Review
Chemistry, Multidisciplinary
Tabish Iqbal, Suryadeep Chakraborty, Subhashini Murugan, Debasis Das
Summary: The dependence on fossil fuels has raised concerns, leading to the interest in developing renewable biofuels. Metalloenzymes play a crucial role in the synthesis of hydrocarbons, derived from fatty acids, and understanding their catalytic mechanisms and substrate specificity is essential for biofuel research.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Ian Dance
Summary: This study investigates the mechanism of the conversion of N-2 to NH3 catalyzed by nitrogenase. The authors propose a detailed mechanism for the reaction, where D-2 first binds to a Fe atom and then two H atoms transfer synchronously to D-2 to form HD. The HD molecules dissociate sequentially and the flanking H atoms are recovered through proton translocation and electron combination. This mechanism is consistent with experimental observations and provides insights into the catalytic process of nitrogenase.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Madhu Sudan Manna, Seok Yeol Yoo, Mohammed Sharique, Hyoju Choi, Bimal Pudasaini, Mu-Hyun Baik, Uttam K. Tambar
Summary: We describe a copper-catalyzed alkylation reaction of unbiased internal allylic carbonates with functionalized alkyl and aryl Grignard reagents. The reactions show high stereospecificity and regioselectivity for S(N)2 or S(N)2' products under two sets of copper-catalyzed conditions, allowing the preparation of a wide range of products with E-alkene selectivity. Density functional theory calculations provide insight into the regioselectivity based on the different behaviors of homo- and heterocuprates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yong Wu, Shanshan Cao, Iskander Douair, Laurent Maron, Xihe Bi
Summary: The [2+1] cycloaddition reaction of a metal carbene with an alkene often suffers from side reactions, leading to lower yields of cyclopropanation products. By adding a low concentration of diazo compound to alkenes, it was found that AgOTf catalysis can efficiently produce cyclopropane products from hindered alkenes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Marin Puget, Viacheslav Shcherbakov, Sergey Denisov, Philippe Moreau, Jean-Pierre Dognon, Mehran Mostafavi, Sophie Le Caer
Summary: The nature of the primary species formed in FEC depends on the amount of FEC in the solution, which will affect its performance in the electrolyte.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Zuzanna Wojdyla, Tomasz Borowski
Summary: Clavaminic acid synthase is a crucial Fe-II/2-oxoglutarate-dependent dioxygenase from Streptomyces clavuligerus, essential for biosynthesis of the beta-lactamase inhibitor clavulanic acid. The enzyme's versatility and selectivity depend on the binding cavity, which interacts differently with substrates for various reactions. Enzyme-substrate interactions affect substrate re-positioning during reactions, with differential effects on hydroxylation and desaturation due to specific residues in the binding cavity.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Zhiyao Duan, Graeme Henkelman
Summary: This study uses global optimization and constant-potential density functional theory to simulate the complete process of Pt dissolution, revealing the formation and dissolution mechanism of a two-dimensional Pt surface oxide. The findings provide a fundamental understanding of Pt dissolution under potential cycling, which is essential for the rational design of durable Pt-based cathodes for fuel cells.
Article
Agricultural Engineering
Misa Mojca Cajnko, Jost Oblak, Miha Grilc, Blaz Likozar
Summary: Enzymes play a crucial role in lignin valorization, with different enzymes involved in various elementary reaction mechanisms. Degradation of lignin depends on enzyme activity and the interaction with proteins in ways that target specific covalent bonds in lignin. Various factors influence enzymatic activity, which must be taken into consideration for optimal functionality and synthesis yields.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Raphael Robidas, Claude Y. Legault
Summary: A mechanism is proposed to explain the formation of benzobicyclo[3.2.0]heptane derivatives from 1,7-enyne derivatives bearing a terminal cyclopropane, which has been previously reported.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Andrea Angeli, Victor Kartsev, Anthi Petrou, Mariana Pinteala, Volodymyr Brovarets, Sergii Slyvchuk, Stepan Pilyo, Athina Geronikaki, Claudiu T. Supuran
Summary: Carbonic anhydrases play a crucial role in living organisms and a series of new compounds were synthesized and tested as potential inhibitors in this study. Some of the derivatives showed interesting inhibitory activity towards tumor-associated isoforms. Computational procedures were also used to investigate the binding mode of these compounds within the active site.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Claire Empel, Sripati Jana, Adithyaraj Koodan, Rene M. Koenigs
Summary: In this study, a photocatalytic orthoalkylation reaction was reported, which achieved the reaction between 2-phenyl pyridines and N-protected maleimides using a catalyst and an additive at room temperature. Experimental and theoretical studies revealed a reaction mechanism that involved both dark and light reactions, with the photochemical excitation facilitating the ligand exchange and protodemetalation reaction.
