Review
Chemistry, Multidisciplinary
Harri Lonnberg
Summary: The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH differs from spontaneous reactions. Comparative kinetic measurements, heavy atom isotope effects, and theoretical calculations help clarify the mechanistic details and provide a basis for more complex catalytic mechanisms.
Article
Chemistry, Multidisciplinary
Olivia Luige, Partha Pratim Bose, Rouven Stulz, Peter Steunenberg, Omar Brun, Shalini Andersson, Merita Murtola, Roger Stromberg
Summary: The study introduces Zn2+-dependent dimethyl-dipyridophenazine PNA conjugates as efficient RNA cleaving artificial enzymes, showing site-specific RNA cleavage with 10 minute half-lives and cleaving clinically relevant RNA models.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Yao Wu, Cong Zhao, Yanzhuang Su, Sason Shaik, Wenzhen Lai
Summary: The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a likely mechanism for this transformation, suggesting the involvement of a triplet Cu-II-superoxide complex and a Cu-I-alkylperoxo intermediate. The results also indicate that the aldehyde oxygen of the final product originates from O-2.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Lange Yakubu Saleh, Mikko Ora, Tuomas Lonnberg
Summary: A water-soluble arylmercury complex has been synthesized and its ability to catalyze the cleavage of the phosphodiester linkage of the RNA model compound has been evaluated. The catalytic reaction is linearly dependent on catalyst concentration and shows relatively low affinity for the substrate.
Review
Chemistry, Multidisciplinary
Bingrui Li, Peng-Fei Cao, Tomonori Saito, Alexei P. Sokolov
Summary: Self-healing materials offer new possibilities for sustainable technologies and improved device longevity. In this overview, we discuss recent developments in intrinsically self-healing polymers, which are mainly based on polymers with dynamic covalent and noncovalent bonds. We describe current self-healing mechanisms and provide examples of systems with different types of dynamic bonds. The most intriguing results are achieved when combining multiple types of dynamic bonds, resulting in materials with high toughness and fast self-healing rates. However, there is a trade-off between self-healing rate and mechanical modulus, and we propose design principles to overcome this trade-off. We also discuss applications and challenges in the field of intrinsically self-healing polymers.
Article
Chemistry, Inorganic & Nuclear
Jorge J. Carbo, Manuel Gomez, Cristina Hernandez-Prieto, Alberto Hernan-Gomez, Avelino Martin, Miguel Mena, Jordi Puiggali-Jou, Josep M. Ricart, Cristina Santamaria
Summary: Hydrogenolysis of alkyl sulfido-bridged tantalum(IV) dinuclear complexes produces Ta(III) tetrametallic sulfide cluster and corresponding alkane. Mechanistic information is obtained through hydrogenation of precursor compounds and DFT calculations. The study of different substrates reveals alternative reaction pathways and the low oxidation states of the synthesized compounds.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Organic
Alberto Mills, Federico Gago
Summary: Ozogamicin, a calicheamicin derivative, selectively targets several types of leukemia cells through tailor-made immunoconjugates, resulting in cell death by double-strand cleavage. The use of calicheamicin epsilon has shown that these sophisticated molecules can cause bending in DNA oligonucleotides, ultimately affecting their circularization ratio. Modeling and simulation of DNA constructs with high and low affinity target sites have shed light on the structural distortions induced by calicheamicin epsilon and provided insights into the preferred structural and dynamic features associated with DNA target selection by calicheamicins.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Changfan Lin, Connor M. Schneps, Siddarth Chandrasekaran, Abir Ganguly, Brian R. Crane
Summary: This study presents a new western-blot-free method to study the binding of CRY to TIM and explores the correlation between the undocking of CTT and TIM affinity. Quantification of the interactions was achieved using pulse-dipolar ESR spectroscopy and molecular dynamics simulations.
Article
Chemistry, Physical
Ruisong Zhu, Guoxuan Li, Zhigang Lei, Chengmin Gui
Summary: This study investigated the thermodynamic feasibility, absorption results, and molecular mechanism of capturing SO2 with mixed ionic liquids (MILs) for [EMIM][SCN] and [EMIM][Cl]. It was found that adding [EMIM][Cl] to [EMIM][SCN] could increase the SO2 absorption capacity, and van der Waals force played a leading role in the process of SO2 absorption. Molecular dynamics simulations further analyzed the interaction between molecules and the distribution state in terms of interaction energy, radial distribution functions (RDFs), and spatial distribution functions (SDFs).
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Hannah K. Wayment-Steele, Do Soon Kim, Christian A. Choe, John J. Nicol, Roger Wellington-Oguri, Andrew M. Watkins, R. Andres Parra Sperberg, Po-Ssu Huang, Eterna Participants, Rhiju Das
Summary: RNA hydrolysis poses challenges for mRNA-based vaccines and therapeutics due to issues in manufacturing, long-term storage, global delivery, and in vivo stability. Redesigning RNAs to form double-stranded regions could reduce hydrolysis, with algorithms like those on the Eterna platform showing promise in creating 'superfolder' mRNAs with increased stability and diverse features beneficial for translation and immunogenicity. Ongoing research aims to maximize mRNA stability and longevity through innovative design strategies and computational approaches.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Applied
Jiangfeng Yu, Yaqing Wang, Yang Yang, Wenzhen Lai
Summary: In this study, DFT calculations were used to investigate the activation of the O-O bond in a Mn-IV-peroxo corrole complex. The results showed that with the assistance of Mn-III-corrole, the O-O bond cleavage can proceed via a binuclear mechanism to produce the high-valent Mn-V-oxo corrole complex.
