Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein by Oscar Herrera-Calderon, Abdulrahman M. Saleh, Andres F. Yepes-Perez, Nada H. Aljarba, Saad Alkahtani, Gaber El-Saber Batiha, Renan Dilton Hañari-Quispe, Haydee Chavez, Josefa Bertha Pari-Olarte, Eddie Loyola-Gonzales, José Santiago Almeida-Galindo, José Francisco Kong-Chirinos, Taoufiq Benali

“…A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). Next, a molecular dynamic study was carried out to monitor the stability during the MD simulations. …”
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Evaluation of Melongosides as Potential Inhibitors of NS2B-NS3 Activator-Protease of Dengue Virus (Serotype 2) by Using Molecular Docking and Dynamics Simulation Approach by Partha Biswas, Ommay Hany Rumi, Dhrubo Ahmed Khan, Md Nasir Ahmed, Nusratun Nahar, Rownak Jahan, Md Nazmul Hasan Zilani, Tridib K Paul, Anamul Hasan, Tohmina Afroze Bondhon, Khoshnur Jannat, Md Nazmul Hasan, Mohammed Rahmatullah

“…However, the 200 ns molecular dynamic simulation experiment indicates significant stability of the protein-ligand interactions with the RMSD values of 2.5 Å, thus suggesting a better docking position and no disruption of the protein-ligand structure. …”
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Novel tetracycline hybrids: synthesis, characterization, docking studies and in-vitro evaluation of antibacterial activity by Mansi Shah, Bhanubhai Suhagia, Sunita Goswami, Sneha Sagar, Arpit Patwari

“…Molecular docking was carried out in order to predict the binding affinity of these compounds to various bacterial enzymes and known protein targets and to establish the structure–activity relationships. Molecular dynamic simulation studies and in silico pharmacokinetic and toxicity prediction studies were done to determine in silico pharmacokinetics and toxicity of compounds. …”
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Computational and In silico study of novel fungicides against combating root rot, gray mold, fusarium wilt, and cereal rust. by Mollah Naimuzzaman, Md Mahabub Hasan, Ajoy Kumer, Abu Yousuf Hossin, Mohammad Harun-Ur-Rashid, Swapan Kumar Roy, Abu Noman Faruq Ahmmed, Jamal Uddin

“…The exploration of potential candidates for fungicides against four fungal proteins that cause some vital plant diseases, namely Phytophthora capsici, Botrytis cinerea, Fusarium oxysporum f. sp. lycopersici, and Puccinia graminis f. sp. tritici, was conducted using in silico, molecular docking simulations, and molecular dynamic (MD) simulation for selecting the nature of binding affinity with actives sites of proteins. …”
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Computational identification of anti-cancer compounds targeting the RNA-binding domain of human FOX-1 protein (RBFOX1) by Muhammad Tahir ul Qamar, Pablo Sanz-Jimenez, Shaima Rabeea Banoon, Xi-Tong Zhu, Fahad M. Aldakheel, Nahlah Makki Almansour, Leen A. Aldaiji, Wafa Abdullah I. Al-Megrin, Faisal Ahmad

“…Results shows that control (3S,5aS,6R,8aS,9R,10S,12R,12aS)-3,6,9-trimethyldecahydro-3H-3,12-epoxy[1,2]dioxepino[4,3-i]isochromen-10-ol (artenimol) reflecting the binding affinities of −7.9 kcal/mol, Top1 (4-[[2-butyl-5-[(E)-2-carboxy-3-thiophen-2-ylprop-1-enyl]imidazol-1-yl]methyl]benzoic acid) shows −8.7 kcal/mol and Top2 (R)-1-carboxy-5-((S)-2-((2R,4S)-4-carboxy-5,5-dimethylthiazolidin-2-yl)-2-(2-phenylacetamido)acetamido)pentan-1-aminium indicating −8.2 k cal/mol. Additional, molecular dynamic simulation studies shows significant stability during RMSD and RMSF analyses over a 100 ns timescale. …”
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Computer-guided identification of novel inhibitors of apoptosis-signaling kinase 1 from Spondia mombim bioactive compounds against colorectal cancer by Olusola Olalekan Elekofehinti, Hannah Oluwaseun Popoola, Adedotun Olayemi Oluwatuyi, Opeyemi Iwaloye, Moses Orimoloye Akinjiyan, Oluwamodupe Cecilia, Frank Abimbola Ogundolie, Olalekan Isaac Olatunde, Oussama Abchir, Samir Chtita, Joao Batista Texeira Rocha

“…These compounds showed modest indices for ADMET parameters. Molecular dynamic simulation validated ellagic acid and (-)-catechin with greater binding stability as leading compounds. …”
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Experimental and computational approach on the corrosion inhibition properties of two newly pyrazole derivatives on carbon steel in acid medium by Nawal Setti, Asma Barrahi, Mohamed Maatallah, Yassine Kaddouri, Taibi Ben Hadda, Halima Outada, Abhinay Thakur, Rachid Touzani, Khalid Karrouchi, Hatem A. Abuelizz, Burak Dikici, Abdelkader Zarrouk, Ali Dafali

“…The DFT calculations and Monte Carlo/Molecular dynamic (MC/MD) simulations were treated and discussed for both compounds Tetra-Pz-Ortho and Tetra-Pz-Para in order to explain their interfacial approach and compared them to experimental results. …”
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Neuroprotective role of epigallocatechin-3-gallate, albeginin and melanoxetin in alzheimer's disease by Arif Malik, Mehreen Hassan, Sulayman Waquar, Muhammad Wasim, Anam Naz, Faryal M. Awan, Muhammad T. Khan, Ali I. Khawaja, Sumera Zaib, Jamshed Iqbal, Ayesha Zahid, Marvi Marvi, Javeid Iqbal, Heng Wang, Dong-Qing Wei

“…Methods: Before conducting experimental work, molecular dynamic (MD) simulations were performed to assess the binding affinity of EGCG, albeginin, and melanoxetin against the selected targets. …”
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Telomerase inhibiting phytochemicals derived from Blumea eriantha for cancer treatment: A comprehensive computational analysis by Rahil Ummar Faruk Abbu, Shaik Mohammad Abdul Fayaz, Divyashree M S, Raghu Chandrashekhar H, Prasanna Kumar Reddy Gayam, Archana Mahadev Rao

“…To further assess the interaction and stability of these phytochemicals and predict their behavior in a biological environment when targeting telomerase, we conducted molecular dynamic simulations using Desmond–Schrödinger. …”
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Antifungal activity and biocompatibility assessment with molecular docking and dynamic simulations of new pyrazole derivatives by Basma T. Abd-Elhalim, Ghada G. El-Bana, Ahmed F. El-Sayed, Ghada E. Abdel-Ghani

“…Additionally, the computational ADMET “Absorption–distribution–metabolism–excretion–toxicity” analysis of these compounds revealed adherence to Lipinski’s rules, indicating favorable physicochemical characteristics. The molecular dynamic simulations of Adenosine 5’-phosphosulfate kinase in P. chrysogenum, UDP-N-acetylglucosamine in A. flavus, and FDC1 in A. niger with 10b also demonstrated the formation of stable complexes with favorable values of Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Solvent Accessible Surface Area (SASA), and Radius of Gyration (Rg). …”
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