A Structural Effect of the Antioxidant Curcuminoids on the Aβ(1–42) Amyloid Peptide by Angelo Santoro, Antonio Ricci, Manuela Rodriquez, Michela Buonocore, Anna Maria D’Ursi

“…The results suggest that the synthetic tetrahydrocurcumin (THC) derivative interacts with the amyloid peptide in all the systems presented, while cyclocurcumin (CYC) and bisdemethoxycurcumin (BMDC) only interact when the peptide is in a less stable conformation. Molecular dynamics simulations helped visualise the curcuminoids’ effect in an aqueous system and hypothesise the importance of the peptide surface exposition to the solvent, differently modulated by the curcumin derivatives.…”
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Structural basis of THC analog activity at the Cannabinoid 1 receptor by Thor S. Thorsen, Yashraj Kulkarni, David A. Sykes, Andreas Bøggild, Taner Drace, Pattarin Hompluem, Christos Iliopoulos-Tsoutsouvas, Spyros P. Nikas, Henrik Daver, Alexandros Makriyannis, Poul Nissen, Michael Gajhede, Dmitry B. Veprintsev, Thomas Boesen, Jette S. Kastrup, David E. Gloriam

“…We leverage this structure for docking and 1000 ns molecular dynamics simulations of THC and 10 structural analogs delineating their spatiotemporal interactions at the molecular level. …”
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Factors governing $${\rm H}_{3}^{+}$$ H 3 + formation from methyl halogens and pseudohalogens by Jacob Stamm, Swati S. Priyadarsini, Shawn Sandhu, Arnab Chakraborty, Jun Shen, Sung Kwon, Jesse Sandhu, Clayton Wicka, Arshad Mehmood, Benjamin G. Levine, Piotr Piecuch, Marcos Dantus

“…We also carry out ab initio molecular dynamics simulations to obtain detailed microscopic insights into the mechanism, yields, and timescales of $${\rm H}_{3}^{+}$$ H 3 + production. …”
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Immunoinformatics Approach to Design a Chimeric CD70-Peptide Vaccine against Renal Cell Carcinoma by Haideh Namdari, Farhad Rezaei, Fatemeh Heidarnejad, Mohammad Yaghoubzad-Maleki, Maryam Karamigolbaghi

“…The chosen vaccine construct underwent diverse assessments such as molecular dynamics simulation, immune response simulation, and in silico cloning. …”
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AI-enhanced 3D-QSAR screening of fragment-based novel designed molecules targeting Phalaris minor ACCase by Bikash Kumar Rajak, Priyanka Rani, Durg Vijay Singh, Nitesh Singh

“…The selected herbicide-like molecules are further processed through fragment-based design to generate a library of new compounds, refined using binding affinity thresholds (-8.5 kcal/mol) and Quantitative Structure-Activity Relationship (QSAR) models. Finally, molecular dynamics (MD) simulations validated the interaction stability of these potential herbicides over 100 ns, yielding four promising candidates optimized for ACCase inhibition. …”
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Designer topological-single-atom catalysts with site-specific selectivity by Weibin Chen, Menghui Bao, Fanqi Meng, Bingbing Ma, Long Feng, Xuan Zhang, Zanlin Qiu, Song Gao, Ruiqin Zhong, Shibo Xi, Xiao Hai, Jiong Lu, Ruqiang Zou

“…In this work, we introduce a design principle of topological-single-atom catalysts (T-SACs) guided by density functional theory (DFT) and Ab initio molecular dynamics (AIMD) calculations, where metal single atoms are arranged in asymmetric configurations that electronic shield topologically misorients d orbitals, minimizing unwanted interactions between reactants and the support surface. …”
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Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes by Reiner Ribarics, Michael Kenn, Rudolf Karch, Nevena Ilieva, Wolfgang Schreiner

“…To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. …”
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Computational design of potent dimeric phenylthiazole NS5A inhibitors for hepatitis C virus by Wissal Liman, Mehdi Oubahmane, Nouhaila Ait Lahcen, Ismail Hdoufane, Driss Cherqaoui, Rachid Daoud, Achraf El Allali

“…Moreover, molecular docking was used to predict the binding affinity of the newly designed inhibitors within the NS5A protein, followed by molecular dynamics simulations to investigate the dynamic interactions over time. …”
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Repurposing antiviral drugs targeting the PARP-1 and HER2 pathways with multifaceted impacts through integrated network analysis and molecular mechanics by Uma Maheshwari Mugundan, Praveen Sekar, Rajanandh Muhasaparur Ganesan

“…The binding affinities observed were -7.92 Kcal/mol for HER2 and -8.08 Kcal/mol for PARP-1 for Efavirenz, and -8.17 Kcal/mol for HER2 and -7.91 Kcal/mol for PARP-1 for Fostemsavir. Subsequent molecular dynamics simulations, conducted over 200 ns, assessed the stability of these drug-protein complexes. …”
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Exploring the impact of the stargazin V143L mutation on the dynamics of the AMPA receptor: stargazin complex by Raquel P. Gouveia, Raquel P. Gouveia, Carlos A. V. Barreto, Carlos A. V. Barreto, Rita Melo, Ana Luísa Carvalho, Ana Luísa Carvalho, Irina S. Moreira, Irina S. Moreira

