Article
Biochemistry & Molecular Biology
Yuri N. Antonenko, Marta I. Jedrzejczyk, Tatyana I. Rokitskaya, Ljudmila S. Khailova, Elena A. Kotova, Adam Huczynski
Summary: A series of SAL derivatives targeting mitochondria were synthesized, and compound 5 exhibited promising anticancer and antimicrobial activity with high permeability on lipid membranes.
BIOELECTROCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Liu-Yi Liu, Tian-Zhu Ma, You-Liang Zeng, Wenting Liu, Hang Zhang, Zong-Wan Mao
Summary: A novel class of G4-binding organic-platinum hybrids, L-1-cispt and L-1-transpt, were designed with spatial matching for G4 binding and G4 DNA reactivity for binding site locking. The study revealed that L-1-cispt and L-1-transpt mediated genomic dysfunction could activate the RIG-I pathway and induce immunogenic cell death. In vivo experiments demonstrated that using L-1-cispt/L-1-transpt-treated cells as therapeutic vaccines stimulated a robust immune response and effectively inhibited tumor growth. These findings highlight the importance of rational combination of spatial recognition and covalent locking in G4-targeting drug design and their potential in immunotherapy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Marc Farag, Cedric Messaoudi, Liliane Mouawad
Summary: ASC-G4 is an algorithm that calculates the advanced structural characteristics of G-quadruplexes (G4). It determines the intramolecular G4 topology and resolves the ambiguity in guanine glycosidic configuration. The algorithm shows that using C3' or C5' atoms is more appropriate than P atoms for calculating groove width in G4, and that minimum groove width is a better measure of available space. ASC-G4 was applied to 207 G4 structures, guiding the calculations. The ASC-G4 website allows users to upload their G4 structures and obtain information on topology, loop types and lengths, snapbacks and bulges, guanine distribution, glycosidic configuration, groove widths, minimum groove widths, tilt and twist angles, backbone dihedral angles, and relevant atom-atom and atom-plane distances for structure evaluation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Polymer Science
Cheng Deng, Hai Yang, Simin Liu, Zhiyong Zhao
Summary: In this study, two types of DNA-dendrimer amphiphiles were successfully constructed, including the G-quadruplex-dendrimer hybrid (G20-Den) and single-stranded DNA-dendrimer hybrid (D20-Den). Both of them self-assembled into nanofibers with a length of several micrometers in MES buffer, and the diameter of G20-Den nanofibers was smaller than that of D20-Den nanofibers due to the compact stacking of G-quadruplex formed in G20-Den hybrids. The catalytic properties of G20-Den nanofiber/hemin, as well as the single-stranded G20/hemin system, were investigated, and they exhibited higher catalytic peroxidation activity than D20-Den nanofiber/hemin. Furthermore, the recycle of these nanofibers can be simply achieved through simple ultrafiltration.
Article
Biochemistry & Molecular Biology
Dao Lin, Yongqi Ke, Hongjia Chen, Yinlong Zhang, Xinjing Tang, Wei Cui, Xiangjun Li, Yujian He, Li Wu
Summary: The control of DNA assembly systems on cells is crucial for precise targeted therapies. In this study, a controllable DNA self-assembly system based on the regulation of G-quadruplex DNA topology by a reduction-sensitive azobenzene ligand is reported. The ligand can induce a complete change of G4 topology in a tissue-specific manner, allowing control of the self-assembly of G4-functionalized DNAs on cells.
Article
Biochemistry & Molecular Biology
Tatyana I. Rokitskaya, Alexander M. Firsov, Ljudmila S. Khailova, Elena A. Kotova, Yuri N. Antonenko
Summary: In this study, the ability of the ionophoric antibiotic salinomycin to perform cation/ H+-exchange was studied by measuring electrical potential on planar bilayer lipid membranes and by examining the fluorescence response of a pH-sensitive dye in liposomes. The results showed that salinomycin has a higher selectivity for potassium and calcium ions, and much lower binding affinity for sodium and lithium ions. These findings can contribute to the understanding of the anti-tumor activity and selective cytotoxicity of salinomycin towards cancer stem cells.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Chemistry, Physical
Ana R. Monteiro, Catarina I. Ramos, Leandro M. O. Lourenco, Sara Fateixa, Joana Rodrigues, Maria G. P. M. S. Neves, Tito Trindade
Summary: The aggregation of phthalocyanines (Pcs) can be weakened by the presence of graphene oxide (GO), which affects their fluorescence. Non-covalently assembled Pcs on GO can be slowly released for long-term detection of G-quadruplexes (G4).
