Article
Chemistry, Multidisciplinary
Nicolai A. Aksenov, Alexander V. Aksenov, Lidiya A. Prityko, Dmitrii A. Aksenov, Daria S. Aksenova, Mezvah A. Nobi, Michael Rubin
Summary: This research paper presents a facile and highly efficient method for synthesizing 2-(3-oxoindolin-2-ylidene)acetonitriles from 4-(2-aminophenyl)-4-oxo-2-phenylbutanenitriles. The method involves nucleophilic intramolecular cyclization and oxidation of the aniline moiety. Overall, this modification improves yields and expands the scope of the reaction.
Article
Biochemistry & Molecular Biology
David Jakubec, Petr Skoda, Radoslav Krivak, Marian Novotny, David Hoksza
Summary: This article presents significant enhancements to PrankWeb, including more accurate evolutionary conservation estimation and the ability to carry out LBS predictions using the AlphaFold model database.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Priya Das, Aditi Mukherjee, Subrata Adak
Summary: This study demonstrates the enrichment of Leishmania GAPDH in extracellular vesicles secreted during infection, which inhibits TNF-alpha expression in macrophages and affects disease progression. The findings highlight the crucial role of GAPDH in parasitic infection.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kristina Tugaeva, Andrey A. Sysoev, Anna A. Kapitonova, Jake L. R. Smith, Phillip Zhu, Richard B. Cooley, Alfred A. Antson, Nikolai N. Sluchanko
Summary: Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins that play a role in virus replication. Using genetic code expansion, it is shown that 14-3-3 binding is triggered by phosphorylation at specific sites on the nucleoprotein. Crystal structures and biochemical data reveal that 14-3-3 binding obstructs a region of the nucleoprotein and inhibits its dephosphorylation. The strength of the 14-3-3/nucleoprotein interaction may be linked to the replicative fitness of the virus.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Dipankar Roy, Andriy Kovalenko
Summary: The 3D-RISM-KH molecular solvation theory plays a crucial role in multiscale modeling, successfully applied in various areas such as protein self-assembly and binding, solvation energy calculations, etc. This enhanced simulation technique has proven applications and can achieve accelerated computation by modifying solvation layers and closure relations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Valentina Noemi Madia, Davide Ialongo, Elisa Patacchini, Cecile Exertier, Lorenzo Antonelli, Gianni Colotti, Antonella Messore, Valeria Tudino, Francesco Saccoliti, Luigi Scipione, Andrea Ilari, Roberta Costi, Roberto Di Santo
Summary: This research focused on the design and synthesis of new compounds structurally related to compound 1, and evaluated their inhibition activity on trypanothione reductase (TR) from Leishmania infantum. The results showed that compounds 2a and 2b were the most potent inhibitors, suggesting the potential of an additional aromatic ring for enzymatic inhibition. Further studies are needed to optimize the activity of these compounds through structure-activity relationships.
Article
Chemistry, Physical
Christopher Paslack, Chandan K. Das, Jurgen Schlitter, Lars Schaefer
Summary: This study focused on analyzing the entropy of water molecules in biomolecules, finding that the decrease in entropy of water molecules in the active site after inhibitor binding is due to changes in hydrogen bonding and stiffening of the hydrogen-bonding network. Additionally, the spectral density calculations used in entropy calculations enable the assignment of changes to specific vibrational modes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Oncology
Mirijam Schaefer, Marie Luise Semmler, Thoralf Bernhardt, Tobias Fischer, Vinodh Kakkassery, Robert Ramer, Martin Hein, Sander Bekeschus, Peter Langer, Burkhard Hinz, Steffen Emmert, Lars Boeckmann
Summary: This review discusses the genetic landscape of squamous cell carcinoma and the potential use of indirubin-based small molecules in cancer therapy. It shows that these small molecules can inhibit cancer cell proliferation by targeting specific genes, thereby providing a potential treatment option for cancer.
Article
Chemistry, Multidisciplinary
Adrian L. Orjuela, Francisco Nunez-Zarur, Jorge Ali-Torres
Summary: Iron complexes are important in biological processes and neurological disorders. The calculation of the standard reduction potential of iron complexes is challenging. This study presents a computational protocol that provides good results compared to experimental values and other methods.
Article
Biochemistry & Molecular Biology
Rafael M. Oliveira, Thaise L. Teixeira, Cassiano C. Rodrigues, Aline A. da Silva, Bruna C. Borges, Rebecca T. S. Brigido, Samuel C. Teixeira, Marlus A. Dos Santos, Joao Paulo S. Servato, Debora de O. Santos, Marcelo J. B. Silva, Luiz R. Goulart, Claudio da Silva
Summary: The study revealed the critical role of gal-3 in the host response to infection by L. (L.) amazonensis, controlling parasite invasion, replication, and formation of endocytic vesicles. Mice with gal-3 deficiency showed an exacerbated inflammatory response.
