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Journal articles on the topic 'Protein-RNA docking'

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Published: 25 May 2024

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1

Arnautova, Yelena A., Ruben Abagyan, and Maxim Totrov. "Protein-RNA Docking Using ICM." Journal of Chemical Theory and Computation 14, no. 9 (2018): 4971–84. http://dx.doi.org/10.1021/acs.jctc.8b00293.

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2

He, Jiahua, Huanyu Tao, and Sheng-You Huang. "Protein-ensemble–RNA docking by efficient consideration of protein flexibility through homology models." Bioinformatics 35, no. 23 (2019): 4994–5002. http://dx.doi.org/10.1093/bioinformatics/btz388.

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AbstractMotivationGiven the importance of protein–ribonucleic acid (RNA) interactions in many biological processes, a variety of docking algorithms have been developed to predict the complex structure from individual protein and RNA partners in the past decade. However, due to the impact of molecular flexibility, the performance of current methods has hit a bottleneck in realistic unbound docking. Pushing the limit, we have proposed a protein-ensemble–RNA docking strategy to explicitly consider the protein flexibility in protein–RNA docking through an ensemble of multiple protein structures, w

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3

Delgado Blanco, Javier, Leandro G. Radusky, Damiano Cianferoni, and Luis Serrano. "Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX." Proceedings of the National Academy of Sciences 116, no. 49 (2019): 24568–73. http://dx.doi.org/10.1073/pnas.1910999116.

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RNA–protein interactions are crucial for such key biological processes as regulation of transcription, splicing, translation, and gene silencing, among many others. Knowing where an RNA molecule interacts with a target protein and/or engineering an RNA molecule to specifically bind to a protein could allow for rational interference with these cellular processes and the design of novel therapies. Here we present a robust RNA–protein fragment pair-based method, termed RnaX, to predict RNA-binding sites. This methodology, which is integrated into the ModelX tool suite (http://modelx.crg.es), take

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Pérez-Cano, Laura, Miguel Romero-Durana, and Juan Fernández-Recio. "Structural and energy determinants in protein-RNA docking." Methods 118-119 (April 2017): 163–70. http://dx.doi.org/10.1016/j.ymeth.2016.11.001.

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5

Zhang, Zhao, Lin Lu, Yue Zhang, et al. "A combinatorial scoring function for protein-RNA docking." Proteins: Structure, Function, and Bioinformatics 85, no. 4 (2017): 741–52. http://dx.doi.org/10.1002/prot.25253.

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6

Zheng, Jinfang, Xu Hong, Juan Xie, Xiaoxue Tong, and Shiyong Liu. "P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking." Bioinformatics 36, no. 1 (2019): 96–103. http://dx.doi.org/10.1093/bioinformatics/btz478.

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AbstractMotivationThe main function of protein–RNA interaction is to regulate the expression of genes. Therefore, studying protein–RNA interactions is of great significance. The information of three-dimensional (3D) structures reveals that atomic interactions are particularly important. The calculation method for modeling a 3D structure of a complex mainly includes two strategies: free docking and template-based docking. These two methods are complementary in protein–protein docking. Therefore, integrating these two methods may improve the prediction accuracy.ResultsIn this article, we compare

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7

Setny, Piotr, and Martin Zacharias. "A coarse-grained force field for Protein–RNA docking." Nucleic Acids Research 39, no. 21 (2011): 9118–29. http://dx.doi.org/10.1093/nar/gkr636.

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Nithin, Chandran, Sunandan Mukherjee, and Ranjit Prasad Bahadur. "A non-redundant protein-RNA docking benchmark version 2.0." Proteins: Structure, Function, and Bioinformatics 85, no. 2 (2016): 256–67. http://dx.doi.org/10.1002/prot.25211.

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Wicaksono, Adhityo, and Arli Aditya Parikesit. "Molecular Docking and Dynamics of SARS-CoV-2 Programmed Ribosomal Frameshifting RNA and Ligands for RNA-Targeting Alkaloids Prospecting." HAYATI Journal of Biosciences 30, no. 6 (2023): 1025–35. http://dx.doi.org/10.4308/hjb.30.6.1025-1035.

