Immunoinformatics design of a novel multiepitope vaccine candidate against non-typhoidal salmonellosis caused by Salmonella Kentucky using outer membrane proteins A, C, and F. by Elayoni E Igomu, Paul H Mamman, Jibril Adamu, Maryam Muhammad, Abubarkar O Woziri, Manasa Y Sugun, John A Benshak, Kingsley C Anyika, Rhoda Sam-Gyang, David O Ehizibolo

“…Molecular docking studies with Toll-like receptors 1, 2, 4, and 5, followed by molecular dynamic simulations, suggested that the vaccine-receptor complexes are energetically feasible, stable, and robust. …”
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Cinnamic acid conjugated with triazole acetamides as anti-Alzheimer and anti-melanogenesis candidates: an in vitro and in silico study by Amir Shervin Shokouhi Asl, Mohammad Hosein Sayahi, Mohammad Hashem Hashempur, Cambyz Irajie, Amir Hossein Alaeddini, Seyedeh Niloufar Ghafouri, Milad Noori, Navid Dastyafteh, Javad Mottaghipisheh, Mehdi Asadi, Bagher Larijani, Mohammad Mahdavi, Aida Iraji

“…Furthermore, molecular docking and molecular dynamic studies of compound 10j were conducted to thoroughly evaluate its mode of action within the BChE active site.…”
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Computer-assisted discovery of natural inhibitors for platelet-derived growth factor alpha as novel therapeutics for thyroid cancer by Hira Khalid, Farah Sattar, Iqra Ahmad, Valdir Ferreira de Paula Junior, Valdir Ferreira de Paula Junior, Umar Nishan, Umar Nishan, Riaz Ullah, Hanna Dib, Khaled W. Omari, Mohibullah Shah, Mohibullah Shah

“…The protein-ligand stability of the top 3 hits, namely cis-Grossamide K, Daturafoliside O, and N-cis-feruloyltyramine, and their interactions at the potential binding site of target protein were confirmed through molecular dynamic simulations. We also analyzed pharmacophoric features for stable binding in the PDGFRA active site. …”
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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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