Article
Biochemistry & Molecular Biology
Vanya D. Barzilova, Josephine Drury, Bryony Rogers, Emily Thomas, Fareen Ahmed, Alice Bradfield, Hannan Al-Lamee, Dharani K. Hapangama
Summary: This study assessed the expression of nucleolin (NCL) in endometrial cancer (EC) and found that it is associated with tumor grading and prognosis. The study also identified dysregulated NCL-associated genes in EC. These findings suggest that NCL could be a potential target for diagnosis, risk stratification, and management of EC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kinjal Bhadresha, Sivakumar Prasanth Kumar, Jpan Brahmbhatt, Chirag Patel, Pujan Pandya, Nayan Jain, Rakesh Rawal
Summary: This study identified theaflavin-3-gallate as a promising natural inhibitor of Hsp90, which can significantly inhibit cell proliferation, induce cell death, reduce cell migration and colony formation in breast cancer cells, and downregulate the expression of several related genes. This compound has the potential to improve the efficacy of existing breast cancer therapies and overall survival of patients.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Biochemistry & Molecular Biology
C. Flores-Kossack, C. Munoz, N. Fuentes, K. Maisey
Summary: In this study, the TCR alpha beta/CD3 complex of rainbow trout was generated through in silico homology modeling, and the structure of different proteins and their potential interactions were characterized. The results show that the structural features described in mammalian TCR/CD3 are also present in the predicted model for trout. Several amino acid interactions between TCR alpha, TCR beta, CD3 gamma delta, and CD3 epsilon were highlighted. In silico structural analyses suggest that the trout TCR alpha beta complex would fit similarly to that described for mammals. These findings explore the implications of the modeled trout complex and leukocyte phenotypes, and further studies are needed to investigate the mechanisms involved.
MOLECULAR IMMUNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Arunima Singh
Summary: A coarse-grained model allows for the simulation of droplet formation using low-complexity RNA sequences.
Article
Oncology
Malin Ljunggren, Caroline E. Weibull, Gabriella Palmer, Emerik Osterlund, Bengt Glimelius, Anna Martling, Caroline Nordenvall
Summary: This population-based study found that women with synchronous metastatic colorectal cancer (mCRC) were less likely to receive metastatic surgery and had slightly higher all-cause mortality compared to men.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Engineering, Biomedical
Zumrat Usmanova, Emin Sunbuloglu
Summary: In this study, a new numerical approach was proposed to simulate long-term orthodontic tooth movement, involving external bone adaptation with strain energy density as the stimulus parameter and bone adaptation modeled by nodal movements at the bone-tooth interface. Contrary to conventional re-meshing algorithms, the proposed method only moves nodes without changing the initial mesh topology, which can accurately predict tooth movement values and validate various orthodontic treatment hypotheses.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2021)
Article
Plant Sciences
Mohammad Khalid, Mohammed H. Alqarni, Ambreen Shoaib, Muhammad Arif, Ahmed Foudah, Obaid Afzal, Abuzer Ali, Amena Ali, Saad S. Alqahtani, Abdulmalik S. A. Altamimi
Summary: The study demonstrated that the alcoholic fraction of S. mangifera fruit extract possesses beneficial effects on rheumatoid arthritis as well as anti-inflammatory potential, and can be used as a possible agent for novel target-based therapies for the management of arthritis. The in vitro and in vivo activities of the extract showed significant reduction in arthritis symptoms, paw diameters, and pro-inflammatory markers, indicating its potential for therapeutic use in arthritis. The molecular docking results suggest that the extract components have critical binding affinity with TNF-alpha, acting as a TNF-alpha antagonist.
