Article
Chemistry, Physical
Ekaterina Maximova, Eugene B. Postnikov, Anastasia Lavrova, Vladimir Farafonov, Dmitry Nerukh
Summary: In this study, the dissociation of ligand isoniazid from a protein catalase was investigated using MD simulations, with a novel method proposed to extrapolate dissociation times to the zero-force limit for comparison with experimental values. The calculated dissociation time was found to quantitatively match the experimental value, despite the extrapolation over multiple orders of magnitude in time.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Hayato Akimoto, Yoshihiro Uesawa, Shigeru Hishinuma
Summary: The study investigated the relationship between the kinetic and thermodynamic binding properties of antihistamines, identifying specific descriptors that determine the rate constants of association and dissociation. The findings suggest that while binding enthalpy and entropy may influence k(off) values, there is no significant relationship with k(on) values. QSAR analyses indicated that descriptors FASA_H and vsurf_CW2 play a crucial role in determining the kinetic and thermodynamic binding properties of antihistamines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Emil Bjorklund, Anna du Rietz, Patrik Lundstrom
Summary: PLIS is an open-source software for determination of protein-ligand dissociation constants, which can be used to characterize biological processes or to shed light on biophysical aspects of interactions. In addition to analyzing experimental data, PLIS includes functionality for generating synthetic data, useful for understanding how different parameters affect the data in order to better analyze experiments.
Article
Chemistry, Analytical
Rouba Nasreddine, Reine Nehme
Summary: Microscale thermophoresis (MST) is a sensitive biophysical tool that allows rapid and accurate determination of the dissociation constant (K-d) between enzymes and small molecules, aiding in the study of binding affinity between biomolecules. The study demonstrated that hyaluronidase maintained enzymatic activity after fluorescent labelling, but showed no affinity with flavonoid compounds under the tested conditions.
MICROCHEMICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Kristof Bozovicar, Barbara Jenko Bizjan, Anze Meden, Jernej Kovac, Tomaz Bratkovic
Summary: The development of a selective short linear peptide ligand of the IgG Fc region, capable of capturing all four IgG subclasses, was reported. This ligand was discovered through in vitro directed evolution and displayed high affinity for IgG, comparable to commercially employed protein A-based resin, after characterization and validation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Claire Andre, Yves Claude Guillaume
Summary: A simple and rapid Nano LC method has been developed for screening arginase inhibitors, using immobilized biotinylated arginase on a neutravidin functionalized nano HPLC capillary column. The miniaturized capillary column significantly decreases the required enzyme amount and achieves high enzyme yield, with reduced non-selective adsorption and excellent repeatability. The immobilized arginase retains high activity over time, making it suitable for recognizing a variety of inhibitor molecules and plant extracts.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Naveen Kumar, Rahul Kaushik, Kam Y. J. Zhang, Vladimir N. N. Uversky, Upasana Sahu, Richa Sood, Sandeep Bhatia
Summary: Multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with flexible amino acid substitutions in the spike protein's receptor binding domain (RBD) continue to evolve. These substitutions alter the binding of SARS-CoV-2 to the human angiotensin-converting enzyme 2 (hACE2) receptor and affect host fitness, transmissibility, and efficacy against therapeutics and vaccines. A computational framework was developed to predict the binding strength of SARS-CoV-2 variants RBD to hACE2 and neutralizing antibodies (NAbs), allowing for the assessment of fitness and the development of effective antibody therapeutics. Analysis of several variants of concern (VOCs) revealed enhanced affinity between VOCs RBD and hACE2. Additionally, the binding affinity of the Omicron variant's RBD towards most RBD-directed NAbs was reduced, consistent with experimental data. By studying the atomic contacts between RBD and NAbs, potential NAbs were identified that may be effective against the Omicron variant.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Abbas Khan, AsfandYar Waheed Randhawa, Ali Raza Balouch, Naila Mukhtar, Abrar Mohammad Sayaf, Muhammad Suleman, Taimoor Khan, Shahid Ali, Syed Shujait Ali, Yanjing Wang, Anwar Mohammad, Dong-Qing Wei
Summary: A computational study identified four compounds that showed potential as antiviral agents against the omicron variant of SARS-CoV-2. These compounds demonstrated good antiviral properties, stability, and structural compactness.
