Prediction of the Binding to the Nuclear Factor NF-Kappa-B by Constituents from <i>Teucrium polium</i> L. Essential Oil by Renilson Castro de Barros, Renato Araújo da Costa, Nesrine Guenane, Boulanouar Bakchiche, Farouk Benaceur, Omer Elkiran, Suelem Daniella Pinho Farias, Vanessa Regina Silva Mota, Maria Fani Dolabela

“…Based on the docking and molecular dynamics results, these molecules have potential as anti-inflammatory and antitumor therapies, with further in vitro and in vivo studies needed to evaluate their activity and toxicity.…”
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Facile universal strategy of presenting multifunctional short peptides for customizing desired surfaces by Ruofei Lu, Bingyang Zhao, Kaiyuan Huo, Hao Liu, Yang Wang, Xingjie Zan, Siwang Hu

“…Polyphenol–peptide interactions were elucidated in detail by assembling polyphenols and peptides possessing different characteristics (charged, uncharged, hydrophobic, and sequence length) in combination with molecular dynamics simulations, and isothermal titration calorimetry further revealed the favorable enthalpy change due to electrostatic interactions is the main driving force for assembling peptides with polyphenols. …”
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Structural bioinformatic study of six human olfactory receptors and their AlphaFold3 predicted water-soluble QTY variants and OR1A2 with an odorant octanoate and TAAR9 with spermid... by Finn Johnsson, Taner Karagöl, Alper Karagöl, Shuguang Zhang

“…Furthermore, we also used AlphaFold3 and molecular dynamics to study the odorant octanoate with OR1A2 and spermidine with TAAR9. …”
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Formation mechanism of multiple spallation and its penetration induced by shear localization in NiTi alloy under implosion loading by Xianye Wu, Xiaoyang Pei, Xiang Chen, Hao Zhang, Jin Wang, Xin Yang, Meizhen Xiang, Shang Gao, Fang Wang

“…This study uses nonequilibrium molecular dynamics simulations to explore the dynamic failures and deformation mechanisms of a cylindrical shell composed of nanocrystalline nickel–titanium alloy under implosion loading. …”
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Network pharmacology uncovers that secoisolariciresinol diglucoside ameliorate premature ovarian insufficiency via PI3K/Akt pathway by Yiqing Zhang, Xialu Liu, Zitong Zheng, Haiqiang Huang, Yurou Wang, Shuqin Wu, Yuan Shu, Yuxin Yang, Yufei Zhong, Pengfei Liao, Yongsong Wang, Zezheng Pan

“…Then, the mechanism by which SDG improves POI is predicted through a combination of network and pharmacology, and its authenticity is further confirmed by experimental verification, molecular docking analysis and molecular dynamics simulation. The results showed that SDG significantly alleviated POI by improving ovarian indices and follicle counts while protecting against CTX-induced ovarian damage by modulating the PI3K/Akt signaling pathway in KGN cells. …”
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Exploring Zinc C295 as a Dual HIV-1 Integrase Inhibitor: From Strand Transfer to 3′-Processing Suppression by Sharif Karim Sayyed, Marzuqa Quraishi, D. S. Prabakaran, Balaji Chandrasekaran, Thiyagarajan Ramesh, Satish Kumar Rajasekharan, Chaitany Jayprakash Raorane, Tareeka Sonawane, Vinothkannan Ravichandran

“…Molecular docking and molecular dynamics simulations were employed to analyse Zinc C295’s interactions with the 3′P allosteric site of HIV-1 integrase. …”
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Core-shell or Janus-like Fe0.5Ni0.5 nanostructures: A theoretical and experimental study by J. Rojas-Nunez, R.M. Freire, A.L. Elias, K. Fujisawa, L. Troncoso, J.C. Denardin, N. Plaza-Alcafuz, S.E. Baltazar

“…In this work, the formation FeNi bimetallic nanoparticles was investigated from an experimental and theoretical point of view. Molecular dynamics simulations were carried out in order to know the most stable arrangement of Fe and Ni atoms. …”
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Synthesis of Novel Benzothiazole–Profen Hybrid Amides as Potential NSAID Candidates by Iliyan Ivanov, Stanimir Manolov, Dimitar Bojilov, Yordan Stremski, Gabriel Marc, Stela Statkova-Abeghe, Smaranda Oniga, Ovidiu Oniga, Paraskev Nedialkov

“…The stability of these predicted complexes was further evaluated through molecular dynamics simulations. The results highlight the compounds’ promising biological activity and strong affinity for HSA. …”
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Molecular modeling to elucidate the dynamic interaction process and aggregation mechanism between natural organic matters and nanoplastics by Chi Zhang, Zhiyu Zhou, Mengning Xi, Haozhe Ma, Junhao Qin, Hanzhong Jia

“…., polyethylene (PE), polyvinyl chloride (PVC), and polystyrene (PS), were investigated. Molecular dynamics (MD) simulations revealed the geometrical change of the spontaneous formation of NOMs-NPs supramolecular assemblies. …”
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Identification of tacrolimus-related genes in familial combined hyperlipidemia and development of a diagnostic model using bioinformatics analysis by Yuan Xu, Hongfei He, Haiyang Li

“…A thorough weighted gene co-expression network analysis was conducted, including a differential expression analysis of the GSE1010 and TRG datasets, to identify intricate patterns of gene co-expression and provide insights on the underlying molecular dynamics within the datasets. Key genes were screened, diagnostic models were constructed, and all genes associated with logFC values were assessed using gene set variation and enrichment analyses. …”
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Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment by Zhuang Wang, Hao Fang, Se Wang, Fan Zhang, Degao Wang