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RNA-ligand docking is a part of computational biology, which is currently lowly recognized compared to the protein-ligand docking procedure commonly applied for drug discovery. This in silico study aims to create a simplified protocol for RNA-ligand docking, which is applicable to RNA-targeting small molecular drug screening. Four alkaloids (berberine, colchicine, nicotine, and tomatine) were subjected to this study and contended against the SARS-CoV-2 genomic RNA -1 PRF component targeting control drug, merafloxacin, including two known intercalator berberine and colchicine, a small alkaloid

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Li, Yaozong, Jie Shen, Xianqiang Sun, Weihua Li, Guixia Liu, and Yun Tang. "Accuracy Assessment of Protein-Based Docking Programs against RNA Targets." Journal of Chemical Information and Modeling 50, no. 6 (2010): 1134–46. http://dx.doi.org/10.1021/ci9004157.

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11

Guilhot-Gaudeffroy, Adrien, Christine Froidevaux, Jérôme Azé, and Julie Bernauer. "Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities." PLoS ONE 9, no. 9 (2014): e108928. http://dx.doi.org/10.1371/journal.pone.0108928.

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12

Huang, Sheng-You, and Xiaoqin Zou. "A nonredundant structure dataset for benchmarking protein-RNA computational docking." Journal of Computational Chemistry 34, no. 4 (2012): 311–18. http://dx.doi.org/10.1002/jcc.23149.

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13

Marium Bibi, Marium Bibi. "Binding Pattern Analysis of Different Allosteric Inhibitors of Hepatitis C Virus (HCV) Polymerase." Journal of the chemical society of pakistan 45, no. 6 (2023): 576. http://dx.doi.org/10.52568/001393/jcsp/45.06.2023.

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To the best of our knowledge, the current study could be considered the first comprehensive one based on the application of molecular docking on the non-nucleoside thumb and palm inhibitors to nonstructural NS5B protein for the detailed evaluation of their binding patterns in the corresponding binding regions in the protein. Non-nucleoside thumb and palm inhibitors were docked into the thumb and palm sites of the nonstructural NS5B protein which is the RNA-dependent RNA polymerase, respectively. Two docking programs, AutoDock 4.2 and AutoDock Vina were employed for the docking of thumb inhibit

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14

Marwal, Avinash, Mukesh Meena, and RK Gaur. "Molecular Docking Studies of Coronavirus Proteins with Medicinal Plant Based Phytochemicals." Defence Life Science Journal 6, no. 1 (2021): 57–63. http://dx.doi.org/10.14429/dlsj.6.15704.

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In this study, we presented an in silico molecular docking between the SARS-CoV-2 four proteins [(a) SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (6M3M), (b) Nsp9 RNA binding protein of SARS CoV-2 (6W4B), (c) The crystal structure of COVID-19 main protease in apo form (6M03), and (d) Structure of the 2019-nCoV HR2 Domain (6LVN)] available in the PDB (Protein Data Bank), and the medicinal plant-based phytochemicals (retrieved from PubChem database) as ligand molecules i.e. Piperine (Black Pepper), Eugenol (Clove), Alliin (Garlic), Gingerol (Ginger) and Curcumin (Turmeric). All

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15

Selvaraj, Jayaraman. "Molecular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus." Bioinformation 17, no. 1 (2021): 167–70. http://dx.doi.org/10.6026/97320630017167.

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It is of interest to document the moelcular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus. Hence, we report the binding features of rutin, Luteolin, Salvianolic acid A, Rosmarinic acid and p-Coumaric acid with the target protein SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) for further consideration.

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Stefaniak, Filip, and Janusz M. Bujnicki. "AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses." PLOS Computational Biology 17, no. 2 (2021): e1008309. http://dx.doi.org/10.1371/journal.pcbi.1008309.

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RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three

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17

da Silva, Joyce Kelly R., Pablo Luis Baia Figueiredo, Kendall G. Byler, and William N. Setzer. "Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation." International Journal of Molecular Sciences 21, no. 10 (2020): 3426. http://dx.doi.org/10.3390/ijms21103426.

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Essential oils have shown promise as antiviral agents against several pathogenic viruses. In this work we hypothesized that essential oil components may interact with key protein targets of the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 Mpro), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 sp

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18

Ma, Hongli, Han Wen, Zhiyuan Xue, Guojun Li, and Zhaolei Zhang. "RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites." PLOS Computational Biology 18, no. 7 (2022): e1010293. http://dx.doi.org/10.1371/journal.pcbi.1010293.

