Article
Biology
Haitao Zhang, Xiaolei Cao, Mei Tang, Guoxuan Zhong, Yuan Si, Haidong Li, Feifeng Zhu, Qinghua Liao, Liuju Li, Jianhui Zhao, Jia Feng, Shuaifeng Li, Chenliang Wang, Manuel Kaulich, Fangwei Wang, Liangyi Chen, Li Li, Zongping Xia, Tingbo Liang, Huasong Lu, Xin-Hua Feng, Bin Zhao
Summary: The human kinome consists of 538 kinases that play essential roles in catalyzing protein phosphorylation. The annotation and visualization of the subcellular distribution of these kinases in the Kinome Atlas (KA) provide insights into their functions and mechanisms, including new kinase localizations and the role of liquid-liquid phase separation in kinase condensate formation. Despite limitations such as potential mislocalization, the subcellular map of the kinome can be utilized to enhance our understanding of regulatory mechanisms involving protein phosphorylation.
Article
Chemistry, Applied
Jia Gao, Shenyu Shi, Qiuying Li, Huili Ma
Summary: Room temperature phosphorescence (RTP) in organic aggregates depends on molecular conformation and packing, which pose challenges in understanding the mechanism of polymorphism-dependent RTP. In this study, different RTP lifetimes were observed in organic polymorphs of DOS compounds (DOS-O and DOS-S). By analyzing molecular and electronic structures, and decay dynamics of T(1) states, it was found that the decreased energy gap of T-1 states due to conformational variation is responsible for the shortened RTP lifetime from DOS-O to DOS-S. This was further supported by the good agreement between theory and experiment in RTP lifetime.
Article
Biochemistry & Molecular Biology
Amy E. Medlock, Wided Najahi-Missaoui, Mesafint T. Shiferaw, Angela N. Albetel, William N. Lanzilotta, Harry A. Dailey
Summary: Ferrochelatase is an important enzyme involved in catalyzing heme synthesis in humans, serving a regulatory and catalytic role in the pathway. Studies on its crystal structures, kinetic properties, and catalytic cycle have provided insights into its functions. However, questions regarding metal ion delivery, active site residue roles, and the catalytic mechanism remain open for further investigation.
BIOCHEMICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Marie Bonnin, Benedicte Favreau, Alexandre Soriano, Nathalie Leonhardt, Julie Oustric, Radia Lourkisti, Patrick Ollitrault, Raphael Morillon, Liliane Berti, Jeremie Santini
Summary: In this study, physiological and biochemical studies on salt stress tolerance were conducted on different citrus genotypes at the polyploidy level. It was found that tetraploid trifoliate orange (PO4x) and Cleopatra mandarin (CL4x) showed better photosynthetic and antioxidant capacities under salt stress compared to their respective diploids (PO2x and CL2x). Thus, tetraploidy may enhance salt stress tolerance in citrus.
Article
Pharmacology & Pharmacy
Yifei Xie, Penghui Yuan, Tianyu Heng, Lida Du, Qi An, Baoxi Zhang, Li Zhang, Dezhi Yang, Guanhua Du, Yang Lu
Summary: Tenoxicam is a new non-steroidal anti-inflammatory drug with superior efficacy and good tolerance. It exists in multiple tautomeric forms and exhibits different forms in cocrystals and salts. The research provides a simple rule to predict the form of Tenoxicam based on the pKa value of the coformer and validates it through experiments. This study is important for understanding the intermolecular interactions and properties of these cocrystals and salts.
Article
Construction & Building Technology
Hongwei Tian, Xiangming Kong, Xia Miao, Lingfei Jiang, Xiaofan Pang
Summary: The dispersing efficiency of PAA, PCE polymers, and AA-co-AMPS copolymers in fresh cement pastes was studied with a focus on their interactions with Ca2+ ions. The presence of side chains in PCE polymers inhibited the ion-bridging effect, while AA-co-AMPS copolymers demonstrated strong resistance against ion-crosslinking effects.