“…To achieve this, we conducted a thorough examination of eight distinct molecular dynamics simulations of AMPA receptor-stargazin complexes, each associated with different conductance levels. …”
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Machine learning-assisted design of Ti–V–Nb–Mo refractory high-entropy alloys with higher ductility and specific yield strength by Yan Li, Junjie Gong, Shilong Liang, Wei Wu, Yongxin Wang, Zheng Chen

“…A dataset of the alloys' performance parameters was established by applying first-principles and molecular dynamics calculations. The combination of the aforementioned dataset with the solid solution strengthening (SSH) model and the D (γs/γusf) parameter enabled the construction of a highly accurate strength-ductility prediction model for the alloys through the use of an XGBoost algorithm. …”
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2-Amino-6-methylbenzothiazole as corrosion inhibitor for low carbon steel in acidic solution: Experimental and theoretical studies by Klodian Xhanari, Muhamed Farruku, Avni Berisha, Bujar Seiti, Kledi Xhaxhiu, Efrosini Kokalari, Alketa Lame

“…Density Functional Theory (DFT) calculations, along with Monte Carlo (MC) and Molecular Dynamics (MD) simulations, were employed to investigate AMBT’s corrosion inhibition behaviour at the molecular level. …”
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In vitro and in silico insights into antimicrobial and anticancer activities of novel imidazo[2,1-b][1,3,4]thiadiazoles by Deepika Dwarakanath, Yogeesha N. Nayak, Ananda Kulal, Samyak Pandey, K Sreedhara Ranganath Pai, Santosh L. Gaonkar

“…Molecular docking was studied to determine the docking poses and binding interaction of the derivatives with the protein bearing PDB: 5BNS and 3ZNR; ADME properties of the derivatives are also inferred which gives insights into the bioavailability. The molecular dynamics simulation of the derivative 3c with HDAC7 protien (PDB: 3ZNR) was evalauted to determine the stability of the interaction between the protein and the ligand.…”
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Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody by Jing Dai, Saeed Izadi, Jonathan Zarzar, Patrick Wu, Angela Oh, Paul J. Carter

“…An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~ 200 anti-GCGR IgG1 variants. …”
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Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein by Ziyuan Niu, Georgios Kementzidis, Miriam Rafailovich, Marcia Simon, Evangelos Papadopoulos, Bertal H. Aktas, Yuefan Deng

“…We performed triplicate and long-time all-atom molecular dynamics simulations to investigate the structures and dynamics of the SARS-CoV-2 spike glycoprotein (S-protein) for a broad range of pH = 1 through 11 and temperatures of 3°C through 75°C. …”
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Unravelling the Methylene Blue Adsorption Mechanism on Doped and Nondoped Polyaniline: A Combined Molecular Modeling and Experimental Investigation by Souad Djellali, Amani Touati, Abderrahmane Semmeq, Maya Kebaili, Michael Badawi, Adrián Bonilla-Petriciolet

“…Static DFT and DFT-based ab initio molecular dynamics were used to characterize the intermolecular interactions of this dye molecule with nondoped and doped PANI. …”
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Challenging the ideal strength limit in single-crystalline gold nanoflakes through phase engineering by Tong Zhang, Yuanbiao Tong, Chenxinyu Pan, Jun Pei, Xiaomeng Wang, Tao Liu, Binglun Yin, Pan Wang, Yang Gao, Limin Tong, Wei Yang

“…First-principles and molecular dynamics (MD) calculations demonstrate that the mechanical properties arise from the unconventional HCP structure as well as the strong surface effect. …”
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Anti-Inflammatory therapeutic potential of Bungur (Lagerstroemia speciosa L.) leaves ethanolic extract against LPS-activated macrophage through TLR4/MD2 signaling: A computational... by Rosyadah Nuraini, Dwijayanti Dinia Rizqi, Annisa Yuslinda, Kamila Fairuz Sarah, Widyananda Muhammad Hermawan, Ulfa Siti Mariyah, Widodo Nashi

“…Molecular docking and molecular dynamics simulations were conducted to evaluate the interaction and stability of selected compounds with TLR4/MD2 complex. …”
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Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii by Fizza Arshad, Asifa Sarfraz, Muhammad Shehroz, Umar Nishan, Asia Perveen, Riaz Ullah, Mohamed A. Ibrahim, Mohibullah Shah

“…Using conserved antigenic peptides, two chimeric vaccine constructs were developed and assessed using molecular docking, molecular dynamics simulations, principal component analysis, MM-GBSA binding free energy, and dynamic cross-correlation matrix studies. …”
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A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth by Marina R. Good, Monica L. Fernández-Quintero, Wei Ji, Alesandra J. Rodriguez, Julianna Han, Andrew B. Ward, Jenna J. Guthmiller

“…We do not observe any binding to α2,6 sialic acids, the receptor used by human seasonal influenza viruses. Using molecular dynamics and a cryo-EM structure of A/Texas/37/2024 H5, we show A/Texas/37/2024 H5 is more flexible within the receptor-binding site compared to a 2.3.4.4b H5 from 2022. …”
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