Article
Chemistry, Organic
Rongqing Guan, He Zhao, Liang Cao, Huanfeng Jiang, Min Zhang
Summary: This study presents a novel reductive alpha-phosphinoylation reaction for the direct construction of novel compounds with various advantages. The strategy is expected to be further utilized in developing direct transformations of inert N-heteroarenes into functional frameworks.
ORGANIC CHEMISTRY FRONTIERS
(2021)
Article
Engineering, Environmental
Nannan Wu, Mingzhu Liu, Bingru Tian, Zunyao Wang, Virender K. Sharma, Ruijuan Qu
Summary: In this study, the oxidation of five phenolic contaminants using ferrate(VI) was investigated to understand the reaction mechanisms. Experimental and theoretical calculations revealed that the reaction rate constants were correlated with the energy of the highest occupied molecular orbital. Electron-donating groups (-R) were found to be more easily oxidized by ferrate(VI) compared to weak electron withdrawing groups (-X) and strong electron-withdrawing groups (-(C=O)-). The dominance of Fe(VI) in the reaction process was determined, and four main reaction mechanisms, including single-oxygen transfer, double-oxygen transfer, ·OH attack, and electron-transfer-mediated coupling reaction, were proposed. Density functional theory calculations suggested that the presence of -(C=O)- facilitated the occurrence of double-oxygen transfer and ·OH attack reactions, while the tendency of single-oxygen transfer and electron-transfer reaction varied with different substituents. Furthermore, the double-oxygen transfer pathway was found to be a common reaction mechanism during the ferrate(VI) oxidation of phenolic compounds.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Physical
B. B. Xiao, L. Yang, H. Y. Liu, X. B. Jiang, B. Aleksandr, E. H. Song, Q. Jiang
Summary: The study systematically investigates the oxygen reduction reaction and oxygen evolution reaction of graphene materials embedded with TMN4 clusters (TM = Fe, Co, Ni) using density functional theory calculations. It demonstrates that the functionalization of graphene can dramatically alter the activity and stability of TMN4 clusters, offering new insights into the design of bifunctional oxygen electrodes.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Katja-Sophia Csizi, Lina Eckert, Christoph Brunken, Thomas B. Hofstetter, Markus Reiher
Summary: In this study, the role of the substrate in the O2 activation process of Rieske dioxygenase was investigated theoretically. The results showed that the presence of substrate did not affect the reaction energies and structural effects at the non-heme FeII center, but played a role in regulating the reactivity of Rieske dioxygenase.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria J. Ramos, Pedro A. Fernandes
Summary: In this study, the catalytic mechanism of RVV-X was determined using a density functional theory/molecular mechanics approach. The results showed that the catalytic process occurs in two steps, involving nucleophilic attack and protonation of the substrate. Zn2+ was found to play a unique role in catalysis by lowering the pKa of the Zn2+-bound water molecule.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Joao Carneiro, Rita P. Magalhaes, Victor de la Oliva M. Roque, Manuel Simoes, Diogo Pratas, Sergio F. Sousa
Summary: This study developed a machine learning multitechnique consensus workflow to predict the protein targets of molecules with confirmed inhibitory activity against biofilm formation by Pseudomonas aeruginosa. The implemented algorithm is freely available and can be improved as more data become available.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2023)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Novo de Oliveira, Saulo Luis Da Silva, Andreimar M. Soares, Ashis K. Mukherjee, Maria Joao Ramos, Pedro A. . Fernandes
Summary: Snake venom-secreted phospholipase A(2) (svPLA(2)) enzymes play a crucial role in envenoming by disrupting the cell membrane's integrity and inducing various pharmacological effects. However, the reaction mechanisms of svPLA(2) are still not fully understood. This review presents and analyzes the most plausible reaction mechanisms, including the single-water mechanism and the assisted-water mechanism. The importance of interfacial activation and a potential catalytic mechanism for noncatalytic PLA(2)-like proteins are also discussed.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Jovana B. Araskov, Natalia Maciejewska, Mateusz Olszewski, Aleksandar Visnjevac, Vladimir Blagojevic, Henrique S. Fernandes, Sergio F. Sousa, Adrian Puerta, Jose M. Padron, Berta Barta Hollo, Miguel Monge, Maria Rodriguez-Castillo, Jose M. Lopez-de-Luzuriaga, Ozlem Uguz, Atif Koca, Tamara R. Todorovic, Nenad R. Filipovic
Summary: In this study, three neutral Zn(II) complexes with pyridine-based TH ligands were synthesized and characterized. The influence of the ligands' charge on the structure, intermolecular interactions, and photophysical properties was investigated. The deprotonation of the ligands mainly affected the relative energies of electronic levels in the complexes, resulting in similar photoluminescence mechanisms and quantum yields. The substituents at the ligands' periphery had localized effects on the selected quantum molecular descriptors of the complexes.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Review
Biochemistry & Molecular Biology
Maria F. Araujo, Elisabete M. S. Castanheira, Sergio F. Sousa
Summary: Insecticides are crucial in controlling the spread of insect-borne diseases and protecting crop health. They are formulated to kill or manage insect populations, but their use can have potential consequences on non-target species, the environment, and human health. It is important to follow recommended instructions and employ integrated pest management practices for responsible and sustainable utilization. This review article provides a comprehensive examination of insecticides, including their modes of action, physiological targets, impacts on the environment and human health, and alternatives.
