Article
Chemistry, Analytical
Jingjing Xu, Qiaoli Yang, Pei Wang, Dan Wu, Xiaohan Yang, Wei Chen, Song Gao, Shenqi Wang
Summary: In this study, an affinity binding based enzyme immobilization strategy was employed to assemble β-galactosidase onto T4 phage for the development of a specific sensing probe for Escherichia coli detection. The assay based on this β-gal T4 phage showed enhanced stability and substrate affinity and was able to quantitatively detect bacteria in water within 2 hours.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Organic
P. K. Hashim, Hisham M. Dokainish, Nobuyuki Tamaoki
Summary: We serendipitously discovered that chaperonin GroEL has the ability to hydrolyze ONPG, a well-known substrate of the enzyme β-galactosidase. The hydrolysis of ONPG by GroEL follows typical enzyme kinetics. Our experiments and molecular docking studies indicate that ONPG binds to the ATP binding site of GroEL.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Food Science & Technology
Zhenshang Xu, Can Li, Yanxin Ye, Ting Wang, Susu Zhang, Xinli Liu
Summary: Transcriptome sequencing revealed the gene expression difference of Lactiplantibacillus plantarum in glucose and lactose medium, identifying that beta-galactosidase LacLM plays a major role in lactose utilization, providing a theoretical foundation for the growth and metabolism of Lp. plantarum in lactose medium.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jennifer M. Podgorski, Krista Freeman, Sophia Gosselin, Alexis Huet, James F. Conway, Mary Bird, John Grecco, Shreya Patel, Deborah Jacobs-Sera, Graham Hatfull, Johann Peter Gogarten, Janne Ravantti, Simon J. White
Summary: Many double-stranded DNA viruses, including tailed bacteriophages and herpesviruses, use the HK97-fold in their major capsid protein. The evolution of capsid structural stability within the actinobacteriophages has been investigated using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and AlphaFold predictions. The actinobacteriophage major capsid proteins can be classified into 15 groups based on their HK97-fold.
Article
Multidisciplinary Sciences
Marc A. Beal, Matthew J. Meier, Angela Dykes, Carole L. Yauk, Iain B. Lambert, Francesco Marchetti
Summary: This study provides a comprehensive and detailed map of amino acid residues affecting the structure and catalytic activity of the beta-gal enzyme, based on the analysis of lacZ mutations.
Article
Biochemistry & Molecular Biology
Keisuke Fukunaga, Yohei Yokobayashi
Summary: In this study, a novel library-vs-library in vitro selection strategy was developed to select synthetic and orthogonal RNA-RBP pairs. The selected pairs exhibited picomolar affinity and >4000-fold selectivity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Sungu Kim, Aparna Krishnamurthy, Pooja Kasiviswanathan, Baskar Ganapathysubramanian, Robbyn K. Anand
Summary: This study demonstrates the use of droplets and ion concentration polarization to rapidly lyse breast cancer cells and enrich low-abundance intracellular analytes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xiaowan Han, Xiangchuan Meng, Xiang Wang, Shan Leng, Qian Liu, Leilei Zhang, Pingping Li, Qingyang Zhang, Hai-Yu Hu
Summary: A new excited-state intramolecular proton transfer-delayed fluorescence (ESIPT-DF) approach was reported to construct analyte-stimulated DF probes. These new classes of ESIPT-DF luminophores, including HBT-PXZ and HBT-PTZ, exhibited significant ESIPT and DF characters. Furthermore, a caged probe HBT-PXZ-Ga was developed and applied to investigate the influence of metal ions on beta-gal activity.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Claudia D'Ercole, Matteo De March, Gianluca Veggiani, Sandra Oloketuyi, Rossella Svigelj, Ario de Marco
Summary: A new adhiron phage display library was created and successfully used to select binders against antigens with different characteristics, resulting in isolated binders specifically targeting membrane epitopes of plant cells. These adhirons exhibited strong binding affinity and were suitable for various experimental applications.