Article
Biology
Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei
Summary: A sequence-based virtual screening method utilizes natural language processing algorithms and optimized deep K-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. It outperforms current methods in multiple datasets and has significant potential in drug discovery and protein engineering.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sebastian Friedrich, Claudia Sieber, Bjoern Drobot, Satoru Tsushima, Astrid Barkleit, Katja Schmeide, Thorsten Stumpf, Jerome Kretzschmar
Summary: The complex formation of Eu(III) and Cm(III) with three coordinating ligands NTA(3-), EDTA(4-), and EGTA(4-) was studied. The complex formation constants were determined by NMR and TRLFS, and the thermodynamic parameters were obtained by ITC. The results showed that the three ligands formed 1:1 complexes with Eu(III) and Cm(III).
Article
Chemistry, Multidisciplinary
Monika Kaminska, Pierrick Bruyat, Carole Malgorn, Marion Doladilhe, Evelyne Cassar-Lajeunesse, Carole Fruchart Gaillard, Melissa De Souza, Fabrice Beau, Robert Thai, Isabelle Correia, Andrzej Galat, Dimitris Georgiadis, Olivier Lequin, Vincent Dive, Sarah Bregant, Laurent Devel
Summary: Activity-based probes can discriminate active enzymes from inactive counterparts, targeting metalloproteases through reversible inhibitors with photo-crosslinkers. Novel probes were developed to covalently modify active matrix metalloproteases without external trigger, allowing for nanogram-scale reactions with recombinant MMPs in complex proteomes. This ligand-directed chemistry successfully labeled active MMP-12 secreted by eukaryote cells, with potential applications for other metalloproteases in unresolved proteomic profiling in vivo.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Environmental Sciences
Rahul Kaushik, Naveen Kumar, Kam Y. J. Zhang, Pratiksha Srivastava, Sandeep Bhatia, Yashpal Singh Malik
Summary: This study investigates the interaction between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and different vertebrate species. The findings suggest that the spike protein of SARS-CoV-2 can bind to ACE2 receptors in a wide range of species, indicating a broad host range and the potential for cross-species transmission and viral evolution. Furthermore, the study identifies genetic determinants that may differentiate susceptible from resistant host species and highlights the importance of surveillance programs to prevent future outbreaks by identifying susceptible hosts.
ENVIRONMENTAL RESEARCH
(2022)
Article
Chemistry, Medicinal
Viet-Khoa Tran-Nguyen, Guillaume Bret, Didier Rognan
Summary: This study conducted an unbiased evaluation of four scoring functions on a high-confidence experimental screening dataset, revealing that rescoring based on simple interaction fingerprints or interaction graphs outperforms advanced machine learning and deep learning scoring functions in most cases. It also highlights the tendency of deep learning methods to predict affinity values within a narrow range centered on the mean value of training samples, and suggests the importance of pre-existing binding modes in detecting the most potent binders.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Analytical
Xiaoshuang He, Xianliang Xu, Yue Sui, Ke Xu, Sicen Wang
Summary: The study established an α(1A)/CMC method for screening active compounds from Tetradium ruticarpum fruits and analyzing the binding characteristics with the receptor. Dehydroevodiamine was identified as a potential active compound through this method.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Review
Chemistry, Physical
Claudio Dalvit, Isabel Gmur, Philip Robler, Alvar D. Gossert
Summary: NMR spectroscopy is widely used for hit identification, but its use in determining the dissociation constant of tight binders is limited. This article provides a theoretical analysis and practical guidelines for determining the binding affinity of strong ligands using NMR experiments. Various methods are discussed, with emphasis on general approaches like competition experiments.
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
(2023)
Article
Surgery
Lorena van den Bogaart, Brian M. Lang, Dionysios Neofytos, Adrian Egli, Laura N. Walti, Katia Boggian, Christian Garzoni, Christoph Berger, Manuel Pascual, Christian van Delden, Nicolas J. Mueller, Oriol Manuel, Matteo Mombelli
Summary: This study describes the epidemiology and outcomes of bacterial foodborne infections in solid organ transplant (SOT) recipients. The infections occurred late post-transplant and were associated with significant morbidity.
AMERICAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Immunology
Janina Linnik, Mohammedyaseen Syedbasha, Hans-Michael Kaltenbach, Dominik Vogt, Yvonne Hollenstein, Lukas Kaufmann, Nathan Cantoni, Sabine Ruosch-Girsberger, Antonia M. S. Mueller, Urs Schanz, Thomas Pabst, Georg Stuessi, Maja Weisser, Joerg Halter, Joerg Stelling, Adrian Egli
Summary: Patients after hematopoietic stem cell transplantation exhibit heterogeneous antibody responses to seasonal influenza vaccination, with factors such as type of immunosuppressive treatment, absolute lymphocyte count, and donor relationship playing a role. While HSCT patients required 2 vaccine doses for adequate responses, they can elicit potent antibody responses over time. However, factors like an unrelated donor, low lymphocyte counts, and certain treatments can lower the odds of responding to vaccination.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Geriatrics & Gerontology
Philipp Kohler, Salome N. Seiffert, Simone Kessler, Gabriela Rettenmund, Eva Lemmenmeier, Laetitia Qalla Widmer, Oliver Nolte, Helena M. B. Seth-Smith, Werner C. Albrich, Baharak Babouee Flury, Celine Gardiol, Stephan Harbarth, Thomas Muenzer, Matthias Schlegel, Christiane Petignat, Adrian Egli, Delphine Hequet
Summary: This study aimed to assess the burden of ESBL-producing Enterobacterales in Swiss long-term care facilities, describe the molecular epidemiology, identify clusters of resistant pathogens, and determine factors associated with colonization. The study found a low prevalence of ESBL-E in Swiss LTCF residents, but identified clusters of residents with identical pathogens within the same institution. The use of PPIs was the only modifiable factor associated with carriage of ESBL producers.
JOURNAL OF THE AMERICAN MEDICAL DIRECTORS ASSOCIATION
(2022)
Article
Chemistry, Multidisciplinary
Marawan Ahmed, Aravindhan Ganesan, Khaled Barakat
Summary: Small molecules targeting hPD-L1 protein have emerged as a promising new generation of immune checkpoints' inhibitors. This study provides an in-depth computational structural analysis of the interactions between five small molecules and hPD-L1, shedding light on the dynamics and molecular mechanisms driving their complex formation. The results highlight the importance of a terminal phenyl ring in hPD-L1 inhibitors.
Letter
Biophysics
Mihaela Sava, Veronika Battig, Sabine Gerull, Jakob R. Passweg, Nina Khanna, Christian Garzoni, Bernhard Gerber, Nicolas J. Mueller, Urs Schanz, Christoph Berger, Yves Chalandon, Christian van Delden, Dionysios Neofytos, Susanne Stampf, Fabian C. Franzeck, Maja Weisser
BONE MARROW TRANSPLANTATION
(2023)
Article
Biochemistry & Molecular Biology
Mowaffaq Adam Ahmed Adam, Laina Zarisa Muhd Kamal, Mahibub Kanakal, Dinesh Babu, Saad Sabbar Dahham, Yasser Tabana, Bronwyn Lok, Brittany M. Bermoy, Muhammad Amir Yunus, Leslie Thian Lung Than, Khaled Barakat, Doblin Sandai
Summary: This study investigated the effects of the fungal toxin AB1 on breast cancer cells and normal breast cells, and found that AB1 can increase the risk of breast cancer development by altering gene expression and epigenetic levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Javier E. Fernandez, Helena M. B. Seth-Smith, Patrice Nordmann, Adrian Egli, Andrea Endimiani, Vincent Perreten
Summary: This study discovered a novel multidrug resistance plasmid pJEF1-OXA-181, which carries carbapenemase and aminoglycoside resistance genes. It highlights the risk of multidrug resistance plasmids spreading in the healthcare system and calls for continuous monitoring of multidrug-resistant bacteria in high-risk patients.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biology
Maryam Jama, Marawan Ahmed, Anna Jutla, Carson Wiethan, Jitendra Kumar, Tae Chul Moon, Frederick West, Michael Overduin, Khaled H. Barakat
Summary: This study utilized computational tools to screen over 6 million compounds and identified three potent allosteric inhibitors of SHP2. The binding affinities of these inhibitors to SHP2 were measured and found to be in the nanomolar range, suggesting their potential as improved allosteric inhibitors of SHP2.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Biology
Bronwyn Lok, Dinesh Babu, Yasser Tabana, Saad Sabbar Dahham, Mowaffaq Adam Ahmed Adam, Khaled Barakat, Doblin Sandai
Summary: The guava tree has long been used in traditional medicine to treat various ailments. Recent studies have shown that it exhibits anticancer activity, making it a potential alternative or adjuvant treatment for human cancers. In vitro and in vivo studies have demonstrated that extracts from the guava plant selectively suppress the growth of human cancer cells without harming normal cells. The availability of the plant also makes it a viable option for cancer treatment in developing countries.