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Valeria Libera, Federico Bianchi, Barbara Rossi, Francesco D'Amico, Claudio Masciovecchio, Caterina Petrillo, Francesco Sacchetti, Alessandro Paciaroni, Lucia Comez
Summary: This study found that during the thermal melting process of G4 structure, the hydrogen-bonded network of water molecules undergoes rearrangement, which is closely related to the DNA rearrangement. Understanding the structural properties of the solvent can contribute to a better understanding of the interaction between G4s and ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Chemical
Ziting Zhu, Hongjian Wang, Chenliang Cao, Jiyu Zou, Meidi Wang, Zhiming Zhang, Yuhan Wang, Yu Cao, Fusheng Pan, Yu Chen, Zhongyi Jiang
Summary: Covalent organic frameworks (COFs) are demonstrated as promising membrane materials for hydrogen peroxide (H2O2) enrichment. By modulating the composition of mixed linkers, the pore size of COF membranes can be tuned for selective separation of water and H2O2. Additionally, introducing hydrophilic linkers enhances the water capture ability of the membranes.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Sifan Chen, Changjia Zhu, Weipeng Xian, Xinyu Liu, XiaoLong Liu, Qinghua Zhang, Shengqian Ma, Qi Sun
Summary: The study presents a facile strategy to fabricate angstrom-sized functional pores by incorporating ionic elements into three-dimensional covalent organic framework channels. The resulting membranes exhibit excellent permselectivity and low membrane resistance, showing potential for harvesting salinity gradient energy. Additionally, a reverse electrodialysis device coupled with positive and negative dye encapsulated COF membranes achieved a power density of up to 51.4 W m(-2), surpassing the commercialization benchmark.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Julien Marquevielle, Aurore De Rache, Brune Vialet, Estelle Morvan, Jean-Louis Mergny, Samir Amrane
Summary: The Caenorhabditis elegans model has provided insights into the role of G-quadruplexes in genomic instability. Telomeric sequences in C. elegans show similarities to those in humans, but even small changes in these sequences can have significant effects on the folded G-quadruplex structure. This study determined the structure of the C. elegans telomeric sequence, revealing an intramolecular two G-tetrads basket type G-quadruplex structure with a C-T base pair in the diagonal loop. The findings shed light on the telomeric structure of the widely used C. elegans animal model.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Xuechen Wang, Xinrui Wang, Shengnan Wei, Shuo Yao, Liang Zhang, Juan Li, Chao Zhao, Juan Wang
Summary: A colorimetric sensor based on hybridization chain reaction (HCR) and G-quadruplex has been developed for the detection of Staphylococcus aureus. The sensor enables rapid and sensitive quantification of S. aureus and can be combined with a smartphone application for on-site detection.
MICROCHEMICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Natalia Bohalova, Jean-Louis Mergny, Vaclav Brazda
Summary: G-quadruplexes are non-B secondary structures with regulatory functions and therapeutic potential. Recent improvements in sequencing methods have allowed for the completion of the first human chromosome assembly, revealing a higher number of G-quadruplex forming sequences than previously thought. This highlights the importance of accurate sequencing in identifying regulatory regions for potential therapeutic interventions.
Article
Engineering, Chemical
Guiliang Li, Wen Wang, Yang Liu, Qile Fang, Na Lu, Jiaping Chen, Shuting Xu, Fu Liu
Summary: This study presents ultrafast water transport and solar-cleaning properties of graphene oxide membranes integrated with Prussian Blue@Covalent Triazine Framework as active mega cubes. The intercalated active mega cubes expand the boundary between graphene oxide and mega cube crystal face, enhancing the photocatalytic activity and stable permeance for organic molecules. The photothermal intensified photocatalysis contributes to foulants degradation, leading to higher reaction rate constant compared to graphene oxide membranes.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Immunology
Sandipan Chakraborty
Summary: This study decodes the effect of key mutations N501Y and E484K in SARS-CoV2 mutants B.1.1.7, B.1.351, and P.1 on the host receptor ACE2 and neutralizing antibody B38 recognition. The mutations enhance the binding affinity to ACE2 while reducing the affinity to neutralizing antibody B38.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Chemistry, Physical
Sucharita Dey, Ankita Saha, Prince Kumar, Chirantan Kar, Sandipan Chakraborty, Pradip K. Sukul
Summary: Picric acid is a dangerous environmental pollutant due to its high solubility in water, posing threats to the environment and public health. The synthesis of water soluble 1,8-naphthalimide (ANDI) and its multimodal sensing applications for nitro explosives such as picric acid (PA) has shown high selectivity and sensitivity, making it a potential material for low cost and light weight explosive sensors in the future.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2022)
Article
Biochemical Research Methods
Ananta Gorai, Ritapa Chaudhuri, Titas Kumar Mukhopadhyay, Ayan Datta, Jyotirmayee Dash
Summary: This study demonstrates the design and synthesis of PNA-like scaffolds incorporating thiazole rings as modified bases. The modified PNA trimer shows selective recognition and high stabilization potential for specific DNA structures, and it effectively suppresses target gene expression by targeting the promoter G4. This research highlights the potential of modified PNAs as flexible tools for selective targeting of noncanonical nucleic acids and modulating gene function.