TOPICS IN CATALYSIS
(2022)
Article
Biochemistry & Molecular Biology
JingRu Chan, Fu Qinqin, Li Jianwei, Chen Ying, Satoru Machida, Chen Wei, Yuren Adam Yuan, Chacko Jobichen
Summary: A novel catalytically active RNase III protein, PsDCR1, was discovered in budding yeast Pichia stipitis. The RNA cleavage activity of PsDCR1 is determined by the stem-loop structure of the RNA substrate, not the sequence motif at the apical loop.
Article
Cell Biology
Isabel Pablos, Yoan Machado, Hugo C. Ramos de Jesus, Yasir Mohamud, Reinhild Kappelhoff, Cecilia Lindskog, Marli Vlok, Peter A. Bell, Georgina S. Butler, Peter M. Grin, Quynh T. Cao, Jenny P. Nguyen, Nestor Solis, Srinivas Abbina, Wioletta Rut, John C. Vederas, Laszlo Szekely, Attila Szakos, Marcin Drag, Jayachandran N. Kizhakkedathu, Karen Mossman, Jeremy A. Hirota, Eric Jan, Honglin Luo, Arinjay Banerjee, Christopher M. Overall
Summary: Research on the main viral protease of SARS-CoV-2 and its relationship with human protein substrates has revealed a large group of substrates, accelerating the exploration of pathophysiology and drug design. The study also demonstrates the interactions between 3CL(pro) and the Hippo pathway and other key effector proteins in human cells.
Article
Biochemistry & Molecular Biology
Anurag T. K. Baidya, Bhanuranjan Das, Bharti Devi, Bengt Langstroem, Hans agren, Taher Darreh-Shori, Rajnish Kumar
Summary: Various investigational studies have found that Proton Pump Inhibitors (PPIs) may increase the risk of developing Alzheimer's disease (AD) and non-AD related dementias. Using computational tools, this study provides mechanistic insights into the interaction between PPIs and the choline acetyltransferase (ChAT) binding pocket, which can help in designing novel ChAT ligands for the diagnosis and treatment of cholinergic dysfunction associated with AD.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Environmental Sciences
Mengqi Wei, Ruina Zhang, Mingjian Zhou, Zhiqiang Yuan, Haiping Yuan, Nanwen Zhu
Summary: The study proposed a new MAICAO(2) process for treating fresh leachate, which showed improved removal efficiencies of COD, TN, NH4+-N, and antibiotics compared to traditional methods. The process utilizes microaeration to enhance degradation of organic acids before anaerobic reactions, resulting in better denitrification efficiency and significant removal of antibiotics.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Chemistry, Organic
Faiza Diaba, Gisela Trenchs
Summary: The first violet light-mediated synthesis of gamma- and delta-lactams from N-alkenyl trichloroacetamides is reported in this paper. The reactions are conducted in tetrahydrofuran or 2-methyltetrahydrofuran as the sole solvent without catalysts or additives, under non-anhydrous conditions in an air atmosphere where the solvent serves as the radical initiator.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Feroze Hussain, Sajjad Ahmed, Ashiq Hussain Padder, Qazi Naveed Ahmed
Summary: This study reports a novel and efficient one-pot synthesis method for mixed phosphorotrithioates, which does not require supplementary additives and shows broad applicability.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Hyunjin Oh, Ikyon Kim
Summary: A new 1,2,4-triazole-pyrrolo[1,2-a]pyrazine hybrid system, 6-acylpyrrolo[1,2-a][1,2,4]triazolo[5,1-c]pyrazine, was synthesized using a catalyst-free method. This method involved sequential exposure of pyrrole-2-carbonitrile-derived substrates to DMF-DMA and acyl hydrazide, resulting in the formation of acylated pyrazine and 1,2,4-triazole rings, enabling the installation of various substituents at specific positions on the core skeleton.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Ming Yan, Si-fan Wang, Yong-po Zhang, Jin-zhong Zhao, Zhuo Tang, Guang-xun Li
Summary: Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. The reaction allows for the gram-scale preparation of sulfinamides and the one-pot synthesis of various sulfonyl amides.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Farzaneh Bandehali-Naeini, Zahra Tanbakouchian, Noushin Farajinia-Lehi, Nicolas Mayer, Morteza Shiri, Martin Breugst
Summary: Two tandem catalytic systems were developed for the synthesis of novel 3,4-disubstituted maleimides using the same Ugi adducts. Different maleimide structures can be synthesized using either Pd or Cu catalysis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Tanya Raghava, Anjan Chattopadhyay, Subhadeep Banerjee, Nivedita Sarkar
Summary: Amine substitution of two ortho fluorine atoms of tetrafluoroterephthalonitrile through SNAr chemistry is easily achievable. But further fluorine substitution is only possible under forcing conditions, yielding valuable fluorophores for bioimaging.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Review
Chemistry, Organic
Anju Chadha, Santosh Kumar Padhi, Selvaraj Stella, Sowmyalakshmi Venkataraman, Thangavelu Saravanan
Summary: Alcohol dehydrogenases are enzymes that use cofactors for oxidation or reduction reactions of alcohols or carbonyl compounds. They are utilized in green chemistry and have applications in the production of pharmaceuticals. Recombinant enzymes have solved the challenge of producing purified enzymes in large quantities. Engineered alcohol dehydrogenases have been used in asymmetric synthesis in industry. Various methods have been established for regenerating expensive cofactors to make the enzymatic process more efficient and economically viable.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)