Article
Biochemistry & Molecular Biology
Linnea Charlotta Hjelm, Hanna Lindberg, Stefan Stahl, John Lofblom
Summary: Affibody molecules are small affinity proteins with excellent properties. A new type of protein scaffold based on a dimeric form of affibodies has been developed, which has a distinct secondary structure content and mode of binding. The scaffold forms a tunnel-like cavity upon binding, encapsulating the target peptide. Selections from a high-complexity phage-displayed library using this scaffold resulted in the identification of high-affinity binders that effectively inhibit amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Christian Fink, Sebastian Beblawy, Andreas M. Enkerlin, Lucas Muhling, Largus T. Angenent, Bastian Molitor
Summary: The study successfully implemented genetic tools for Methanothermobacter thermautotrophicus Delta H, including shuttle vectors, neomycin resistance cassette, and cryptic plasmid, and demonstrated heterologous gene expression and DNA transfer between Escherichia coli and Methanothermobacter thermautotrophicus Delta H. The research findings laid the foundation for optimizing methane production and high-value platform chemicals production.
Article
Biochemistry & Molecular Biology
Xuguo Duan, Shuyue Luan
Summary: This study successfully expressed the natural intracellular beta-galactosidase (lacZBa) from Bacillus aryabhattai extracellularly in Bacillus subtilis, achieving high yield in secretion. The expression of lacZBa in B. subtilis showed improved acid resistance, pH stability, and thermostability compared to E. coli. The optimal medium composition was determined using single-factor experiments and response surface methodology, resulting in significantly enhanced extracellular expression of beta-galactosidase.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Bruna Coelho de Andrade, Adriano Gennari, Gaby Renard, Brenda Da Rolt Nervis, Edilson Valmir Benvenutti, Tania Maria Haas Costa, Sabrina Nicolodi, Nadya Pesce da Silveira, Jocelei Maria Chies, Giandra Volpato, Claucia Fernanda Volken de Souza
Summary: This study synthesized iron magnetic nanoparticles functionalized with histidine and nickel for the immobilization of His-tagged recombinant enzymes, particularly beta-galactosidase. The immobilized enzyme showed increased substrate affinity and thermal stability, leading to efficient lactose hydrolysis with high recovery rates. The nanoparticles demonstrated potential applications in oriented immobilization of other high-molecular-weight enzymes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biology
Phil Huss, Anthony Meger, Megan Leander, Kyle Nishikawa, Srivatsan Raman
Summary: The study systematically dissected the functional role of every residue in the tip domain of T7 phage RBP. Substitution patterns revealed host-specific differences and molecular adaptation to individual hosts. Gain-of-function and host-constricting variants were discovered, showcasing the therapeutic utility of engineered T7 variants against a urinary tract pathogen.
Article
Genetics & Heredity
Igor Bychkov, Antonina Kuznetsova, Galina Baydakova, Leonid Gorobets, Vladimir Kenis, Alena Dimitrieva, Alexandra Filatova, Vyacheslav Tabakov, Mikhail Skoblov, Ekaterina Zakharova
Summary: This article presents a unique case of pure MBD associated with the insertion of a mobile genetic element. The study identifies the molecular genetic mechanism of pathogenesis and demonstrates the potential of blocking cryptic exon to restore normal splicing, opening up possibilities for personalized genetic therapy.
