Article
Biochemistry & Molecular Biology
Chandran Remya, K. Dileep, Eeda Koti Reddy, Kumar Mantosh, Kesavan Lakshmi, Reena Sarah Jacob, Ayyiliyath M. Sajith, E. Jayadevi Variyar, Shaik Anwar, Kam Y. J. Zhang, C. Sadasivan, R. Omkumar
Summary: Research aimed to develop novel high affinity multitarget directed ligands (MTDLs) against AChE and NMDAR, with reduced hepatotoxicity, identified several promising compounds with potential therapeutic value, among which MTDL-201 appears to be a potential candidate for immediate preclinical evaluations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Beata Dabrowska-Bouta, Grzegorz Sulkowski, Mikolaj Salek, Malgorzata Frontczak-Baniewicz, Lidia Struzynska
Summary: Silver nanoparticles have strong antimicrobial properties, but also exhibit neurotoxicity by affecting the NMDA receptor complex and signaling pathways in immature rats, potentially leading to health hazards in children and infants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Hongmei Ning, Chong Li, Zhihong Yin, Dongfang Hu, Yaming Ge, Lingli Chen
Summary: The study revealed that high concentrations of fluoride (1.5, 2, and 2.5 mM) exerted significant toxic effects on the cellular morphologies and neural formation of primary cultured cortical neurons.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Jan Voldrich, Marika Matousova, Marketa Smidkova, Barbora Slavikova, Hana Chodounska, Eva Kudova, Helena Mertlikova-Kaiserova
Summary: The goal of this study was to evaluate the efficacy of mixed cortical and hippocampal primary rat postnatal neuronal culture for identifying NMDAR antagonists. The authors found that this model is comparable to other commonly used primary rat neuronal models and is a convenient and robust tool for NMDAR antagonist screening.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2022)
Article
Cell Biology
Rafael Rivas-Santisteban, Iu Raich, David Aguinaga, Carlos A. Saura, Rafael Franco, Gemma Navarro
Summary: The study discovered a direct interaction between PrPC and NMDAR, which alters the functionality of the receptor. Significant overexpression of NMDAR-PrPC complexes was observed in the AD model, and PrPC exacerbates the axonal transport of Tau and pTau proteins.
Article
Clinical Neurology
Dror Shir, Jonathan Graff-Radford, Mary M. Machulda, Nha Trang Thu Pham, Clifford R. Jack, Val J. Lowe, Jennifer L. Whitwell, Keith A. Josephs
Summary: This study found that primary occipital posterior cortical atrophy (PCA) is characterized by an older age at onset, more color perception dysfunction, less severe ideomotor apraxia, and less hypometabolism in the temporo-parietal meta-ROI compared to established phenotypes.
EUROPEAN JOURNAL OF NEUROLOGY
(2022)
Article
Multidisciplinary Sciences
A. F. Garcia, E. A. Crummy, I. G. Webb, M. N. Nooney, S. M. Ferguson
Summary: Processing within the anterior cingulate cortex is crucial for appropriate behavior, and dysfunction following chronic drug use is thought to play a major role in drug addiction. Two types of cortical pyramidal projection neurons regulate distinct features of a drug experience, its positive and negative aspects, respectively, supporting a revised theory of cortical function in addiction.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Rosaria Perone, Claudia Albertini, Elisa Uliassi, Flaminia Di Pietri, Pedro de Sena Murteira Pinheiro, Sabrina Petralla, Nicola Rizzardi, Romana Fato, Lenka Pulkrabkova, Ondrej Soukup, Anna Tramarin, Manuela Bartolini, Maria Laura Bolognesi
Summary: By merging donepezil with idebenone, a novel multi-target-directed ligand (MTDL) was designed targeting A beta and oxidative pathways, demonstrating promising bioactivity and drug-like properties.