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RNA molecules can adopt stable secondary and tertiary structures, which are essential in mediating physical interactions with other partners such as RNA binding proteins (RBPs) and in carrying out their cellular functions. In vivo and in vitro experiments such as RNAcompete and eCLIP have revealed in vitro binding preferences of RBPs to RNA oligomers and in vivo binding sites in cells. Analysis of these binding data showed that the structure properties of the RNAs in these binding sites are important determinants of the binding events; however, it has been a challenge to incorporate the struct

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19

Yan, Yumeng, Di Zhang, Pei Zhou, Botong Li, and Sheng-You Huang. "HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy." Nucleic Acids Research 45, W1 (2017): W365—W373. http://dx.doi.org/10.1093/nar/gkx407.

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20

Sharma, Arun Dev, Inderjeet Kaur, and Amrita Chauhan. "Targeting H3N2 influenza virus RNA dependent RNA polymerase dependent inhibitory activity by principal components from latex of Calotropis gigantean." Trends in Horticulture 6, no. 2 (2023): 2940. http://dx.doi.org/10.24294/th.v6i2.2940.

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The H3N2 influenza virus is spiking dramatically, which is a major concern worldwide and in India. The multifunctional hetero-trimer influenza virus RNA-dependent RNA polymerase (RdRP) is involved in the generation of viral mRNA and is crucial for viral infectivity, which is directly related to the virus’s ability to survive. The goal of the current work was to use molecular docking to determine how the RdRP protein might be affected by powerful bioactive chemicals found in Calotropis gigantia latex. By applying CB-dock 2 analysis and 2D interactions, an in-silico docking study was conducted u

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21

Emmanuel Chuks Oranu, Esther Oluchukwu Eze, Adanna Ijeawele, et al. "Validation of the binding affinities and stabilities of ivermectin and moxidectin against Sars-CoV-2 receptors using molecular docking and molecular dynamics simulation." GSC Biological and Pharmaceutical Sciences 26, no. 1 (2024): 303–14. http://dx.doi.org/10.30574/gscbps.2024.26.1.0030.

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

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22

Ivashkina, Natalia, Benno Wölk, Volker Lohmann, et al. "The Hepatitis C Virus RNA-Dependent RNA Polymerase Membrane Insertion Sequence Is a Transmembrane Segment." Journal of Virology 76, no. 24 (2002): 13088–93. http://dx.doi.org/10.1128/jvi.76.24.13088-13093.2002.

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ABSTRACT The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) belongs to a class of membrane proteins termed tail-anchored proteins. Here, we show that the HCV RdRp C-terminal membrane insertion sequence traverses the phospholipid bilayer as a transmembrane segment. Moreover, the HCV RdRp was found to be retained in the endoplasmic reticulum (ER) or an ER-derived modified compartment both following transient transfection and in the context of a subgenomic replicon. An absolutely conserved GVG motif was not essential for membrane insertion but possibly provides a docking site for tra

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23

Asadzadeh, Homayoun, Ali Moosavi, Georgios Alexandrakis та Mohammad R. K. Mofrad. "Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-α Protein". BioMed Research International 2021 (16 липня 2021): 1–11. http://dx.doi.org/10.1155/2021/9926128.

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Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting

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24

Kappel, Kalli, and Rhiju Das. "Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking." Structure 27, no. 1 (2019): 140–51. http://dx.doi.org/10.1016/j.str.2018.10.001.

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25

Thakur, Priti, Jowad Atway, Patrick A. Limbach, and Balasubrahmanyam Addepalli. "RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site." International Journal of Molecular Sciences 23, no. 13 (2022): 7021. http://dx.doi.org/10.3390/ijms23137021.

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Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5–1% cleavage levels for a given dinucleotide sequence combination. While RNase M

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26

Ebenezer, Oluwakemi, Nkululeko Damoyi, Maryam A. Jordaan, and Michael Shapi. "Unveiling of Pyrimidindinones as Potential Anti-Norovirus Agents—A Pharmacoinformatic-Based Approach." Molecules 27, no. 2 (2022): 380. http://dx.doi.org/10.3390/molecules27020380.

