bioactivity as well as docking performance among 50K small molecules is chose. This compound can inhibit CCL18 treatment as well as tumor associated macrophage co-culture mediated migration and invasion. Besides, it can also inhibit the phophorylation of PYK2 and Src without inhibition the expression of PITPNM3. Conclusions: Our findings identify the first-in-class anti-PITPNM3 small molecule inhibitors. These compounds can inhibit PITPNM3 signaling pathway and reverse breast cancer metastasis.

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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 performed in the non-nucleoside reverse transcriptase inhibitory binding pocket of the enzyme HIV-1 reverse transcriptase (protein data bank [PDB] ID-1RT2), using AutoDock 4.2.6 and to identify the important pharmacophoric features required for the development of effective non-nucleoside reverse transcriptase inhibitors, pharmacophore analysis was performed. The findings of this study can be used as a valuable tool for identifying and developing potent and effective inhibitors.

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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, conservation, and toxicity analysis. T – cell-based vaccine development against NiV was screened for eight epitopes of Indian - Asian origin. Results: Two epitopes, SPVIAEHYY and LVNDGLNII, have been screened and selected for further docking study based on toxicity and conservancy analyses. These epitopes showed a significant score of -1.19 kcal/mol and 0.15 kcal/mol with HLA- B*35:03 and HLA- DRB1 * 07:03, respectively by using allele - Class I and Class II from AutoDock. These two peptides predicted by the reverse vaccinology approach are likely to induce immune response mediated by T – cells. Conclusion: Simulation using GROMACS has revealed that LVNDGLNII epitope forms a more stable complex with HLA molecule and will be useful in developing the epitope-based Nipah virus vaccine.

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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 activation. A new problem arises because the reverse transcriptase in HIV-1 undergoes a cross mutation and causes nevirapine resistance. Previous research using an in vitro approach showed the ability to inhibit the process of replication, attachment, and internalization of the virus shown by Zingiber officinale var. Roscoe, then another ability is that these herbal plants can trigger cell stimulation for interferon-β secretion. This study aims to screen the chemical compounds of Zingiber officinale var Roscoe for the discovery of new antiretrovirals through computational study. Zingiber officinale var. Roscoe is predicted to act as an antiretroviral agent through with a mechanism of HIV-1 reverse transcriptase activity inhibition at Pro95, Tyr181, Val179, Leu100, Tyr188, Val106, Leu234, Phe227, Tyr318, Asn103, Gly99 residues, β-sitosterol is predicted to act as a drug-like molecule, the antiretroviral potential of Zingiber officinale var. Roscoe must undergo further analysis to provide strong scientific evidence.

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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 to determine the most probable binding mode and to obtain reliable conformations for molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA (q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis of hybrid docking-based and ligand-based alignment. Results: The predictive ability of CoMFA and CoMSIA models was further validated using a test set of eight compounds with predictive r2 pred values of 0.843 and 0.723, respectively. Conclusion: The information obtained from the 3D contour maps can be used in designing new SDABO derivatives with improved HIV-1 inhibitory activity.

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Mukherjee, Taniya, Isha Sangal, Biswajit Sarkar, Qais Almaamari, and Tamer M. Alkadash. "How Effective Is Reverse Cross-Docking and Carbon Policies in Controlling Carbon Emission from the Fashion Industry?" Mathematics 11, no. 13 (2023): 2880. http://dx.doi.org/10.3390/math11132880.

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The present consumer behavior is manipulated by “fast fashion”, where purchasing new, trendy, affordable clothes is preferred over recycling old ones. This changing mannerism has escalated the GHG emissions from the fashion industry. Energy-intensive raw material production, preparation, and processing contribute to considerable emissions. The management of the returned goods from the primary market and further processing through the secondary outlets indulge in reverse logistics. In this paper, efforts are made to minimize the total cost and the carbon emission amount during the process of managing the return articles from the primary market to the reverse distribution center, further processing of the articles at the secondary outlet, and the return of the unsold or excess articles from the secondary outlet. Reverse cross-docking has been implemented in managing the return articles, while environmental concerns over GHG emissions have been addressed by investing in green technology under a strict carbon cap policy. In this research, return articles from the primary and secondary markets, rework of the returned articles, and disposal of the impaired returned articles have been considered. The carbon emission cost at all stages of transportation, rework, or disposal has also been incorporated into this model. A constrained mixed integer linear programming model is proposed and solved considering green investment. A numerical example has been formulated to investigate the effect of green technology on the total cost. The results portray that, though the total cost increases by nearly 2% due to investment in green technology, it ensures a considerable drop of 23% in the carbon emission amount. Also, the result is successful in establishing that reverse cross-docking is a better option than traditional warehousing in terms of minimizing the cost.