Article
Chemistry, Medicinal
Massimiliano Runfola, Michele Perni, Xiaoting Yang, Maria Marchese, Andrea Bacci, Serena Mero, Filippo M. Santorelli, Beatrice Polini, Grazia Chiellini, Daniela Giuliani, Antonietta Vilella, Martina Bodria, Eleonora Daini, Eleonora Vandini, Simon Rudge, Sheraz Gul, Michale O. J. Wakelam, Michele Vendruscolo, Simona Rapposelli
Summary: In order to treat Alzheimer's disease, researchers designed a compound called SG2 with pleiotropic effects such as promoting autophagic flux, neuroprotection, and metabolic reprogramming. In animal model experiments, SG2 showed the ability to promote recovery in the AD model and improve learning abilities. This compound has been confirmed to have low toxicity, serving as a potential starting point for the development of AD drugs.
Article
Neurosciences
Yaqin Lu, Yusheng Yang, Wanqiang Chen, Nicole Du, Yansheng Du, Huiying Gu, Qi Liu
Summary: Minocycline and doxycycline, two second-generation tetracyclines, have different effects in protecting neurons against excitotoxicity. Minocycline can directly block excitotoxicity by inhibiting intracellular calcium concentration induced by NMDA or glutamate, while doxycycline is ineffective in this aspect.
Article
Cell Biology
Dmitry A. Sibarov, Zoia D. Zhuravleva, Margarita A. Ilina, Sergei I. Boikov, Yulia D. Stepanenko, Tatiana V. Karelina, Sergei M. Antonov
Summary: Na/K-ATPase plays a crucial role in maintaining ionic gradients and functioning as a signal transducer. Ouabain at subnanomolar concentrations provides neuroprotection against calcium overload and apoptosis. This study investigates the role of lipid rafts in the interactions between Na/K-ATPase, sodium-calcium exchanger (NCX), and N-methyl-D-aspartate receptors (NMDARs). Results showed that ouabain attenuated NMDA-evoked calcium responses and prevented an increase in mEPSC frequency, suggesting the involvement of cholesterol-rich membrane microdomains in these effects. It is concluded that cardiotonic steroids can regulate synaptic transmission and impact the efficacy of neurological medications.
Article
Multidisciplinary Sciences
Xiaocen Fan, Jiachen Song, Chaonan Ma, Yanbo Lv, Feifei Wang, Lan Ma, Xing Liu
Summary: This study found that increased norepinephrine release from the locus coeruleus to the medial prefrontal cortex during contextual fear conditioning is crucial for memory tagging and remote memory storage. It is regulated by the ventrolateral periaqueductal grey and can be promoted by activating beta1-adrenergic receptor signaling in juvenile mice.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
David Wasilewski, Nelson David Villalba-Moreno, Inke Stange, Markus Glatzel, Diego Sepulveda-Falla, Susanne Krasemann
Summary: This study improved an in vitro co-culture assay to investigate the impact of reactive astrocytes on neuronal morphology in the context of Alzheimer's disease (AD). The findings highlight the role of different cell types in AD pathology.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Seiji Ishii, Toru Sasaki, Shahid Mohammad, Hye Hwang, Edwin Tomy, Fahad Somaa, Nobuyuki Ishibashi, Hideyuki Okano, Pasko Rakic, Kazue Hashimoto-Torii, Masaaki Torii
Summary: Primary cilia play a crucial role in protecting immature neurons from environmental stress by activating signaling pathways that inhibit degeneration of dendritic arbors and caspase-mediated cleavage of cytoskeletal proteins in stress-exposed neurons.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Medicinal
Zixuan Cheng, Siaw San Hwang, Mrinal Bhave, Taufiq Rahman, Xavier Chee Wezen
Summary: In this study, a combination strategy of deep-learning-based QSAR modeling and hybrid-based consensus scoring was used to screen for potential inhibitors against PLK1 and p38 gamma. Compound 4 was identified as a potent PLK1 inhibitor that inhibited PLK1 activity and liver cancer cell growth in the nanomolar range. Compound 14 was found to inhibit both PLK1 and p38 gamma activities and showed promising inhibitory effects on human hepatocellular carcinoma and hepatoblastoma cells in vitro.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Stefania Demuro, Conall Sauvey, Shailesh K. Tripathi, Rita M. C. Di Martino, Da Shi, Jose A. Ortega, Debora Russo, Beatrice Balboni, Barbara Giabbai, Paola Storici, Stefania Girotto, Ruben Abagyan, Andrea Cavalli