NPJ GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Prateek Pathak, Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The present investigation estimated the electron properties of EGFR proteins-ligand complexes using AlteQ approach and established the relationship between electron properties and pharmacological activity. The study found that the inhibitory activity of EGFR is closely related to intermolecular contacts between protein and ligands.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Vladislav Naumovich, Maria Grishina, Jurica Novak, Prateek Pathak, Vladimir Potemkin, Mohd Shahbaaz, Magda H. Abdellattif
Summary: This study investigates the interaction between human dihydrofolate reductase (hDHFR) and inhibitors, aiming to identify factors that can reduce side effects and enhance drug activity. Through calculation of electronic properties and statistical analysis, the researchers found that changes in volume and electron number correlated with hDHFR inhibition potency. Molecular dynamics simulations were also used to gain deeper insights into the structural inhibition. The AlteQ approach allowed for the quantitative evaluation of factors influencing activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Prem Prakash Sharma, Sumit Kumar, Kumar Kaushik, Archana Singh, Indrakant K. Singh, Maria Grishina, Kailash C. Pandey, Pushpendra Singh, Vladimir Potemkin, Poonam, Geeta Singh, Brijesh Rathi
Summary: Plasmepsin V is an essential protease for the survival of the malaria parasite Plasmodium falciparum, with inhibition showing potential as a drug target. Through molecular docking, a new compound has been identified as a potent inhibitor, which warrants further experimental validation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Jurica Novak, Hrvoje Rimac, Shivananda Kandagalla, Prateek Pathak, Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The study identified a more favorable allosteric binding site on the SARS-CoV-2 3CL protease, which could be a better target for non-covalent inhibitors to prevent dimerization and activation. The tyrosine kinase inhibitors radotinib and nilotinib, used for leukemia treatment, showed potential binding to this allosteric site, as confirmed by molecular dynamics simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shivananda Kandagalla, Jurica Novak, Sharath Belenahalli Shekarappa, Maria A. Grishina, Vladimir A. Potemkin, Bhimanagoud Kumbar
Summary: Kyasanur forest disease (KFD) is a tick-borne, neglected tropical disease caused by KFD virus (KFDV). This study evaluated the effectiveness of FDA approved drugs and natural compounds against KFDV proteins using in silico drug repurposing method.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Mohd Shahbaaz, Dmitry A. Maslov, Aleksey A. Vatlin, Valery N. Danilenko, Maria Grishina, Alan Christoffels
Summary: In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical infrastructures.
Article
Chemistry, Medicinal
Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The aim of this study was to determine the significance of the 3CLpro enzyme of SARS-CoV-2 as a target for COVID-19 and evaluate the accuracy of drug modeling methods. The authors developed a model using the AlteQ approach to assess the reliability of 3CLpro complexes with ligands, which showed high correlation coefficients and can be utilized to determine the reliability of docked 3CLpro complexes with ligands.
FUTURE MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Prateek Pathak, Vikas Kumar, Habibullah Khalilullah, Maria Grishina, HariOm Singh, Amita Verma
Summary: The study demonstrates that debelalactone can protect tissues, alleviate chronic hepatic inflammation and oxidative stress induced by diethyl nitrosamine in Wistar rats. It significantly reduces parameters associated with liver and non-liver functions, and improves body weight of treated animals. Moreover, debelalactone restores antioxidant markers and inflammatory mediators to normal levels, reduces liver tissue abnormalities and inflammation, and inhibits precancerous cells.
Review
Chemistry, Medicinal
Ankit Kumar Singh, Adarsh Kumar, Harshwardhan Singh, Pankaj Sonawane, Harshali Paliwal, Suresh Thareja, Prateek Pathak, Maria Grishina, Mariusz Jaremko, Abdul-Hamid Emwas, Jagat Pal Yadav, Amita Verma, Habibullah Khalilullah, Pradeep Kumar
Summary: Cancer is a complex disease, and the efficacy of conventional anticancer drugs varies. The hybrid approach of combining two drugs into a single molecule shows potential in improving treatment efficacy and reducing drug resistance. Recent research has identified promising hybrid molecules with anticancer properties. This study provides valuable knowledge for researchers working on complex diseases like cancer.
Article
Biochemistry & Molecular Biology
Ashok Kumar Mandal, Samrat Paudel, Anisha Pandey, Parasmani Yadav, Prateek Pathak, Maria Grishina, Mariusz Jaremko, Abdul-Hamid Emwas, Habibullah Khalilullah, Amita Verma
Summary: The study investigated the antioxidant and anticancer activities of Psidium guajava L. essential oil, demonstrating its potential therapeutic value against breast cancer. The bioactive compounds in the oil showed promising properties in inhibiting tumor growth and exhibited drug likeness properties according to ADME analysis, suggesting their potential for novel drug discovery.
Review
Chemistry, Medicinal
Adarsh Kumar, Ankit Kumar Singh, Harshwardhan Singh, Veena Vijayan, Deepak Kumar, Jashwanth Naik, Suresh Thareja, Jagat Pal Yadav, Prateek Pathak, Maria Grishina, Amita Verma, Habibullah Khalilullah, Mariusz Jaremko, Abdul-Hamid Emwas, Pradeep Kumar
Summary: Cancer is a major healthcare challenge worldwide, calling for the development of safer and target-specific anticancer drugs. This study summarizes the use of nitrogen-containing heterocycles in cancer treatment, providing insights into their pharmacological properties and mechanisms of action.