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The RNA-dependent RNA polymerase (RdRp) receptor is an attractive target for treating human norovirus (HNV). A computer-aided approach like e-pharmacophore, molecular docking, and single point energy calculations were performed on the compounds retrieved from the Development Therapeutics Program (DTP) AIDS Antiviral Screen Database to identify the antiviral agent that could target the HNV RdRp receptor. Induced-fit docking (IFD) results showed that compounds ZINC1617939, ZINC1642549, ZINC6425208, ZINC5887658 and ZINC32068149 bind with the residues in the active site-B of HNV RdRp receptor via

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He, Jiahua, Jun Wang, Huanyu Tao, Yi Xiao, and Sheng-You Huang. "HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures." Nucleic Acids Research 47, W1 (2019): W35—W42. http://dx.doi.org/10.1093/nar/gkz412.

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AbstractInteractions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA–RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)–nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported f

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Adasme, Melissa F., Katja L. Linnemann, Sarah Naomi Bolz, et al. "PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA." Nucleic Acids Research 49, W1 (2021): W530—W534. http://dx.doi.org/10.1093/nar/gkab294.

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Abstract With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA

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NAWAZ, A., and B. IJAZ. "ANTIVIRAL SCREENING OF AZADIRACHTA INDICA PHYTOCHEMICALS AS DENGUE NS5 INHIBITOR: A MOLECULAR DOCKING APPROACH." Biological and Clinical Sciences Research Journal 2023, no. 1 (2023): 560. http://dx.doi.org/10.54112/bcsrj.v2023i1.560.

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Dengue has been an alarming viral infection in tropical and subtropical regions of the world for the past few decades, resulting in millions of deaths. There is no effective drug to treat this arbovirus-based infection. Dengue virus non-structural protein NS5 contains N terminus methyl transferase domain and C terminus RNA-dependent RNA polymerase domain, which is involved in viral RNA replication and serves as a potential target. The current in-silico study aims to find new potential dengue virus NS5 protein inhibitors. The designed library containing eight compounds from Azadirachta Indica w

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YIP, Ryan Pak Hong, Doris Ching Ying Kwok, Louis Tung Faat Lai, et al. "SRPK2 Mediates HBV Core Protein Phosphorylation and Capsid Assembly via Docking Interaction." PLOS Pathogens 20, no. 2 (2024): e1011978. http://dx.doi.org/10.1371/journal.ppat.1011978.

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Members of the serine–arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral nucleocapsid assembly. Among them, SRPK2 exhibits higher kinase activity toward Cp. In this study, we identified Cp sites that are phosphorylated by SRPK2 and demonstrated that the kinase utilizes an SRPK-specific docking groove to interact with and regulate the phosphorylation of the C-terminal arginine rich domain of Cp. We determined that direct interaction between the docking groove of SRPK2 and unphospho

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31

Dickerhoff, Jonathan, Kassandra R. Warnecke, Kaibo Wang, Nanjie Deng, and Danzhou Yang. "Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA." International Journal of Molecular Sciences 22, no. 19 (2021): 10801. http://dx.doi.org/10.3390/ijms221910801.

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G-quadruplexes are four-stranded nucleic acid secondary structures of biological significance and have emerged as an attractive drug target. The G4 formed in the MYC promoter (MycG4) is one of the most studied small-molecule targets, and a model system for parallel structures that are prevalent in promoter DNA G4s and RNA G4s. Molecular docking has become an essential tool in structure-based drug discovery for protein targets, and is also increasingly applied to G4 DNA. However, DNA, and in particular G4, binding sites differ significantly from protein targets. Here we perform the first system

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32

Li, Gang, Wei Zhou, Xiurong Zhao, and Ying Xie. "In Silico Molecular Docking and Interaction Analysis of Traditional Chinese Medicines Against SARS-CoV-2 Receptor." Natural Product Communications 16, no. 5 (2021): 1934578X2110150. http://dx.doi.org/10.1177/1934578x211015030.

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The novel coronavirus, 2019-nCoV, has led to a major pandemic in 2020 and is responsible for more than 2.9 million officially recorded deaths worldwide. As well as synthetic anti-viral drugs, there is also a need to explore natural herbal remedies. The Traditional Chinese Medicines (TCMs) system has been used for thousands of years for the prevention, diagnosis, and treatment of several chronic diseases. In this paper, we performed an in silico molecular docking and interaction analysis of TCMs against SARS-CoV-2 receptor RNA-dependent RNA polymerase (RdRp). We obtained the 5 most effective pl

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Sharma, Arun Dev, and Inderjeet Kaur. "Targeting H3N2 Influenza Virus RNA-dependent RNA Polymerase by Using Bioactives from Essential Oils from Eucalyptus polybrachtea, Cymbopogon citratus and Cymbopogon khasianus." Biology, Medicine, & Natural Product Chemistry 12, no. 2 (2023): 515–24. http://dx.doi.org/10.14421/biomedich.2023.122.515-524.

