A1, an innovative fluorinated CXCR4 inhibitor, redefines the therapeutic landscape in colorectal cancer by Hossein Khorramdelazad, Kowsar Bagherzadeh, Ali Rahimi, Ali Darehkordi, Alireza Najafi, Milad Karimi, Majid Khoshmirsafa, Gholamhossein Hassanshahi, Elaheh Safari, Reza Falak

“…This study focuses on investigating the potential of N, N''-thiocarbonylbis (N'-(3,4-dimethyl phenyl)-2,2,2-trifluoroacetimidamide) (A1), a novel fluorinated CXCR4 inhibitor, through a comprehensive analysis encompassing in silico, in vitro, and in vivo studies. Methods The molecular dynamic simulation method was employed to compute A1 binding affinity and energy for the CXCR4 receptor compared to AMD3100. …”
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Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 by López-Orozco Wendolyne, Mendoza-Huizar Humberto Luis, Álvarez-Romero Giaan Arturo, Torres-Valencia Jesús Martín, Sanchez-Zavala Maricruz

“…Additionally, the molecular docking study revealed that, alliin is able to dock to the protease Mpro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. …”
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London dispersion forces and steric effects within nanocomposites tune interaction energies and chain conformation by Baode Zhang, Snežana D. Zarić, Sonja S. Zrilić, Iosif Gofman, Barbara Heck, Günter Reiter

“…Calculation of the interaction energy and chain conformations of each PI upon CNT was performed by accurate density functional theory (DFT) calculations and molecular dynamic simulation (MDS). OPI chain adopt helically wrapping conformation around CNT with relatively strong interaction energy. …”
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Exploring Substituted Tetrazoloquinazoline: Biological Activities, Molecular Docking Analysis, and Anti-Breast Cancer MCF7/HER2 Effects by Neni Frimayanti, Ihsan Ikhtiarudin, Rahma Dona, Rahul Oktarizal, Aprilia Cindy Nurfatimah

“…This research aims to synthesize substituted tetrazoloquinazoline and evaluate its potential as an anticancer agent using molecular docking studies with the Molecular Operating Environment (MOE) software. Furthermore, molecular dynamic was also performed to analyze the binding stability of this protein-ligand complex. …”
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Senyawa Fucodiphlorethol Dan Phloroglucinol Alga Coklat Sebagai Inhibitor Lipase Secara In Silico by Yohanes Bare, Dewi Ratih Tirto Sari, Marsiana Coo Mogi, Maria Marcelina Dua Nurak

“…Therefore, we predicted that both of fucodiphlorethol and phloroglucinol inhibit lipase allosterically by altering the protein structure conformations. molecular docking analysis suggested that fucodiphlorethol and phloroglucinol have potential antiobesity effect by inhibiting lipase. Molecular dynamic are needed for further investigation.…”
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Investigation on the Binding and Conformational Change of All-trans-Retinoic Acid with Peptidyl Prolyl cis/trans Isomerase Pin1 Using Spectroscopic and Computational Techniques by GuoFei Zhu, ShaoLi Lyu, Yang Liu, Chao Ma, Wang Wang

“…Circular dichroism, fluorescence spectra, and computational simulations revealed that ATRA interacted with residues Lys63 and Arg69 of Pin1 to affect its conformational changes. Molecular dynamic simulation, principal component analysis, and free energy landscape monitored the dynamical conformational characteristics of ATRA binding to Pin1. …”
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Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease by Atatreh Noor, Hasan Shaima, Ali Bassam R., Ghattas Mohammad A.