Article
Chemistry, Applied
Alessandro Triolo, Fabrizio Lo Celso, Javier Perez, Olga Russina
Summary: The mechanism of efficient solvation of cyclodextrins in green solvents was investigated, and it was found that 1-ethyl-3-methylimidazolium acetate is an excellent solvent for native cyclodextrins. Simulation techniques revealed the intimate interactions between the ionic species and cyclodextrins, providing an excellent solvation environment.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemistry & Molecular Biology
Khadidja Adjir, Amina C. Berrekhchi-Berrahma, Majda Sekkal-Rahal
Summary: This study investigates the structure-biological activity relationship of indirubin and its derivatives using computational methods. The results show that the derivatives have easier interaction with the environment compared to the parent compound. The relationship between absorption spectra and chemical structure is also discussed.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Priyanka Bose, Nofar Baron, Durgeshwar Pullaiahgari, Anat Ben-Zvi, Michal Shapira
Summary: Most cellular mRNAs in eukaryotes are translated through a cap-dependent pathway. Leishmania, a parasitic protozoan, has a wide range of cap-binding complexes that play various roles in survival. LeishIF3d, a protein in Leishmania, has been found to have a non-canonical cap-binding activity that is required for translation, although it does not offer an alternative translation pathway in the mammalian life form of the parasite.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biophysics
Rohit Joshi, Pavel Pohl, Dita Strachotova, Petr Herman, Tomas Obsil, Veronika Obsilova
Summary: Nedd4-2, a ubiquitin ligase, is involved in the endocytosis and degradation of target molecules through interactions with 14-3-3 proteins. The binding of 14-3-3 induces structural rearrangement of Nedd4-2, affecting the mobility and emission properties of certain domains. In contrast, the active site of the HECT domain becomes more mobile upon 14-3-3 binding.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Medicinal
Xiaoyang Qu, Lina Dong, Jinyan Zhang, Yubing Si, Binju Wang
Summary: This study incorporates the features extracted from protein-bound waters into machine learning-based scoring functions using the HydraMap method. The results show that this approach consistently improves the performance of the scoring functions, including their scoring, ranking, and docking power.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
George Lambrinidis, Cedric Gouedard, Sotiria Stasinopoulou, Angeliki Angelopoulou, Vassiliki Ganou, Aggeliki K. Meligova, Dimitra J. Mitsiou, Panagiotis Marakos, Nicole Pouli, Emmanuel Mikros, Michael N. Alexis
Summary: Raloxifene analogues bearing a bulky basic side chain amino group showed higher ER antagonism in post-menopausal endometrium than raloxifene itself, particularly compound 13b. Compound 13b demonstrated potential for providing safer endometrial treatment for menopausal syndrome.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Anezia Kourkoulou, Iliana Zantza, Konstantina Foti, Emmanuel Mikros, George Diallinas
Summary: Members of the NAT family are symporters specific for the uptake of purines, pyrimidines, or L-ascorbic acid. This study reveals the roles of partially conserved residues in determining the specificity of the UapA transporter. Results show that UapA specificity is genetically modifiable, allowing for speculation on the flexible mechanism of transport.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Medicinal
Marina Bantzi, Fiona Augsburger, Jeremie Loup, Yan Berset, Sofia Vasilakaki, Vassilios Myrianthopoulos, Emmanuel Mikros, Csaba Szabo, Christian G. Bochet
Summary: A study identified a novel 3-MST inhibitor HMPSNE with micromolar potency, along with derivatives, showing inhibitory effects on colon cancer cell proliferation.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Cell Biology
Zoi Spyropoulou, Angelos Papaspyropoulos, Nefeli Lagopati, Vassilios Myrianthopoulos, Alexandros G. Georgakilas, Maria Fousteri, Athanassios Kotsinas, Vassilis G. Gorgoulis
Summary: Cockayne syndrome is a DNA repair syndrome with symptoms like neurodegeneration and premature aging, mainly caused by mutations in the CSB gene. Besides its role in DNA repair pathways, CSB is also involved in DNA transcription, mitochondrial biology, telomere maintenance, and p53 regulation.
Article
Biochemical Research Methods
Stavros Beteinakis, Anastasia Papachristodoulou, Emmanuel Mikros, Maria Halabalaki
Summary: NMR-based metabolic profiling is widely used in food and plant sciences, but appropriate pre-processing procedures greatly affect the obtained metabolic profile. This study provides a detailed guide for untargeted NMR-based metabolic profiling of table olives, showing that pre-processing and sample preparation stages have a significant impact on the metabolic profile and spectral quality.
