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458 Publications visible to you, out of a total of 458
Prediction of drug-protein binding kinetics

Abstract

Not specified

Author: Abraham Muñiz‐Chicharro

Date Published: 3rd Apr 2025

Publication Type: Doctoral Thesis

The need to implement FAIR principles in biomolecular simulations.

Abstract

Not specified

Authors: R. E. Amaro, J. Aqvist, I. Bahar, F. Battistini, A. Bellaiche, D. Beltran, P. C. Biggin, M. Bonomi, G. R. Bowman, R. A. Bryce, G. Bussi, P. Carloni, D. A. Case, A. Cavalli, C. A. Chang, T. E. 3rd Cheatham, M. S. Cheung, C. Chipot, L. T. Chong, P. Choudhary, G. A. Cisneros, C. Clementi, R. Collepardo-Guevara, P. Coveney, R. Covino, T. D. Crawford, M. Dal Peraro, B. L. de Groot, L. Delemotte, M. De Vivo, J. W. Essex, F. Fraternali, J. Gao, J. L. Gelpi, F. L. Gervasio, F. D. Gonzalez-Nilo, H. Grubmuller, M. G. Guenza, H. V. Guzman, S. Harris, T. Head-Gordon, R. Hernandez, A. Hospital, N. Huang, X. Huang, G. Hummer, J. Iglesias-Fernandez, J. H. Jensen, S. Jha, W. Jiao, W. L. Jorgensen, S. C. L. Kamerlin, S. Khalid, C. Laughton, M. Levitt, V. Limongelli, E. Lindahl, K. Lindorff-Larsen, S. Loverde, M. Lundborg, Y. L. Luo, F. J. Luque, C. I. Lynch, A. D. Jr MacKerell, A. Magistrato, S. J. Marrink, H. Martin, J. A. McCammon, K. Merz, V. Moliner, A. J. Mulholland, S. Murad, A. N. Naganathan, S. Nangia, F. Noe, A. Noy, J. Olah, M. L. O'Mara, M. J. Ondrechen, J. N. Onuchic, A. Onufriev, S. Osuna, G. Palermo, A. R. Panchenko, S. Pantano, C. Parish, M. Parrinello, A. Perez, T. Perez-Acle, J. R. Perilla, B. M. Pettitt, A. Pietropaolo, J. P. Piquemal, A. B. Poma, M. Praprotnik, M. J. Ramos, P. Ren, N. Reuter, A. Roitberg, E. Rosta, C. Rovira, B. Roux, U. Rothlisberger, K. Y. Sanbonmatsu, T. Schlick, A. K. Shaytan, C. Simmerling, J. C. Smith, Y. Sugita, K. Swiderek, M. Taiji, P. Tao, D. P. Tieleman, I. G. Tikhonova, J. Tirado-Rives, I. Tunon, M. W. van der Kamp, D. van der Spoel, S. Velankar, G. A. Voth, R. Wade, A. Warshel, V. V. Welborn, S. D. Wetmore, T. J. Wheeler, C. F. Wong, L. W. Yang, M. Zacharias, M. Orozco

Date Published: 2nd Apr 2025

Publication Type: Journal

Prediction of Binding Kinetics of the Interleukin-13-Interleukin-13 Receptor alpha1 Complex

Abstract

Not specified

Editor:

Date Published: 31st Jan 2025

Publication Type: Master's Thesis

Structural bioinformatics approach to exploring transient binding pockets in proteins

Abstract

Not specified

Editor:

Date Published: 18th Dec 2024

Publication Type: Bachelor's Thesis

Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos

Abstract

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Authors: Jessica Guerra, Mirella Belleri, Giulia Paiardi, Chiara Tobia, Davide Capoferri, Marzia Corli, Elisa Scalvini, Marco Ghirimoldi, Marcello Manfredi, Rebecca C. Wade, Marco Presta, Luca Mignani

Date Published: 1st Dec 2024

Publication Type: Journal

Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD

Abstract (Expand)