CONSTRUCTION AND BUILDING MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Rajkumar Misra, Thangavel Vijayakanth, Linda J. W. Shimon, Lihi Adler-Abramovich
Summary: In this study, the atomistic details of helical secondary structure formation and super helical assembly of two heptapeptides composed of sequentially arranged Phe residues were revealed using helix promoting Aib residues.
CHEMICAL COMMUNICATIONS
(2022)
Article
Materials Science, Multidisciplinary
Kang-Jia Wang, Jing-Hua Liu
Summary: The study investigates the nonlinear oscillators with coordinate dependent mass using He's frequency-amplitude formulation combined with the average residuals. The results show that this method is simple and effective, and can provide new perspectives for the study of nonlinear oscillator theory.
RESULTS IN PHYSICS
(2022)
Article
Chemistry, Applied
Yaqing Xiao, Yingnan Liu, Shufang Kang, Huaide Xu
Summary: This study found that incorporating cellulose nanocrystals (CNC) into soy protein isolate films can effectively improve the film properties, including tensile strength, barrier properties, and water resistance. The appropriate addition of CNC can promote the construction of a more homogeneous and compact film structure, while excessive addition may weaken the functional properties.
Review
Chemistry, Analytical
Muhammad Waris, Engin Kocak, Ekrem Murat Gonulalan, L. Omur Demirezer, Sedef Kir, Emirhan Nemutlu
Summary: Plant-based metabolomics studies aim to discover new active compounds, determine vegetation period, investigate adulteration, evaluate correlation activity and metabolite levels, and monitor quality control of medicinal plants. However, the chemical differences of primary and secondary metabolites in complex natural products present challenges for analysis, ranging from sample collection to preparation, and from analysis to metabolite annotation and quantification. A comprehensive evaluation of current and new trends in plant metabolomics helps researchers in designing their studies holistically.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Construction & Building Technology
Muhammad Riaz Ahmad, Mehran Khan, Aiguo Wang, Zuhua Zhang, Jian-Guo Dai
Summary: This study investigated the feasibility of using flue gas residues (FGR) and commercial sodium silicate (CSS) as hybrid activators (HA) for the preparation of alkali-activated materials (AAMs). The results showed that the use of hybrid activators led to the formation of more C-A-S-H gel compared to the control paste, which contained a higher amount of N-A-S-H gel. The analysis also revealed the presence of calcium-rich cross-linked gel (C-(N)-A-S-H) in all the pastes.
CONSTRUCTION AND BUILDING MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Janmejaya Rout, Bikash Chandra Swain, Suchismita Subadini, Padmaja Prasad Mishra, Harekrushna Sahoo, Umakanta Tripathy
Summary: This study investigated the binding of vitamin B12 to hemoglobin using optical spectroscopy and computational methods, revealing quenching of hemoglobin's intrinsic fluorescence and resulting conformational changes. The study may have implications for treating pernicious anemia, hereditary transcobalamin deficiency, and improving athletic performance.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Engineering, Chemical
Abolfazl Malti, Arash Kardani, Abbas Montazeri
Summary: The study reveals a reverse correlation between solidification time and amorphous content, with the process controlled by dislocation slip at temperatures from 600-1000 K and by surface diffusion and thermal twinning beyond 1000 K. Optimal parameters are identified as a combination of dislocation slip and surface diffusion at 1000 K with 100 ps sintering. Temperature-dependent MSD diagrams are monitored for a detailed analysis of sintering dynamics.