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A dramatic surge of H3N2 influenza virus is of grave concern worldwide and particularly in India. H3N2 cause acute respiratory infection, however, a few drugs are available for its mitigation. Subsequently, researchers have been involved in efforts to discover novel antiviral mechanisms that can lay the basis for new anti-influenza drugs. Influenza virus RNA-dependent RNA polymerase (RdRP) is a multi-functional hetero-trimer, implicated in the production of viral mRNA, hence plays a major role in viral infectivity thus directly associated with survival of the virus. RdRP have been cited as ana

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34

Mustafa, Ghulam, Hafiza Salaha Mahrosh, Mahwish Salman, et al. "In Silico Analysis of Honey Bee Peptides as Potential Inhibitors of Capripoxvirus DNA-Directed RNA Polymerase." Animals 13, no. 14 (2023): 2281. http://dx.doi.org/10.3390/ani13142281.

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The genus Capripoxvirus belongs to the Poxviridae family. The sheeppox, goatpox, and lumpy skin disease viruses are three species of this genus with 96% identity in their genomes. These are financially devastating viral infections among cattle, which cause a reduction in animal products and lead to a loss in livestock industries. In the current study, the phylogenetic analysis was carried out to reveal the evolutionary relationships of Capripoxvirus species (i.e., sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV)) with other viruses from the Poxviridae family wit

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Dawood, Ali A. "Influence of SARS-CoV-2 variants’ spike glycoprotein and RNA-dependent RNA polymerase (nsp12) mutations on remdesivir docking residues." Medical Immunology (Russia) 24, no. 3 (2022): 617–28. http://dx.doi.org/10.15789/1563-0625-ios-2486.

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Rapid emergence and evolution of novel SARS-CoV-2 variants has raised concerns about their potential impact on efficiency of currently available vaccines. Among the most significant target mutations in the virus are those of the spike glycoprotein. Remdesivir, which inhibits the polymerase activity of the RNAdependent RNA polymerase RdRp, is the only medicine approved by FDA for treatment of COVID-19 (nsp12). The docking features of the flexible ligand (remdesivir) with the stiff receptors was investigated in the present study (S protein and RdRp interaction). In various studies, the spike gly

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Bui, Thanh Tung, Bao Kim Nguyen, Minh Ngoc Le, The Toan Nguyen, and The Hai Pham. "In silico screening of drug inhibitors of SARS-CoV-2RNA-dependent RNA polymerase target." Ministry of Science and Technology, Vietnam 63, no. 4 (2021): 47–54. http://dx.doi.org/10.31276/vjste.63(4).47-54.

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Objectives: the COVID-19 pandemic triggering acute respiratory syndrome has become a major global health concern. After one year into this pandemic, special therapies for COVID-19 remain an unprecedented challenge to mankind and finding drugs to treat this disease is extremely urgent. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) enzyme that regulates viral replication has been examined as a potential therapeutic target for the inhibition of SARS-CoV-2 infection. In this study, the authors evaluated the ability of RNA-dependent RNA polymerase drug inhibitors by using an in silico molecula

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Yamkela, Mthembu, Zingisa Sitobo, and Xolani H. Makhoba. "In Silico Analysis of SARS-CoV-2 Non-Structural Proteins Reveals an Interaction with the Host’s Heat Shock Proteins That May Contribute to Viral Replications and Development." Current Issues in Molecular Biology 45, no. 12 (2023): 10225–47. http://dx.doi.org/10.3390/cimb45120638.

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The non-structural protein 2 (NSP2) is an RNA-binding protein involved in coronavirus genome replication, and it often decreases human immune response to promote viral invasion and development. It is believed that the NSP2 associates itself with polyamines and heat shock proteins inside the host cell to proceed with viral development. This study aimed to investigate how the SARS-CoV-2 virus’ key non-structural proteins (NSP2) utilize polyamines and heat shock proteins using a molecular docking approach and molecular dynamics (MD). ClusPro and HADDOCK servers were used for the docking and Disco

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Wang Erickson, Anna F., Padraig Deighan, Shanshan Chen, et al. "A novel RNA polymerase‐binding protein that interacts with a sigma‐factor docking site." Molecular Microbiology 105, no. 4 (2017): 652–62. http://dx.doi.org/10.1111/mmi.13724.

