Monitoring Anthracycline Cancer Drug-Nucleosome Interaction by NMR using a Specific Isotope Labeling Approach for Nucleosomal DNA
We describe the synthesis of segmental one-strand 13C-thymidine labeled 601-DNA, the assignment of the methyl signals, and demonstrate its use to observe site-specific binding events in the nucleosome by aclarubicin, an anthracycline cancer drug that intercalates into the DNA minor grooves. Our results highlight intrinsic conformational heterogeneity in the 601 DNA sequence and show that aclarubicin binds an exposed AT-rich region near the DNA end. Overall, our data point to a model where the drug invades the nucleosome from the terminal ends inward, eventually resulting in histone eviction and nucleosome disruption.PMID:3...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Clara L van Emmerik Vincenzo Lobbia Jacques Neefjes Frank H T Nelissen Hugo van Ingen Source Type: research
Novel Triazole-Containing "Dipeptides": Synthesis, Molecular Docking And Analgesic Activity Studies
Chembiochem. 2024 Mar 13:e202300837. doi: 10.1002/cbic.202300837. Online ahead of print.ABSTRACTDipeptides of a new structure based on β-triazolalanines and (L)-α-amino acids were synthesized and optimal conditions were developed that ensure both chemical and optical purity of the final products. Molecular docking was carried out and possible intermolecular interactions of dipeptides with potential targets were established. Based on these studies, the analgesic property of chosen dipeptides was studied and it was found that some compounds possess revealed antinociceptive activity in the tail-flick test.PMID:38477021 | DO...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Tariel V Ghochikyan Arusyak G Zhamharyan Shushanik G Afrikyan Vardges R Frangyan Armen Galstyan Source Type: research
Research Progress on the Assembly of Large DNA Fragments
This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and ...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Wei Tan Qing Miao Xuemei Jia Ying Liu Shuai Li Dayong Yang Source Type: research
Efficient Transferase Engineering for SAM Analog Synthesis from Iodoalkanes
Chembiochem. 2024 Mar 13:e202400079. doi: 10.1002/cbic.202400079. Online ahead of print.ABSTRACTS-Adenosyl-l-methionine (SAM) is an important cosubstrate in various biochemical processes, including selective methyl transfer reactions. Simple methods for the (re)generation of SAM analogs could expand the chemistry accessible with SAM-dependent transferases and go beyond methylation chemistry. Here we present an efficient enzyme engineering strategy to synthesize different SAM analogs from "off-the-shelf" iodoalkanes through enzymatic alkylation of S-adenosyl-l-homocysteine (SAH). This was achieved by mutating multiple hydro...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Kai H Sch ülke Jana S Fr öse Alina Klein Marc Garcia-Borr às Stephan C Hammer Source Type: research
Porphyrin-BODIPY Dyad: Enhancing Photodynamic Inactivation via Antenna Effect
Chembiochem. 2024 Mar 13:e202400138. doi: 10.1002/cbic.202400138. Online ahead of print.ABSTRACTA porphyrin-BODIPY dyad (P-BDP) was obtained through covalent bonding, featuring a two-segment design comprising a light-harvesting antenna system connected to an energy acceptor unit. The absorption spectrum of P-BDP resulted from an overlap of the individual spectra of its constituent parts, with the fluorescence emission of the BODIPY unit experiencing significant quenching (96%) due to the presence of the porphyrin unit. Spectroscopic, computational, and redox investigations revealed a competition between photoinduced energy...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Mar ía Eugenia Pérez Javier Esteban Durantini Sol Romina Martinez Andr és Matías Durantini Mar ía Elisa Milanesio Edgardo N Durantini Source Type: research
Monitoring Anthracycline Cancer Drug-Nucleosome Interaction by NMR using a Specific Isotope Labeling Approach for Nucleosomal DNA
We describe the synthesis of segmental one-strand 13C-thymidine labeled 601-DNA, the assignment of the methyl signals, and demonstrate its use to observe site-specific binding events in the nucleosome by aclarubicin, an anthracycline cancer drug that intercalates into the DNA minor grooves. Our results highlight intrinsic conformational heterogeneity in the 601 DNA sequence and show that aclarubicin binds an exposed AT-rich region near the DNA end. Overall, our data point to a model where the drug invades the nucleosome from the terminal ends inward, eventually resulting in histone eviction and nucleosome disruption.PMID:3...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Clara L van Emmerik Vincenzo Lobbia Jacques Neefjes Frank H T Nelissen Hugo van Ingen Source Type: research
Novel Triazole-Containing "Dipeptides": Synthesis, Molecular Docking And Analgesic Activity Studies
Chembiochem. 2024 Mar 13:e202300837. doi: 10.1002/cbic.202300837. Online ahead of print.ABSTRACTDipeptides of a new structure based on β-triazolalanines and (L)-α-amino acids were synthesized and optimal conditions were developed that ensure both chemical and optical purity of the final products. Molecular docking was carried out and possible intermolecular interactions of dipeptides with potential targets were established. Based on these studies, the analgesic property of chosen dipeptides was studied and it was found that some compounds possess revealed antinociceptive activity in the tail-flick test.PMID:38477021 | DO...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Tariel V Ghochikyan Arusyak G Zhamharyan Shushanik G Afrikyan Vardges R Frangyan Armen Galstyan Source Type: research