“…Molecular interactions between carbon nanoparticles (CNPs) and a double-stranded deoxyribonucleic acid (dsDNA) fragment were investigated using molecular dynamics (MD) simulations. Six types of CNPs including fullerenes (C60 and C70), (8,0) single-walled carbon nanotube (SWNT), (8,0) double-walled carbon nanotube (DWNT), graphene quantum dot (GQD), and graphene oxide quantum dot (GOQD) were studied. …”
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AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins by Olivia S. Pratt, Luc G. Elliott, Margaux Haon, Shahram Mesdaghi, Rebecca M. Price, Adam J. Simpkin, Daniel J. Rigden

“…The instability of some predictions is demonstrated by molecular dynamics. Importantly, other deep learning-based structure prediction tools predict different structures or β-solenoids with much lower confidence suggesting that AF2 alone has an unreasonable tendency to predict confident but unrealistic β-solenoids for perfect repeat sequences. …”
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Atomistic Insight into the Effects of Collision Angle on the Characteristics of Cu-Ta Joining by Explosive Welding by Van-Thuc Nguyen, Nguyen Quang Hien, Pham Minh Duc, Tran Duy Nam, Van Huong Hoang, Van Thanh Tien Nguyen

“…This study aims to examine how the collision angle affects the Cu-Ta weld generated by the explosive welding method using molecular dynamics modeling. When two blocks collide, the metallic substrates melt rapidly. …”
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Enhancing water solubility of phytosterols through Co-amorphization with food-grade coformers by Yuxin Li, Yingting Luo, Xuening Song, Yuzhuo Wang, Simiao Liu, Fazheng Ren, Lingyan Kong, Hao Zhang

“…Fourier-transform infrared, Raman, and 1H NMR spectroscopies, along with molecular dynamics simulations, revealed strong intermolecular interactions between PS and Nic. …”
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Pharmacological Mechanism of Zuojin Pill for Gastroesophageal Reflux Disease: A Network Pharmacology Study by Mi Lv, Jinke Huang, Jiayan Hu, Wenxi Yu, Ping Liu, Kunli Zhang, Fengyun Wang

“…Therefore, we employed network pharmacology (NP), molecular docking (MD), and molecular dynamics simulation (MDS) to investigate the pharmacological mechanisms of ZJP against GERD. …”
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Multilevel Precision-Based Rational Design of Chemical Inhibitors Targeting the Hydrophobic Cleft of Apical Membrane Antigen 1 (AMA1) by Umashankar Vetrivel, Shalini Muralikumar, B Mahalakshmi, K Lily Therese, HN Madhavan, Mohamed Alameen, Indhuja Thirumudi

“…These two compounds surpassed all the precision levels of docking and also the stringent post docking and cumulative molecular dynamics evaluations. Moreover, the backbone flexibility of hotspot residues in the hydrophobic cleft, which has been previously reported to be essential for accommodative binding of RON2 to AMA1, was also highly perturbed by these compounds. …”
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A DFT study of lithium intercalation and metallization on oxygen-vacancy containing TiO2(110) by J. Juan, M.G. Sandoval, P. Bechthold, E.A. González, P.V. Jasen

“…When more Lithium is considered, new Li-O bonds are formed. Ab initio molecular dynamics simulations (AIMD) are performed, to check the stability of the system. …”
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Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks by Wesley Cardoso Generoso, Alana Helen Santana Alvarenga, Isabelle Taira Simões, Renan Yuji Miyamoto, Ricardo Rodrigues de Melo, Ederson Paulo Xavier Guilherme, Fernanda Mandelli, Clelton Aparecido Santos, Rafaela Prata, Camila Ramos dos Santos, Felippe Mariano Colombari, Mariana Abrahão Bueno Morais, Rodrigo Pimentel Fernandes, Gabriela Felix Persinoti, Mario Tyago Murakami, Leticia Maria Zanphorlin

“…Combining X-ray crystallography, molecular dynamics simulations, and machine learning, we have identified intricate molecular rearrangements within the active site that enable the Cβ atom of the substrate to approach the heme iron, thereby promoting oleate decarboxylation. …”
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Novel inhibitors of the (VIBVN) NAT protein identified through pharmacophore modeling by Wei Wei, Xionghao Li, Ning Hou, Aowei Xie, Huicong Liang, Ting Gao, Xiaoli Jing, Liqin Li, Jiejie Hao, Ximing Xu

“…From this process, we identified two hit compounds, AK-968-11563024 and AG-205-36710025, with IC50 values of 18.86 µM and 33.27 µM, respectively. Molecular dynamics simulations further elucidated the binding mechanism between (VIBVN)NAT and AK-968-11563024. …”
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Novel Antibacterial 4-Piperazinylquinoline Hybrid Derivatives Against <i>Staphylococcus aureus</i>: Design, Synthesis, and In Vitro and In Silico Insights by Gabriele La Monica, Annamaria Gallo, Alessia Bono, Federica Alamia, Antonino Lauria, Rosa Alduina, Annamaria Martorana

“…Further in silico docking and molecular dynamics studies highlighted strong interactions of <b>5k</b> with bacterial enzymes, such as tyrosyl-tRNA synthetase, pyruvate kinase, and DNA gyrase B, suggesting potential modes of action. …”
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