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Pérez-Cano, Laura, Brian Jiménez-García, and Juan Fernández-Recio. "A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data." Proteins: Structure, Function, and Bioinformatics 80, no. 7 (2012): 1872–82. http://dx.doi.org/10.1002/prot.24075.

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Lee, Gwangho, Gun Hyuk Jang, Ho Young Kang, and Giltae Song. "Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach." PLOS ONE 16, no. 6 (2021): e0253760. http://dx.doi.org/10.1371/journal.pone.0253760.

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Oligonucleotide-based aptamers, which have a three-dimensional structure with a single-stranded fragment, feature various characteristics with respect to size, toxicity, and permeability. Accordingly, aptamers are advantageous in terms of diagnosis and treatment and are materials that can be produced through relatively simple experiments. Systematic evolution of ligands by exponential enrichment (SELEX) is one of the most widely used experimental methods for generating aptamers; however, it is highly expensive and time-consuming. To reduce the related costs, recent studies have used in silico

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Ren, Yixin, Sihui Long, and Shuang Cao. "Molecular Docking and Virtual Screening of an Influenza Virus Inhibitor That Disrupts Protein–Protein Interactions." Viruses 13, no. 11 (2021): 2229. http://dx.doi.org/10.3390/v13112229.

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Influenza is an acute respiratory infection caused by the influenza virus, but few drugs are available for its treatment. Consequently, researchers have been engaged in efforts to discover new antiviral mechanisms that can lay the foundation for novel anti-influenza drugs. The viral RNA-dependent RNA polymerase (RdRp) is an enzyme that plays an indispensable role in the viral infection process, which is directly linked to the survival of the virus. Methods of inhibiting PB1–PB2 (basic polymerase 1–basic polymerase 2) interactions, which are a key part of RdRp enzyme activity, are integral in t

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Praveen, Rajkumar. "Insights from the molecular docking aided interaction analysis of HfQ with small RNAs." Bioinformation 18, no. 4 (2022): 425–31. http://dx.doi.org/10.6026/97320630018425.

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Hfq, RNA binding protein, is widely found in most of the prokaryotes. It plays a key role in gene regulation by binding with small RNA and facilitates mRNA pairing there by suppress or boost translation according to RNA structures. Interaction between sRNAs and HfQ in Salmonella SL1344 were screened using Co-Immuno Precipitation (HfQ-CoIP) studies earlier. We have formulated an In silico approach, to model the 3D structures of 155 sRNA and studied their interactions with HfQ proteins. We have reported the key interacting PHE42, LEU7, VAL27, PHE39 and PRO21 residues of HfQ binds with many small

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Sharp, Kumar. "Alternatives to Remdesivir: Drug repurposing for inhibition of SARS-CoV2 RNA dependent RNA polymerase." Journal of Pharmacological and Pharmaceutical Research 1, no. 1 (2024): 32. http://dx.doi.org/10.5455/jppr.20240402024133.

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Background & Objectives: Even after more than a year of the beginning of COVID-19 pandemic, a specific treatment for the disease has not been discovered. Vaccination programmes are being rolled out as the fastest pace possible but achievement of herd immunity will take time. Many drugs like favipiravir, remdesivir and tocilizumab are being used for the treatment of this disease but reports published by the World Health Organization and the New England Journal of Medicine shows that they do not produce any significant clinical results. In this study, by molecular docking a large set of drug

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Abdelaal Ahmed Mahmoud M. Alkhatip, Ahmed, Michail Georgakis, Lucio R. Montero Valenzuela, et al. "Metal-Bound Methisazone; Novel Drugs Targeting Prophylaxis and Treatment of SARS-CoV-2, a Molecular Docking Study." International Journal of Molecular Sciences 22, no. 6 (2021): 2977. http://dx.doi.org/10.3390/ijms22062977.