Summary: The human kinome plays a crucial role in various pathways and its dysregulation is associated with central nervous system-related disorders. Simultaneously modulating multiple protein kinases through pharmacological approaches may lead to superior therapeutic effects compared to traditional single target, single drug approaches.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Francesco Di Palma, Sergio Decherchi, Fatima Pardo-Avila, Sauro Succi, Michael Levitt, Gunnar von Heijne, Andrea Cavalli
Summary: This study used all-atom molecular dynamics simulations to investigate the interactions between the XBP1u AP and the mammalian ribosome exit tunnel, shedding light on the ribosome stalling mechanism. The results provide an unprecedented atomistic picture of this biological process and offer insights into the key AP-ribosome interactions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Catia R. Lopes, Ines M. Amaral, Marlene F. Pereira, Joao P. Lopes, Daniela Madeira, Paula M. Canas, Rodrigo A. Cunha, Paula Agostinho
Summary: This study found that astrocytes play an important role in regulating hippocampal long-term depression (LTD) and long-term potentiation (LTP) in early Alzheimer's disease (AD). Additionally, it was discovered that astrocytes are responsible for the shift from LTD to LTP in AD conditions, suggesting that targeting astrocytes may help restore memory and synaptic plasticity deficits in early AD.
JOURNAL OF NEUROCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Tobias Muhlethaler, Lampros Milanos, Jose Antonio Ortega, Thorsten B. Blum, Dario Gioia, Bibhas Roy, Andrea E. Prota, Andrea Cavalli, Michel O. Steinmetz
Summary: This study developed an antitubulin small molecule, Todalam, through two rounds of chemical synthesis based on a crystallographic fragment screen. Todalam binds to a novel tubulin site, disrupts microtubule networks, induces cell death, and synergizes with vinblastine. It destabilizes microtubules by inhibiting the conformational switch in alpha-tubulin and sequestering tubulin dimers. This work demonstrates the importance of using tubulin-binding fragments for innovative antitubulin drug and chemical probe discovery campaigns.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Pedro Valada, Sofia Alcada-Morais, Rodrigo A. Cunha, Joao Pedro Lopes
Summary: Theobromine, a metabolite of caffeine, affects synaptic transmission and plasticity by antagonizing adenosine receptors, resulting in improved cognitive function and neuroprotection against disease-related conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ana Patricia Simoes, Francisco Q. Goncalves, Daniel Rial, Samira G. Ferreira, Joao Pedro Lopes, Paula M. Canas, Rodrigo A. Cunha
Summary: CD73 plays a key role in the regulation of fear memory and synaptic plasticity in the amygdala, suggesting it as a potential therapeutic target for interfering with abnormal fear-like emotional processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Pedro Valada, Sonja Hinz, Christin Vielmuth, Catia R. Lopes, Rodrigo A. Cunha, Christa E. Mueller, Joao Pedro Lopes
Summary: Inosine has neuroprotective effects by indirectly modifying the activity of adenosine receptors and controlling synaptic transmission and plasticity. It acts as a ligand of adenosine receptors with low affinity and shows higher affinity towards the rat A(3) receptor. The impact of inosine on synaptic transmission and plasticity is mediated by modification of extracellular levels of adenosine through equilibrative nucleoside transporters.
PURINERGIC SIGNALLING
(2023)
Article
Biochemistry & Molecular Biology
Catia R. Lopes, Andreia Oliveira, Ingride Gaspar, Matilde S. Rodrigues, Joana Santos, Eszter Szabo, Henrique B. Silva, Aangelo R. Tome, Paula M. Canas, Paula Agostinho, Rui A. Carvalho, Rodrigo A. Cunha, Ana Patricia Simoes, Joao Pedro Lopes, Samira G. Ferreira
Summary: Moderate caffeine intake can antagonize adenosine receptors and protect neurons without affecting behavior and synaptic plasticity. It increases the metabolic competence of synapses and enhances their antioxidant capacity.