“…Consequently, > 580,000 ligands were processed via several filtration and docking steps, then the top 21 compounds were analysed extensively via MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. …”
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Inherent stochasticity, noise and limits of detection in continuous and time-gated fluorescence systems. by Nicholas H Vitale, Arjang Hassibi, Hyongsok Tom Soh, Boris Murmann, Thomas H Lee

“…Both the ensemble and stochastic models presented in this work have been verified using Monte Carlo molecular dynamic simulations that utilize the Gillespie algorithm. …”
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Self-Healing Effect of Various Capsule-Core Materials on Asphalt Materials by Suhua Chen, Qi Liu, Yanqiu Bi, Bin Yu, Jiupeng Zhang

“…To further investigate the self-healing mechanism of microcapsules and exclude the interference of capsule-wall materials, a bi-plate test and a molecular model of asphalt and capsule-core materials were established using dynamic shear rheometer (DSR) and molecular dynamic (MD) simulation. Firstly, the models of asphalt-rejuvenator-asphalt and asphalt-epoxy resin-asphalt were established to simulate the interface of asphalt and capsule-core materials. …”
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Computational and GC-MS screening of bioactive compounds from Thymus Vulgaris targeting mycolactone protein associated with Buruli ulcer by Muhammad Naveed, Imran Ali, Tariq Aziz, Ayesha Saleem, Zeerwah Rajpoot, Sameera Khaleel, Ayaz Ali Khan, Mitub Al-harbi, Thamer H. Albekairi

“…The ADMET analysis predicted that the compound borneol crosses the PGP + through the Blood Brain Barrier and gastrointestinal tract without violating Lipinski’s rule of 5 having high water solubility, and log p-value of 2.29. The molecular dynamic simulation was performed and showed the Eigenvalue of 1.332692e-04. …”
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Rational design, synthesis, in vitro, and in-silico studies of pyrazole‑phthalazine hybrids as new α‑glucosidase inhibitors by Mehrdad Roshan, Roghieh Mirzazadeh, Azadeh Tajmir-Riahi, Mohammad Sadegh Asgari

“…All of the pharmacophoric features used in the hybrid design were found to be involved in the interaction with the enzyme’s active site, as expected. Moreover, molecular dynamic simulation and the absorption, distribution, metabolism, and excretion (ADME) have been performed.…”
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In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. by Abu Tayab Moin, Nurul Amin Rani, Rajesh B Patil, Tanjin Barketullah Robin, Md Asad Ullah, Zahidur Rahim, Md Foyzur Rahman, Talha Zubair, Mohabbat Hossain, A K M Moniruzzaman Mollah, Nurul Absar, Mahboob Hossain, Mohammed Abul Manchur, Nazneen Naher Islam

“…Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. …”
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A new potential of sodium anthraquinone-2-sulfonate as a corrosion inhibitor for carbon steel in 0.5 M H2SO4 by Nikolay Akatyev, Roza Kenzhegalieva, Meruyet Khapiyeva, Gauhar Uzakbay, Aruzhan Talapova, Ruben Vardanyan

“…Density functional theory DFT/B3LYP/6-311+G(d,p) and molecular dynamic simulation (MD) were applied for theoretical studies to evaluate the inhibiting effect and understand the mechanism of interaction of inhibitor molecules with Fe (110) surface. …”
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The Impact of Pore Structure on Kerogen Geomechanics by Saad Alafnan

“…Eight units were initially placed in a low-density cell. Then, a molecular dynamic protocol was followed to form a final structure with a density of 1.1 g/cc; the range of density values was consistent with what has been reported in the literature. …”
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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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Synthesis, In vitro antimicrobial activity, and In silico bioinformatical approach of xanthone-fatty acid esters against Staphylococcus aureus, Escherichia coli, and Candida albica... by Yehezkiel Steven Kurniawan, Ervan Yudha, Jumina, Harno Dwi Pranowo, Eti Nurwening Sholikhah

“…Furthermore, both molecular docking and molecular dynamic simulations indicated good stability of xanthyl laurate in the active site of each protein receptor through hydrogen bond and other non-covalent interactions. …”
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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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Predicting the adsorption of -perfluorohexane in BAM-P109 standard activated carbon by molecular simulation using SAFT- Mie coarse-grained force fields by Carmelo Herdes, Esther Forte, George Jackson, Erich A Müller

“…The parameters of the SAFT- γ Mie force field are estimated directly from the vapour pressure and saturated liquid density data of the pure fluids using the equation of state, and further validated by molecular dynamic simulations. The coarse-grained intermolecular potential models are then used to obtain the adsorption isotherm kernels for argon, carbon dioxide, and n -perfluorohexane in graphite slit pores of various widths using Grand Canonical Monte Carlo simulations. …”
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