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SARS-CoV-2 currently lacks effective first-line drug treatment. We present promising data from in silico docking studies of new Methisazone compounds (modified with calcium, Ca; iron, Fe; magnesium, Mg; manganese, Mn; or zinc, Zn) designed to bind more strongly to key proteins involved in replication of SARS-CoV-2. In this in silico molecular docking study, we investigated the inhibiting role of Methisazone and the modified drugs against SARS-CoV-2 proteins: ribonucleic acid (RNA)-dependent RNA polymerase (RdRp), spike protein, papain-like protease (PlPr), and main protease (MPro). We found th

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Ivan, Jeremias, Rizky Nurdiansyah, and Arli Aditya Parikesit. "Computational modeling of AGO-mediated molecular inhibition of ARF6 by miR-145." Indonesian Journal of Biotechnology 25, no. 2 (2020): 102. http://dx.doi.org/10.22146/ijbiotech.55631.

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Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AG

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Rehman, Muhammad Fayyaz ur, Shahzaib Akhter, Aima Iram Batool, et al. "Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World." Antibiotics 10, no. 8 (2021): 1011. http://dx.doi.org/10.3390/antibiotics10081011.

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The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 pro

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Santiago-Frangos, Andrew, Kathrin S. Fröhlich, Jeliazko R. Jeliazkov, et al. "Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation." Proceedings of the National Academy of Sciences 116, no. 22 (2019): 10978–87. http://dx.doi.org/10.1073/pnas.1814428116.

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We have solved the X-ray crystal structure of the RNA chaperone protein Hfq from the alpha-proteobacterium Caulobacter crescentus to 2.15-Å resolution, resolving the conserved core of the protein and the entire C-terminal domain (CTD). The structure reveals that the CTD of neighboring hexamers pack in crystal contacts, and that the acidic residues at the C-terminal tip of the protein interact with positive residues on the rim of Hfq, as has been recently proposed for a mechanism of modulating RNA binding. De novo computational models predict a similar docking of the acidic tip residues against

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Prabahar, Archana, Subashini Swaminathan, Arul Loganathan, and Ramalingam Jegadeesan. "Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants." Advances in Bioinformatics 2015 (October 18, 2015): 1–9. http://dx.doi.org/10.1155/2015/198214.

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Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. TMV enters the host cell and produces the capping enzyme RNA polymerase. The viral genome replicates further to produce multiple mRNAs which encodes several proteins, including the coat protein and an RNA-dependent RNA polymerase (RdRp), as well as the movement protein. TMV replicase domain was chosen for the virtual screening studies against small molecules derived from ligand databases such as PubChem and ChemBank. Catalytic sites of the RdRp domain

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Sari, Dewi Ratih Tirto, Heny Yusuf, Laily Sifaiyah, Nur Dina Camelia, and Yohanes Bare. "Kajian Farmakoinformatika Senyawa Brazilin dan 3-O-Methyl Brazilin Caesalpinia sappan Sebagai Terapi Demam Berdarah Dengue." al-Kimiya 9, no. 1 (2022): 19–25. http://dx.doi.org/10.15575/ak.v9i1.17613.

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Demam berdarah Dengue (DBD) merupakan penyakit tropis yang diakibatkan oleh gigitan nyamuk yang terinfeksi oleh virus DENV. Beberapa tanaman herbal dapat digunakan untuk mengatasi demam berdarah baik upaya preventif maupun kuratif. Kayu secang merupakan salah satu tanaman herbal kayu yang memiliki berbagai aktivitas biologis, utamanya sebagai immunomodulator dan antivirus. Penelitian ini bertujuan untuk mengidentifikasi aktivitas brazilin dan 3-O-methyl brazilin sebagai obat terapi demam berdarah melalui kajian komputasi. Pendekatan molecular docking digunakan dalam studi penelitian ini. Senya

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Alhossary, Amr, Yaw Awuni, Chee Keong Kwoh, and Yuguang Mu. "Proposing drug fragments for dengue virus NS5 protein." Journal of Bioinformatics and Computational Biology 16, no. 03 (2018): 1840017. http://dx.doi.org/10.1142/s0219720018400176.

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Dengue fever is a febrile illness caused by Dengue Virus, which belongs to the Flaviviridae family. Among its proteome, the nonstructural protein 5 (NS5) is the biggest and most conserved. It has a primer-independent RNA-dependent RNA polymerase (RdRp) domain at its C-Terminus. Zou et al. studied the biological relevance of the two conserved cavities (named A and B) within the NS5 proteins of dengue virus (DENV) and West Nile Virus (WNV) using mutagenesis and revertant analysis and found four mutations located at cavity B having effects on viral replication. They recommended Cavity B, but not

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