Article
Biochemistry & Molecular Biology
Andrey G. Baranovskiy, Alisa E. Lisova, Lucia M. Morstadt, Nigar D. Babayeva, Tahir H. Tahirov
Summary: This study reveals how the human primosome counts the length of RNA-DNA primers and terminates DNA elongation. The key regulator in this process is p58(C), which plays a crucial role in all steps of RNA-DNA primer synthesis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Arif Jamal Siddiqui, Vikash Kumar, Sadaf Jahan, Mohammed Merae Alshahrani, Ahmed Abdullah Al Awadh, Maqsood Ahmed Siddiqui, Walid Sabri Hamadou, Abdelmushin Abdelgadir, Juhi Saxena, Riadh Badraoui, Mejdi Snoussi, Mohd Adnan
Summary: Two drugs, C22 and C27, have been found to selectively inhibit human ELOVL1 enzyme, blocking the binding of long-chain fatty acids. This study provides important insights for the discovery and design of novel, selective, and potent ELOVL1 inhibitors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Jade Fogha, Julien Diharce, Alan Obled, Samia Aci-Seche, Pascal Bonnet
Article
Biochemistry & Molecular Biology
Nicolas Bosc, Christophe Muller, Laurent Hoffer, David Lagorce, Stephane Bourg, Carine Derviaux, Marie-Edith Gourdel, Jean-Christophe Rain, Thomas W. Miller, Bruno O. Villoutreix, Maria Miteva, Pascal Bonnet, Xavier Morelli, Olivier Sperandio, Philippe Roche
ACS CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Medicinal
Nada Ibrahim, Pascal Bonnet, Jean-Daniel Brion, Jean-Francois Peyrat, Jerome Bignon, Helene Levaique, Beatrice Josselin, Thomas Robert, Pierre Colas, Stephane Bach, Samir Messaoudi, Mouad Alami, Abdallah Hamze
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Chemistry, Applied
Soukaina Faarasse, Said El Kazzouli, Otmane Bourzikat, Stephane Bourg, Samia Aci-Seche, Pascal Bonnet, Franck Suzenet, Gerald Guillaumet
Summary: Direct and site-selective C5 and C7 palladium-catalyzed C-H arylations of 4-azaindazole N-oxide have been achieved, leading to the synthesis of potential medicinal compounds.
ADVANCED SYNTHESIS & CATALYSIS
(2021)
Article
Chemistry, Medicinal
Fiona M. Hunter, A. Patricia Bento, Nicolas Bosc, Anna Gaulton, Anne Hersey, Andrew R. Leach
Summary: The safety of marketed drugs is a significant concern, and the curated drug safety dataset in ChEMBL can help support a wide range of safety-related drug discovery questions, making it a valuable resource for drug development.
CHEMICAL RESEARCH IN TOXICOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Nicolas Bosc, Eloy Felix, Ricardo Arcila, David Mendez, Martin R. Saunders, Darren V. S. Green, Jason Ochoada, Anang A. Shelat, Eric J. Martin, Preeti Iyer, Ola Engkvist, Andreas Verras, James Duffy, Jeremy Burrows, J. Mark F. Gardner, Andrew R. Leach
Summary: The research team developed a consensus in silico model for identifying anti-malarial molecules and addressed the challenge of data integration by sharing QSAR models. They developed an open-source software platform and launched a website called MAIP for the wider community to freely use for predicting potential malaria inhibiting compounds.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Oliver Wieder, Melaine Kuenemann, Marcus Wieder, Thomas Seidel, Christophe Meyer, Sharon D. Bryant, Thierry Langer
Summary: This work introduces a novel GNN architecture, called D-GIN, which improves the accuracy of predicting molecular properties in drug discovery. By combining different sub-architectures and strategies, the model shows increased predictive power and addresses limitations in evaluating deep-learning models.