Article
Pharmacology & Pharmacy
Shinde Bhagatsing Devidas, Shubham Nilkanth Rahmatkar, Rahul Singh, Nitisha Sendri, Rituraj Purohit, Damanpreet Singh, Pamita Bhandari
Summary: A new anthraquinone compound, 1-Hydroxy-5,5-dimethyl-5,6,7,8-tetrahydro-9,10-anthraquinone, isolated from ethylacetate extract of Juglans regia L., showed potent acetylcholinesterase inhibition activity and neuroprotective effects in various assays, suggesting its potential for ameliorating cognitive impairment.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Almerinda Agrelli, Niedja Fittipaldi Vasconcelos, Rayane Cristine Santos da Silva, Carina Lucena Mendes-Marques, Isabel Renata de Souza Arruda, Priscilla Stela Santana de Oliveira, Luzia Rejane Lisboa Santos, Audrey Nunes de Andrade, Ronald Rodrigues de Moura, Lucas Coelho Bernardo-Menezes, Natalia Pereira da Silva, Giovanna Machado
Summary: The study focused on using in silico methods to identify peptides with potential for improving osseointegration of TiO2 implants, by docking analysis and MD simulations. 82 promising peptides were discovered, and three showed the highest binding stability during the simulations, offering a more efficient and time-saving approach for in vitro studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Toxicology
Danlei Wang, Maartje H. Rietdijk, Lenny Kamelia, Peter J. Boogaard, Ivonne M. C. M. Rietjens
Summary: Developmental toxicity testing is traditionally animal-intensive, but a new in vitro-in silico approach, combining data from the mouse embryonic stem cell test and physiologically based kinetic modeling, successfully predicted the developmental toxicity of polycyclic aromatic hydrocarbons like benzo[a]pyrene. The study demonstrated the feasibility of using this approach to predict developmental toxicity of related PAHs without extensive animal testing, showing promising potential for future toxicology research.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Apsara Kavital, M. B. Hiremath, A. H. M. Vishwanath Swamy, Santosh B. Patil
Summary: This research investigates the hypoglycemic activity of Syzygium cumini seed extracts using in vitro, in vivo, and in silico methods. The results show that the extracts are able to inhibit both alpha-amylase and alpha-glucosidase enzymes, suggesting their potential use in the management of diabetes mellitus.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Medicine, Research & Experimental
Joseph Piscitelli, Bart Hens, Irena Tomaszewska, Lance Wollenberg, Kevin Litwiler, Mark McAllister, Micaela Reddy
Summary: In vitro, in vivo, and in silico data were generated to study the effect of food and coadministration with a proton-pump inhibitor (PPI) on Encorafenib, and to optimize the clinical dose and evaluate safety. The results showed that food had a minimal impact on the pharmacokinetics of Encorafenib, while coadministration with a PPI also had negligible effects. Modeling studies demonstrated complete absorption of Encorafenib when formulated as an amorphous solid dispersion. The TIM-1 and physiologically based pharmacokinetic model results were consistent with the observed clinical data, suggesting their potential as valuable tools for future research.
MOLECULAR PHARMACEUTICS
(2023)
Article
Medicine, Research & Experimental
Joseph Piscitelli, Bart Hens, Irena Tomaszewska, Lance Wollenberg, Kevin Litwiler, Mark McAllister, Micaela Reddy
Summary: In vitro, in vivo, and in silico data were generated to evaluate the effects of food and coadministration with a proton-pump inhibitor (PPI) on the oral absorption and efficacy of Encorafenib. The results showed that both food and coadministration with a PPI had no significant impact on the absorption and efficacy of the drug, indicating that no dose adjustment is necessary in clinical practice.
MOLECULAR PHARMACEUTICS
(2023)
Article
Pharmacology & Pharmacy
Jawad Khan, Gowhar Ali, Umer Rashid, Rasool Khan, Muhammad Saeed Jan, Rahim Ullah, Sajjad Ahmad, Sumra Wajid Abbasi, Atif Ali Khan Khalil, Robert D. E. Sewell
Summary: CHD demonstrated potential anti-nociceptive and anti-inflammatory properties, likely mediated through GABAergic and opioidergic interactions, and supported by COX-2 and 5-LOX enzyme inhibition as well as reduced expression of pro-inflammatory cytokines.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Karuppusamy Arunachalam, Amilcar Sabino Damazo, Antonio Macho, Monica Steffi Matchado, Eduarda Pavan, Fabiana de Freitas Figueiredo, Darley Maria Oliveira, Carrie A. Duckworth, Parimelazhagan Thangaraj, Marco Leonti, Domingos Tabajara de Oliveira Martins
Summary: Canthin-6-one has anti-inflammatory and antioxidant effects on colitis, reducing intestinal damage and improving inflammatory markers. It has the potential therapeutic benefit for inflammatory bowel disease by regulating molecular immune mediators.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Melissa Dolan, Michalis Mastri, Amanda Tracz, James G. Christensen, Gurkamal Chatta, John M. L. Ebos
Article
Biochemical Research Methods
Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullino, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sebastien Benzekry
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Oncology
Masanori Oshi, Eriko Katsuta, Li Yan, John M. L. Ebos, Omar M. Rashid, Ryusei Matsuyama, Itaru Endo, Kazuaki Takabe
Editorial Material
Oncology
Joseph Ciccolini, Sebastien Benzekry, Fabrice Barlesi
BRITISH JOURNAL OF CANCER
(2020)
Article
Pharmacology & Pharmacy
Sebastien Benzekry
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2020)
Article
Oncology
Sebastien Benzekry, Mathieu Grangeon, Melanie Karlsen, Maria Alexa, Isabella Bicalho-Frazeto, Solene Chaleat, Pascale Tomasini, Dominique Barbolosi, Fabrice Barlesi, Laurent Greillier
Summary: By studying the determinants of response to immune-checkpoint inhibition in advanced non-small cell lung cancer patients, it was found that hemoglobin levels and performance status were the strongest predictors, and neutrophil-to-lymphocyte ratio was also associated with outcome.