BIOCONJUGATE CHEMISTRY
(2022)
Editorial Material
Chemistry, Medicinal
Sandipan Chakraborty
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sandipan Chakraborty, Aditi Saha, Chiranjeet Saha, Sanjana Ghosh, Trisha Mondal
Summary: The recent surge in COVID-19 cases can be attributed to the emergence of omicron variants. By studying the binding affinities of different classes of RBD-specific antibodies, this study reveals that omicron variants achieve antibody escape abilities through specific mutations at immunogenic hotspots. This has important implications for vaccine therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sandipan Chakraborty, Sanjana Ghosh, Trisha Mondal
Summary: By combining evolutionary bioinformatics and molecular dynamics simulation, researchers identified the origin of the ACE2 usage trait in coronaviruses and found that SARS-CoV2 has a different lineage from other human ACE2-user CoVs. The high binding affinity of SARS-CoV2 to ACE2 is primarily due to the formation of more hydrogen bonds.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Chemistry, Physical
Srijon Ghosh, Sandipan Chakraborty, Arnab Ghosh, Kritiman Marjit, Goutam Ghosh, Amitava Patra
Summary: A detailed understanding of the relaxation dynamics of conjugated polymer nanoparticles (PNPs) is important for optimizing their light-harvesting applications. In this study, the intermolecular interactions and ultrafast relaxation processes of poly(3-hexylthiophene-2,5-diyl) (P3HT) PNPs were investigated using molecular dynamics simulations and ultrafast transient absorption spectroscopy. The results showed that increasing the polymer chain concentration led to enhanced intermolecular interactions, which significantly affected the vibrational relaxation and energy funneling processes.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Multidisciplinary
Ritapa Chaudhuri, Thumpati Prasanth, Jyotirmayee Dash
Summary: This study demonstrates for the first time that noncanonical DNA can be used to direct the synthesis of gene modulators through macrocyclization-like reactions. The planar G-quartets present in DNA G-quadruplexes provide a reaction platform for the synthesis of peptidomimetic macrocycles. By utilizing the innate fluorescence of the formed macrocycle, its cellular localization and formation process can be monitored. This research opens up new possibilities for targeted therapeutic applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Prasun Pal, Sandipan Chakraborty, Biman Jana
Summary: This study explores the correlation between solvent accessible surface areas and hydrogen bonds within proteins, finding a linear relationship. The number of protein-water hydrogen bonds per unit solvent accessible surface area is consistent across different protein structure classes, while the number of intramolecular hydrogen bonds varies. The study also shows a linear decrease in solvation free energy with solvent accessible surface area. This research provides a basis for designing new proteins with improved functionality.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Prasun Pal, Rahul Aich, Sandipan Chakraborty, Biman Jana
Summary: This study provides an atomistic overview of the differential antifreeze activities of different classes of antifreeze proteins (AFPs) and identifies ice surface coverage as a critical factor in ice growth inhibition.
Article
Biochemistry & Molecular Biology
Harshavardhan Bhuktar, Sharda Shukla, Kumar Reddy Kakularam, Srikanth Battu, Manupati Srikanth, Susmita Srivastava, Raghavender Medishetti, Pooja Ram, P. C. Jagadish, Mahaboobkhan Rasool, Sandipan Chakraborty, Nooruddin Khan, Pallu Reddanna, Srinivas Oruganti, Manojit Pal
Summary: The lipoxygenase enzyme 12R-LOX plays a critical role in immune modulation and can be a potential drug target for skin related inflammatory diseases. In this study, 2-aryl quinoline derivatives were designed and synthesized as inhibitors of 12R-LOX. Compound 4a and 7b emerged as potential inhibitors, showing selectivity towards 12R-LOX.
BIOORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Rahul Aich, Prasun Pal, Sandipan Chakraborty, Biman Jana
Summary: This study investigates the mechanism of ice nucleation by ice-nucleating proteins (INPs) using molecular dynamics simulations. The hydration layer around the ice-nucleating surface of an INP is found to be highly ordered, with slower dynamics compared to a non-ice-binding protein. The ice-binding surface of INP shows more evident ordering of the hydration layer compared to an antifreeze protein. The structural synergies observed in the INP make it a better template for ice nucleation than AFP, although both efficiently bind to the ice surface.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Medicinal
Sandipan Chakraborty, Chiranjeet Saha
Summary: Researchers have developed a screening platform to identify SARS-CoV-2 mutants with enhanced ACE2 binding abilities. They found four mutations (F490K, S494K, G504F, and P499L) that formed stable complexes with more hydrogen bonds and salt-bridge interactions with ACE2. Simulation data suggests that these mutations allosterically alter the packing of the RBM interface, resulting in significantly higher rupture force for RBD-ACE2 contacts.
MOLECULAR INFORMATICS
(2023)
Article
Chemistry, Medicinal
Sandipan Chakraborty, Chiranjeet Saha
Summary: In this study, we identified four RBD mutants with enhanced ACE2 binding ability using a multi-tier screening platform. Compared to wild-type RBD, these mutants form more stable complexes with ACE2 and require a higher rupture force to break the RBD-ACE2 contacts.
MOLECULAR INFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Sunny Mukherjee, Sucharita Das, Navneeth Sriram, Sandipan Chakraborty, Mahesh Kumar Sah
Summary: This study aims to resolve the tertiary structure of MCM7 and repurpose FDA-approved drugs for cancer therapy by targeting MCM7 protein. The results reveal the potential of vitamin D and vitamin K as oncoprotein inhibitors for cancer therapy via inhibition of MCM7.