Research Progress on the Assembly of Large DNA Fragments
This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and ...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Wei Tan Qing Miao Xuemei Jia Ying Liu Shuai Li Dayong Yang Source Type: research
Efficient Transferase Engineering for SAM Analog Synthesis from Iodoalkanes
Chembiochem. 2024 Mar 13:e202400079. doi: 10.1002/cbic.202400079. Online ahead of print.ABSTRACTS-Adenosyl-l-methionine (SAM) is an important cosubstrate in various biochemical processes, including selective methyl transfer reactions. Simple methods for the (re)generation of SAM analogs could expand the chemistry accessible with SAM-dependent transferases and go beyond methylation chemistry. Here we present an efficient enzyme engineering strategy to synthesize different SAM analogs from "off-the-shelf" iodoalkanes through enzymatic alkylation of S-adenosyl-l-homocysteine (SAH). This was achieved by mutating multiple hydro...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Kai H Sch ülke Jana S Fr öse Alina Klein Marc Garcia-Borr às Stephan C Hammer Source Type: research
Porphyrin-BODIPY Dyad: Enhancing Photodynamic Inactivation via Antenna Effect
Chembiochem. 2024 Mar 13:e202400138. doi: 10.1002/cbic.202400138. Online ahead of print.ABSTRACTA porphyrin-BODIPY dyad (P-BDP) was obtained through covalent bonding, featuring a two-segment design comprising a light-harvesting antenna system connected to an energy acceptor unit. The absorption spectrum of P-BDP resulted from an overlap of the individual spectra of its constituent parts, with the fluorescence emission of the BODIPY unit experiencing significant quenching (96%) due to the presence of the porphyrin unit. Spectroscopic, computational, and redox investigations revealed a competition between photoinduced energy...
Source: Chembiochem - March 13, 2024 Category: Biochemistry Authors: Mar ía Eugenia Pérez Javier Esteban Durantini Sol Romina Martinez Andr és Matías Durantini Mar ía Elisa Milanesio Edgardo N Durantini Source Type: research
Bioluminescence The Vibrant Glow of Nature and its Chemical Mechanisms
Chembiochem. 2024 Mar 12:e202400106. doi: 10.1002/cbic.202400106. Online ahead of print.ABSTRACTBioluminescence, the mesmerizing natural phenomenon where living organisms produce light through chemical reactions, has long captivated scientists and laypersons alike, offering a rich tapestry of insights into biological function, ecology, evolution as well as the underlying chemistry. This comprehensive review systematically explores the phenomenon of bioluminescence, addressing its historical context, geographic dispersion, and ecological significance with a focus on their chemical mechanisms. We discuss terrestrial biolumin...
Source: Chembiochem - March 12, 2024 Category: Biochemistry Authors: Stefan Schramm Dieter Wei ß Source Type: research
Binding dynamics of a stapled peptide targeting the transcription factor NF-Y
In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.PMID:384709...
Source: Chembiochem - March 12, 2024 Category: Biochemistry Authors: Canan Durukan Federica Arbore Rasmus Klintrot Carlo Bigiotti Ioana M Ilie Jocelyne Vreede Tom N Grossmann Sven Hennig Source Type: research
Bioluminescence The Vibrant Glow of Nature and its Chemical Mechanisms
Chembiochem. 2024 Mar 12:e202400106. doi: 10.1002/cbic.202400106. Online ahead of print.ABSTRACTBioluminescence, the mesmerizing natural phenomenon where living organisms produce light through chemical reactions, has long captivated scientists and laypersons alike, offering a rich tapestry of insights into biological function, ecology, evolution as well as the underlying chemistry. This comprehensive review systematically explores the phenomenon of bioluminescence, addressing its historical context, geographic dispersion, and ecological significance with a focus on their chemical mechanisms. We discuss terrestrial biolumin...
Source: Chembiochem - March 12, 2024 Category: Biochemistry Authors: Stefan Schramm Dieter Wei ß Source Type: research
Binding dynamics of a stapled peptide targeting the transcription factor NF-Y
In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.PMID:384709...
Source: Chembiochem - March 12, 2024 Category: Biochemistry Authors: Canan Durukan Federica Arbore Rasmus Klintrot Carlo Bigiotti Ioana M Ilie Jocelyne Vreede Tom N Grossmann Sven Hennig Source Type: research
Strategies for the Construction of Multicyclic Phage Display Libraries
Chembiochem. 2024 Mar 11:e202400072. doi: 10.1002/cbic.202400072. Online ahead of print.ABSTRACTPeptide therapeutics have gained great interest due to their multiple advantages over small molecule and antibody-based drugs. Peptide drugs are easier to synthesize, have the potential for oral bioavailability, and are large enough to target protein-protein interactions that are undruggable by small molecules. However, two major limitations have made it difficult to develop novel peptide therapeutics not derived from natural products, including the metabolic instability of peptides and the difficulty of reaching antibody-like p...
Source: Chembiochem - March 11, 2024 Category: Biochemistry Authors: Fa-Jie Chen Nicole Pinnette Jianmin Gao Source Type: research