Article
Biochemistry & Molecular Biology
Catia R. Lopes, Joana S. Silva, Joana Santos, Matilde S. Rodrigues, Daniela Madeira, Andreia Oliveira, Ana Moreira-de-Sa, Vanessa S. Lourenco, Francisco Q. Goncalves, Henrique B. Silva, Ana Patricia Simoes, Anabela P. Rolo, Paula M. Canas, Angelo R. Tome, Carlos M. Palmeira, Joao Pedro Lopes, Rodrigo A. Cunha, Paula Agostinho, Samira G. Ferreira
Summary: Alzheimer's disease predominantly affects women and is characterized by metabolic deregulation and synaptic failure. In a study on female APPswe/PS1dE9 mice, a model for early AD, it was found that these mice exhibited learning and memory deficits, increased anxiety-like behavior, and signs of fear generalization. The prefrontal cortex showed decreased long-term potentiation and reduced levels of sirtuin-1 and sestrin-2, while synaptic markers remained unchanged. However, activation of sirtuin-1 did not restore abnormal cortical plasticity in APP/PS1 female mice; instead, its inhibition increased plasticity. These findings suggest that mood and memory dysfunction in early AD may be associated with a decrease in synaptic plasticity and sirtuin-1 levels in the prefrontal cortex.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
S. Decherchi, G. Ciccotti, A. Cavalli
Summary: We address the problem of estimating free energy from the perspectives of regularization and Bayes estimation theory. By utilizing prior knowledge of the free energy, we reformulate the Bennett acceptance ratio method and present a numerical algorithm to solve it. Additionally, we provide a closed formula to estimate confidence in the prior. Finally, the derived estimators are tested on a toy model.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Riccardo Aguti, Mattia Bernetti, Stefano Bosio, Sergio Decherchi, Andrea Cavalli
Summary: Allostery is a crucial feature of biomolecular systems, impacting their functioning through intricate interplays between residues and protein structures. Computational approaches for correlation estimation provide insights into these complexes but can lead to different conclusions and outcomes. This article compares three computational methods on pharmaceutical targets, revealing consensus in some aspects but also highlighting the importance of different notions in identifying specific pockets and communications.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
S. Decherchi, A. Cavalli
Summary: Optimal transport theory is a growing field of mathematics with numerous applications. In this work, we utilize optimal transport for computational free energy estimation and demonstrate its effectiveness in optimizing barriers of alchemical transformations through analytical and simulation-based approaches.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Chemistry, Multidisciplinary
Francesco Di Palma, Carlo Abate, Sergio Decherchi, Andrea Cavalli
Summary: Drug discovery is challenging and prone to failure. Computational methods for identifying ligandable pockets are recommended due to their inexpensiveness and speed, especially when supported by machine learning methodologies. However, the outcome of these methods depends on the input data and the modeling assumptions made.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Catia R. Lopes, Francisco Q. Goncalves, Simao Olaio, Angelo R. Tome, Rodrigo A. Cunha, Joao Pedro Lopes
Summary: Adenosine regulates synaptic transmission and plasticity through A(1) and A(2A) receptors. Supramaximal activation of A(1)R blocks hippocampal synaptic transmission, and A(2A)R activation decreases A(1)R-mediated inhibition during high-frequency-induced LTP.
Article
Chemistry, Medicinal
Sarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli
Summary: Tyrosine kinases play critical roles in cellular machinery, and dysregulation of their active or inactive forms is associated with diseases like cancer. This study aimed to comprehensively understand the flexibility-activity relationships of tyrosine kinases, focusing on pockets and fluctuations. By conducting molecular dynamics simulations, pocket and residue fluctuation analysis, and using a complementary machine learning approach, we studied 43 different tyrosine kinases. We found that the inactive forms often exhibit increased flexibility, particularly at the DFG motif level. Notably, using long simulations and a decision tree, we identified a semi-quantitative fluctuation threshold of the DGF+3 residue, beyond which the kinase is more likely to be in the inactive form.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)