PHYTOCHEMICAL ANALYSIS
(2022)
Article
Cell Biology
Despina Smirlis, Florent Dingli, Valentin Sabatet, Aileen Roth, Uwe Knippschild, Damarys Loew, Gerald F. Spaeth, Najma Rachidi
Summary: Leishmaniasis is a severe public health problem caused by Leishmania, a protozoan parasite. This study identified the signaling kinase L-CK1.2 as an important factor for the survival and host subversion of the parasite. Using a combination of phosphatase treatment, in vitro kinase assay, and SILAC-based mass spectrometry, the researchers identified 225 host substrates of L-CK1.2 and revealed their enrichment in biological processes related to viral and symbiotic interaction, actin cytoskeleton organization, and apoptosis. These findings provide important insights into the mechanism of host subversion by Leishmania and other intracellular pathogens.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Microbiology
Dimitra K. Toubanaki, Antonia Efstathiou, Evdokia Karagouni
Summary: This review summarizes the current knowledge of gene expression responses to nervous necrosis virus (NNV) infection in different fish species based on transcriptomic analysis data. The review describes the infected host species, developmental stages, and tissues, and highlights the genes and pathways that are most affected by viral infection. These transcriptome studies provide insights into the host reaction mechanisms to viral infections, enabling the development of healthier and sustainable aquaculture systems.
Article
Cell Biology
Ioanna Dagla, Aikaterini Iliou, Dimitra Benaki, Evagelos Gikas, Emmanuel Mikros, Tina Bagratuni, Efstathios Kastritis, Meletios A. Dimopoulos, Evangelos Terpos, Anthony Tsarbopoulos
Summary: Vaccination is highly effective in mitigating the COVID-19 pandemic. However, individual immune responses to mRNA vaccines vary significantly. Metabolomics analysis reveals distinct plasma metabolic profiles associated with immune response levels, indicating the potential of certain metabolites as predictive markers for vaccine response.
Article
Chemistry, Medicinal
Maria A. Theodoropoulou, Giorgos S. Koutoulogenis, Linlin Zhang, Ifigeneia Akrani, Emmanuel Mikros, Rolf Hilgenfeld, George Kokotos
Summary: The development of novel agents to combat COVID-19 is crucial. This study focused on identifying an inhibitor that can simultaneously target both SARS-CoV-2 M-pro and PLA(2). Evaluation of various PLA(2) inhibitors revealed that the known potent inhibitor GK241 also weakly inhibits SARS-CoV-2 M-pro. Molecular docking and dynamics calculations provided insights into the interaction between GK241 and SARS-CoV-2 M-pro. The structure of 2-Oxoamide GK241 may serve as a lead for the development of dual PLA(2) and SARS-CoV-2 M-pro inhibitors.
Article
Biochemistry & Molecular Biology
Karim Zuhra, Maria Petrosino, Barkha Gupta, Theodora Panagaki, Marco Cecconi, Vassilios Myrianthopoulos, Roger Schneiter, Emmanuel Mikros, Tomas Majtan, Csaba Szabo
Summary: Epigallocatechin gallate (EGCG) is the main bioactive component of green tea and it inhibits cystathionine beta-synthase (CBS), a major H2S-generating enzyme. EGCG blocks a substrate access channel to pyridoxal-5'-phosphate and inhibits cellular H2S production in cancer cells and Down syndrome fibroblasts. This potent inhibition of CBS-derived H2S production may contribute to the pharmacological effects of EGCG in various pathophysiological conditions.
NITRIC OXIDE-BIOLOGY AND CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Argyro Vontzalidou, Sapfo-Maria Dimitrakoudi, Konstantinos Tsoukalas, Grigoris Zoidis, Eliza Chaita, Evanthia Dina, Christina Cheimonidi, Ioannis P. Trougakos, George Lambrinidis, Alexios-Leandros Skaltsounis, Emmanuel Mikros, Nektarios Aligiannis
Summary: A number of stilbenoid and chalconoid derivatives were synthesized and evaluated for their ability to modulate tyrosinase activity and scavenge free radicals. The results showed that certain compounds exhibited potent tyrosinase inhibitory activity, while others enhanced the enzymatic activity. Moreover, some compounds demonstrated significant anti-melanogenic effects or melanogenic effects, as well as strong free radical scavenging activity.
Article
Biochemistry & Molecular Biology
Mohan Ghorasaini, Konstantina Ismini Tsezou, Aswin Verhoeven, Yassene Mohammed, Panayiotis Vlachoyiannopoulos, Emmanuel Mikros, Martin Giera
Summary: In this study, a workflow combining nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis was developed for lipid analysis in human plasma samples. The study found good agreement and correlation between the two platforms in lipid quantification and diagnostic performance. The research also provided insight into lipoprotein and lipid interactions and disease relevance.
Article
Food Science & Technology
Gabriela Belen Lemus Ringele, Stavros Beteinakis, Anastasia Papachristodoulou, Evangelos Axiotis, Emmanuel Mikros, Maria Halabalaki
Summary: Honey is a natural, healthy commodity and is considered one of the most complex foods produced by nature. NMR-based metabolite profiling combined with chemometrics was used in the quality control of Greek honeys, and STOCSY was employed for the first time as a tool for honey biomarker identification.
Meeting Abstract
Pharmacology & Pharmacy
D. Nikolakis, A. Banos, A. Filia, V Myrianthopoulos, P. Garantziotis, P. Verginis, E. Mikros, D. Boumpas
EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY
(2022)