Letter
Biophysics
Katharina Baur, Andreas Buser, Lukas T. Jeker, Nina Khanna, Heinz Laeubli, Dominik Heim, Jan C. Dirks, Corinne C. Widmer, Thomas Volken, Jakob R. Passweg, Andreas Holbro
BONE MARROW TRANSPLANTATION
(2023)
Article
Immunology
Dionysios Neofytos, Susanne Stampf, Linard D. Hoessly, Matilde D'Asaro, Gael Nguyen Tang, Katia Boggian, Cedric Hirzel, Nina Khanna, Oriol Manuel, Nicolas J. Mueller, Christian Van Delden
Summary: This retrospective study analyzed data from the Swiss Transplant Cohort Study registry to describe the epidemiology of bacteremia in solid organ transplant recipients (SOTr) during the first year post-transplant. The incidence of bacteremia varied among different organ transplant types and has decreased in recent years. Risk factors for bacteremia included age, diabetes, cardiopulmonary diseases, transplant complications, rejection, and fungal infections.
OPEN FORUM INFECTIOUS DISEASES
(2023)
Article
Immunology
Matteo Mombelli, Dionysios Neofytos, Uyen Huynh-Do, Javier Sanchez-Cespedes, Susanne Stampf, Dela Golshayan, Suzan Dahdal, Guido Stirnimann, Aurelia Schnyder, Christian Garzoni, Reto M. Venzin, Lorenzo Magenta, Melanie Schonenberger, Laura Walti, Cedric Hirzel, Aline Munting, Michael Dickenmann, Michael Koller, John-David Aubert, Jurg Steiger, Manuel Pascual, Thomas F. Mueller, Mace Schuurmans, Christoph Berger, Isabelle Binet, Jean Villard, Nicolas J. Mueller, Adrian Egli, Elisa Cordero, Christian van Delden, Oriol Manuel
Summary: The use of MF59-adjuvanted or high-dose influenza vaccine in solid-organ transplant recipients was safe and resulted in a higher vaccine response rate.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Ophthalmology
Nan-Ji Lu, Hendrik Koliwer-Brandl, Mark Hillen, Adrian Egli, Farhad Hafezi
Summary: This study aimed to compare the efficacy of riboflavin/UV-A light and rose bengal/green light in treating Staphylococcus aureus and Pseudomonas aeruginosa infections. The results demonstrated that rose bengal/green light had significantly higher bacterial killing ratios compared to riboflavin/UV-A light.
TRANSLATIONAL VISION SCIENCE & TECHNOLOGY
(2023)
Article
Medicine, General & Internal
Alix T. Coste, Adrian Egli, Jacques Schrenzel, Beatrice Nickel, Andrea Zbinden, Reto Lienhard, Alexis Dumoulin, Martin Risch, Gilbert Greub
Summary: The IVDR regulation poses a major challenge for diagnostic microbiology laboratories due to its complexity and risks. The emergence of new pathogens further complicates the regulation, negatively impacting the development of new diagnostic tests. Additionally, the regulation affects the availability and costs of diagnostic tests, posing a risk to public health.
Article
Microbiology
T. C. Scheier, J. Franz, M. Boumasmoud, F. Andreoni, B. Chakrakodi, B. Duvnjak, A. Egli, W. Zingg, A. Ramette, A. Wolfensberger, R. D. Kouyos, S. D. Brugger
Summary: This study evaluated the application of FT-IR spectroscopy in VREfm outbreak investigations. The results showed that FT-IR spectroscopy had reproducible basic performance, and its readouts showed high agreement with WGS analysis in clinical outbreak investigations. FT-IR spectroscopy had a higher discriminatory power than MLST in outbreak investigations. Therefore, FT-IR spectroscopy is a promising technique that can assist in outbreak investigations with an affordable cost and a turnaround time of less than one day.
MICROBIOLOGY SPECTRUM
(2023)