Article
Chemistry, Multidisciplinary
Laia Miret-Casals, Sander van de Putte, Dorien Aerssens, Julien Diharce, Pascal Bonnet, Annemieke Madder
Summary: In this study, a coiled-coil peptide dimer was used as a model system to investigate the reactivity of furan. Novel cross-link partners of furan warheads for site-specific cross-linking were discovered, and it was demonstrated that the activation of furan could lead to covalently connected coiled-coil motifs. The study also revealed the reaction of the activated furan warhead with cysteine and tyrosine, expanding the versatility of furan cross-link methodology.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sreenivas Avula, Xudan Peng, Xingfen Lang, Micky Tortorella, Beatrice Josselin, Stephane Bach, Stephane Bourg, Pascal Bonnet, Frederic Buron, Sandrine Ruchaud, Sylvain Routier, Cleopatra Neagoie
Summary: A library of simplified Lamellarin isosters, substituted indolo[2,3-c]quinolone-6-ones, was developed and evaluated for their inhibitory activity on Haspin kinase. Two derivatives exhibited good selectivity and interesting cell effects on osteosarcoma cell line.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Patrick Penner, Virginie Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey
Summary: Fragment-based drug design is a commonly used method in drug development, and growing fragments into viable ligands is a significant challenge. FastGrow is an application based on a shape search algorithm that can rapidly address this challenge and also offers additional features, making it a comprehensive structure-based modeling tool. Through evaluation in various scenarios and comparison with other software, FastGrow has demonstrated its competitiveness and effectiveness.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Medicinal
Sonia Ziada, Julien Diharce, Eric Raimbaud, Samia Aci-Seche, Pierre Ducrot, Pascal Bonnet
Summary: Drug-target residence time is a crucial factor in drug discovery, but determining the residence time cost-effectively in the early stages remains a challenge. This study presents an efficient computational protocol based on targeted molecular dynamics, which can rank drug candidates and provide insights into ligand-target dissociation mechanisms.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Rohit Arora, Joannes T. M. Linders, Samia Aci-Seche, Thomas Verheyen, Erika Van Heerde, Dirk Brehmer, Apirat Chaikuad, Stefan Knapp, Pascal Bonnet
Summary: The mutation V600E in B-Raf leads to mitogen activated protein kinase (MAPK) pathway activation, uncontrolled cell proliferation, and tumorigenesis. ATP competitive type I B-Raf inhibitors efficiently block the MAPK pathways in B-Raf mutant cells but induce conformational changes in the wild type B-Raf (wtB-Raf) kinase domain causing paradoxical hyperactivation. Type II inhibitors prevent heterodimerization by binding the kinase in the DFG-out conformation.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Barbara Zdrazil, Eloy Felix, Fiona Hunter, Emma J. Manners, James Blackshaw, Sybilla Corbett, Marleen de Veij, Harris Ioannidis, David Mendez Lopez, Juan F. Mosquera, Maria Paula Magarinos, Nicolas Bosc, Ricardo Arcila, Tevfik Kiziloren, Anna Gaulton, A. Patricia Bento, Melissa F. Adasme, Peter Monecke, Gregory A. Landrum, Andrew R. Leach
Summary: ChEMBL is a curated resource of bioactive molecules with drug-like properties. It has evolved significantly in size and diversity of data types over time. The inclusion of new datasets has expanded the bioactivity data available and added new features to ChEMBL.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Frederic Buron, Nuno Rodrigues, Thibault Saurat, Marie Aude Hiebel, Stephane Bourg, Pascal Bonnet, Reine Nehme, Philippe Morin, Nathalie Percina, Justine Corret, Beatrice Vallee, Remy le Guevel, Marie-Lise Jourdan, Helene Benedetti, Sylvain Routier
Summary: This study focuses on the synthesis, enzymatic activities, in silico docking, and cellular activities of various uncommon 2,4,7 trisubstituted pyrido[3,2-d]pyrimidines on PI3K and mTOR. By altering the substituents at the C-7 position, compounds with improved kinase efficiency were identified, with some showing promising activity on PI3K alpha. The most effective compounds induced micromolar cytotoxicity on cancer cell lines with overactivated PI3K pathway.
Article
Medicine, Research & Experimental
Katharine Briggs, Nicolas Bosc, Tima Camara, Carlos Diaz, Phil Drew, William C. Drewe, Jan Kors, Erik van Mulligen, Manuel Pastor, Francois Pognan, Jordi Ramon Quintana, Sirarat Sarntivijai, Thomas Steger-Hartmann
Summary: Pre-competitive data sharing in the pharmaceutical industry can reduce time and costs for bringing new drugs to market, improve toxicological prediction, and decrease animal usage. Applying the FAIR Guiding Principles can enhance the benefits of data sharing.
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION
(2021)