Abstract The dissociation rate, or its reciprocal, the residence time (τ), is a crucial parameter for understanding the duration and biological impact of biomolecular interactions. Accurate prediction …tions. Accurate prediction of τ is essential for understanding protein-protein interactions (PPIs) and identifying potential drug targets or modulators for tackling diseases. Conventional molecular dynamics simulation techniques are inherently constrained by their limited timescales, making it challenging to estimate residence times, which typically range from minutes to hours. Building upon its successful application in protein-small molecule systems, τ-Random Acceleration Molecular Dynamics (τRAMD) is here investigated for estimating dissociation rates of protein-protein complexes. τRAMD enables the observation of unbinding events on the nanosecond timescale, facilitating rapid and efficient computation of relative residence times. We tested this methodology for three protein-protein complexes and their extensive mutant datasets, achieving good agreement between computed and experimental data. By combining τRAMD with MD-IFP (Interaction Fingerprint) analysis, dissociation mechanisms were characterized and their sensitivity to mutations investigated, enabling the identification of molecular hotspots for selective modulation of dissociation kinetics. In conclusion, our findings underscore the versatility of τRAMD as a simple and computationally efficient approach for computing relative protein-protein dissociation rates and investigating dissociation mechanisms, thereby aiding the design of PPI modulators.

Authors: Giulia D’Arrigo, Daria B. Kokh, Ariane Nunes-Alves, Rebecca C. Wade

Date Published: 1st Dec 2024

Publication Type: Journal

Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer’s disease

Abstract (Expand)

Abstract Background Neural stem cell (NSC) proliferation and differentiation in the mammalian brain decreases to minimal levels postnatally. Nevertheless, neurogenic niches persist in the adult cortex …rtheless, neurogenic niches persist in the adult cortex and hippocampus in rodents, primates and humans, with adult NSC differentiation sharing key regulatory mechanisms with development. Adult neurogenesis impairments have been linked to Alzheimer’s disease (AD) pathology. Addressing these impairments by using neurotrophic factors is a promising new avenue for therapeutic intervention based on neurogenesis. However, this possibility has been hindered by technical difficulties of using in-vivo models to conduct screens, including working with scarce NSCs in the adult brain and differences between human and mouse models or ethical limitations. Methods Here, we use a combination of mouse and human stem cell models for comprehensive in-vitro characterization of a novel neurogenic compound, focusing on the brain-derived neurotrophic factor (BDNF) pathway. The ability of ENT-A011, a steroidal dehydroepiandrosterone derivative, to activate the tyrosine receptor kinase B (TrkB) receptor was tested through western blotting in NIH-3T3 cells and its neurogenic and neuroprotective action were assessed through proliferation, cell death and Amyloid-β (Aβ) toxicity assays in mouse primary adult hippocampal NSCs, mouse embryonic cortical NSCs and neural progenitor cells (NPCs) differentiated from three human induced pluripotent stem cell lines from healthy and AD donors. RNA-seq profiling was used to assess if the compound acts through the same gene network as BDNF in human NPCs. Results ENT-A011 was able to increase proliferation of mouse primary adult hippocampal NSCs and embryonic cortical NSCs, in the absence of EGF/FGF, while reducing Aβ-induced cell death, acting selectively through TrkB activation. The compound was able to increase astrocytic gene markers involved in NSC maintenance, protect hippocampal neurons from Αβ toxicity and prevent synapse loss after Aβ treatment. ENT-A011 successfully induces proliferation and prevents cell death after Aβ toxicity in human NPCs, acting through a core gene network shared with BDNF as shown through RNA-seq. Conclusions Our work characterizes a novel BDNF mimetic with preferable pharmacological properties and neurogenic and neuroprotective actions in Alzheimer’s disease via stem cell-based screening, demonstrating the promise of stem cell systems for short-listing competitive candidates for further testing.

Authors: Despoina Charou, Thanasis Rogdakis, Alessia Latorrata, Maria Valcarcel, Vasileios Papadogiannis, Christina Athanasiou, Alexandros Tsengenes, Maria Anna Papadopoulou, Dimitrios Lypitkas, Matthieu D. Lavigne, Theodora Katsila, Rebecca C. Wade, M. Zameel Cader, Theodora Calogeropoulou, Achille Gravanis, Ioannis Charalampopoulos

Date Published: 1st Dec 2024

Publication Type: Journal

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