Article
Multidisciplinary Sciences
Anne Rodallec, Cristina Vaghi, Joseph Ciccolini, Raphaelle Fanciullino, Sebastien Benzekry
Summary: This study identified the most accurate formula for estimating tumor volume in xenografted mice with human breast cancer cells. The formula 1/6 π x L x W x (L + W)/2 is recommended for tumors under 1500mm(3).
Article
Biochemical Research Methods
Arturo Alvarez-Arenas, Wilfried Souleyreau, Andrea Emanuelli, Lindsay S. Cooley, Jean-Christophe Bernhard, Andreas Bikfalvi, Sebastien Benzekry
Summary: This article presents a method to extract more information from distant metastasis-free survival (DMFS) curves using a mathematical model. The model depends on parameters that quantify tumor growth and metastatic dissemination, and the parameters are determined using least-squares minimization. The study found that including the percentage of patients with metastasis at diagnosis was critical to the robust estimation of the parameters. The impact and identifiability of covariates and their coefficients in the model were also studied.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Oncology
Veronica Torres-Estay, Michalis Mastri, Spencer Rosario, Patricia Fuenzalida, Carolina E. Echeverria, Emilia Flores, Anica Watts, Javier Cerda-Infante, Viviana P. Montecinos, Paula C. Sotomayor, Julio Amigo, Carlos Escudero, Francisco Nualart, John M. L. Ebos, Dominic J. Smiraglia, Alejandro S. Godoy
Summary: This study investigates the paracrine crosstalk between vascular endothelial cells and prostate cancer cells. The results indicate that endothelial cells secrete signals that promote the proliferation and growth of prostate cancer cells and selectively increase the migration, invasion, and metastatic potential of aggressive prostate cancer cells. Molecular analyses show that endothelial cells induce epigenetic changes in migratory pathways in aggressive prostate cancer cells. The findings suggest that the interaction between endothelial cells and prostate cancer cells may play an important role in the progression of prostate cancer.
Article
Computer Science, Interdisciplinary Applications
Celestin Bigarre, Francois Bertucci, Pascal Finetti, Gaetan Macgrogan, Xavier Muracciole, Sebastien Benzekry
Summary: This study proposes a novel mathematical model to predict the risk of metastatic relapse in early-stage breast cancer patients. By using mixed-effects modeling, the researchers identified two mathematical parameters representing growth and dissemination abilities. They found that Ki67 and Thymidine Kinase-1 were associated with growth, while nodal status and Plasminogen Activator Inhibitor-1 were associated with dissemination.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Oncology
Sebastien Benzekry, Coline Sentis, Carole Coze, Laetitia Tessonnier, Nicolas Andre
Summary: A mechanistic model of metastasis in HRNB was established, using patient-specific parameters and clinical variables, to improve survival prediction and refine patient stratification. The addition of a computational biomarker significantly enhanced the prediction of overall survival, showing promising results for prognosis ability.
JCO CLINICAL CANCER INFORMATICS
(2021)
Article
Oncology
Chiara Nicolo, Cynthia Perier, Melanie Prague, Carine Bellera, Gaetan Macgrogan, Olivier Saut, Sebastien Benzekry
JCO CLINICAL CANCER INFORMATICS
(2020)
Article
Pharmacology & Pharmacy
Benjamin K. Schneider, Arnaud Boyer, Joseph Ciccolini, Fabrice Barksi, Kenneth Wang, Sebastien Benzekry, Jonathan P. Mochel
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2019)
Article
Oncology
Michalis Mastri, John M. L. Ebos
MOLECULAR & CELLULAR ONCOLOGY
(2019)