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Rotich, Winnie, Nicholas J. Sadgrove, Eduard Mas-Claret, Guillermo F. Padilla-González, Anastasia Guantai, and Moses K. Langat. "HIV-1 Reverse Transcriptase Inhibition by Major Compounds in a Kenyan Multi-Herbal Composition (CareVid™): In Vitro and In Silico Contrast." Pharmaceuticals 14, no. 10 (2021): 1009. http://dx.doi.org/10.3390/ph14101009.

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CareVid is a multi-herbal product used in southwest Kenya as an immune booster and health tonic and has been anecdotally described as improving the condition of HIV-positive patients. The product is made up of roots, barks and whole plant of 14 African medicinal plants: Acacia nilotica (L.) Willd. ex Delile (currently, Vachelia nilotica (L.) P.J.H Hurter & Mabb.), Adenia gummifera (Harv.) Harms, Anthocleista grandiflora Gilg, Asparagus africanus Lam., Bersama abyssinica Fresen., Clematis hirsuta Guill. & Perr., Croton macrostachyus Hochst. ex Delile, Clutia robusta Pax (accepted as Clutia kilimandscharica Engl.), Dovyalis abyssinica (A. Rich.) Warb, Ekebergia capensis Sparm., Periploca linearifolia Quart.-Dill. & A. Rich., Plantago palmata Hook.f., Prunus africana Hook.f. Kalkman and Rhamnus prinoides L’Her. The objective of this study was to determine the major chemical constituents of CareVid solvent extracts and screen them for in vitro and in silico activity against the HIV-1 reverse transcriptase enzyme. To achieve this, CareVid was separately extracted using CH2Cl2, MeOH, 80% EtOH in H2O, cold H2O, hot H2O and acidified H2O (pH 1.5–3.5). The extracts were analysed using HPLC–MS equipped with UV diode array detection. HIV-1 reverse transcriptase inhibition was performed in vitro and compared to in silico HIV-1 reverse transcriptase inhibition, with the latter carried out using MOE software, placing the docking on the hydrophobic pocket in the subdomain of p66, the NNRTI pocket. The MeOH and 80% EtOH extracts showed strong in vitro HIV-1 reverse transcriptase inhibition, with an EC50 of 7 μg·mL−1. The major components were identified as sucrose, citric acid, ellagic acid, catechin 3-hexoside, epicatechin 3-hexoside, procyanidin B, hesperetin O-rutinoside, pellitorine, mangiferin, isomangiferin, 4-O-coumaroulquinic acid, ellagic acid, ellagic acid O-pentoside, crotepoxide, oleuropein, magnoflorine, tremulacin and an isomer of dammarane tetrol. Ellagic acid and procyanidin B inhibited the HIV-1 reverse transcription process at 15 and 3.2 µg/mL−1, respectively. Docking studies did not agree with in vitro results because the best scoring ligand was crotepoxide (ΔG = −8.55 kcal/mol), followed by magnoflorine (ΔG = −8.39 kcal/mol). This study showed that CareVid has contrasting in vitro and in silico activity against HIV-1 reverse transcriptase. However, the strongest in vitro inhibitors were ellagic acid and procyanidin B.

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Islam, Sk Injamamul, Saloa Sanjida, Sheikh Sunzid Ahmed, et al. "Core Proteomics and Immunoinformatic Approaches to Design a Multiepitope Reverse Vaccine Candidate against Chagas Disease." Vaccines 10, no. 10 (2022): 1669. http://dx.doi.org/10.3390/vaccines10101669.

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Chagas disease is a tropical ailment indigenous to South America and caused by the protozoan parasite Trypanosoma cruzi, which has serious health consequences globally. Insect vectors transmit the parasite and, due to the lack of vaccine availability and limited treatment options, we implemented an integrated core proteomics analysis to design a reverse vaccine candidate based on immune epitopes for disease control. Firstly, T. cruzi core proteomics was used to identify immunodominant epitopes. Therefore, we designed the vaccine sequence to be non-allergic, antigenic, immunogenic, and to have better solubility. After predicting the tertiary structure, docking and molecular dynamics simulation (MDS) were performed with TLR4, MHC-I, and MHC-II receptors to discover the binding affinities. The final vaccine design demonstrated significant hydrogen bond interactions upon docking with TLR4, MHC-I, and MHC-II receptors. This indicated the efficacy of the vaccine candidate. A server-based immune simulation approach was generated to predict the efficacy. Significant structural compactness and binding stability were found based on MDS. Finally, by optimizing codons on Escherichia coli K12, a high GC content and CAI value were obtained, which were then incorporated into the cloning vector pET2+ (a). Thus, the developed vaccine sequence may be a viable therapy option for Chagas disease.

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Sree Latha, Ramaswamy, Ramadoss Vijayaraj, Ettayapuram Ramaprasad Azhagiya Singam, Krishnaswamy Chitra, and Venkatesan Subramanian. "3D-QSAR and Docking Studies on the HEPT Derivatives of HIV-1 Reverse Transcriptase." Chemical Biology & Drug Design 78, no. 3 (2011): 418–26. http://dx.doi.org/10.1111/j.1747-0285.2011.01162.x.

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