Article
Biochemistry & Molecular Biology
Joao P. M. De Sousa, Nuno C. S. A. Oliveira, Pedro A. Fernandes
Summary: (S)-Norcoclaurine is a crucial compound for the biosynthesis of benzylisoquinoline alkaloids, including various drugs. The genetic modification of (S)-norcoclaurine synthase has been proven to be an effective strategy for large-scale bioproduction of (S)-norcoclaurine in heterologous hosts such as bacteria or yeast.
Article
Chemistry, Physical
Rui P. P. Neves, Bruno Araujo, Maria J. Ramos, Pedro A. Fernandes
Summary: The bacterium Rhodococcus erythropolis (strain IGTS8) has a significant potential in the industry for its ability to remove sulfur from crude oil through the 4S metabolic pathway. The rate-limiting enzyme DszC is prone to feedback inhibition. Molecular docking and dynamics simulations were used to identify binding sites wherein two products of the pathway induce feedback inhibition. The study revealed four potential binding sites, and the proposed mechanism of feedback inhibition involves disturbance of oligomerization and weakening of key interactions within DszC.
Article
Pharmacology & Pharmacy
Carlos F. M. Silva, Teresa Leao, Filipa Dias, Ana M. Tomas, Diana C. G. A. Pinto, Eduardo F. T. Oliveira, Ana Oliveira, Pedro A. Fernandes, Artur M. S. Silva
Summary: Leishmaniasis is a neglected disease mainly affecting people in developing countries, with approximately 350 million people at risk. The lack of vaccines and chemotherapy has led to an increase in the incidence of the disease. A computational study focusing on a specific enzyme of the parasite has identified potential inhibitors, indicating the promise of using these compounds for developing novel antileishmanial drugs.
Article
Chemistry, Medicinal
Mariana Novo Belchor, Caroline Ramos da Cruz Costa, Airam Roggero, Laila L. F. Moraes, Ricardo Samelo, Isabelly Annunciato, Marcos Antonio de Oliveira, Sergio F. Sousa, Marcos Hikari Toyama
Summary: In this study, in silico tools were used to evaluate the potential of quercetin methylated derivatives in inhibiting snake venom toxins and phospholipase A2. The results showed that certain residues, including Leu2, Phe5, Tyr28, glycine in the calcium-binding loop, His48, and Asp49, were the main targets for inhibition. These findings are important for further research on the anti-inflammatory effects of quercetin derivatives.
Article
Chemistry, Medicinal
Joas T. S. Coimbra, Pedro A. Fernandes, Maria J. Ramos
Summary: Due to antibiotic resistance, it is crucial to explore new antibiotics and/or strategies to counter resistance. This study used molecular dynamics simulations and quantum mechanics/molecular mechanics methods to investigate the degradation of a streptogramin B antibiotic by Vgb lyase and assess the impact of point mutations on the reaction. The findings provide valuable insights into the linearization reactions of cyclic antibiotics and aid in the development of novel strategies against antibiotic resistance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Microbiology
E. Mauro, D. Lapaillerie, C. Tumiotto, C. Charlier, F. Martins, S. F. Sousa, M. Metifiot, P. Weigel, K. Yamatsugu, M. Kanai, H. Munier-Lehmann, C. Richetta, M. Maisch, J. Dutrieux, J. Batisse, M. Ruff, O. Delelis, P. Lesbats, V. Parissi
Summary: Researchers used AlphaLISA technology to monitor the interaction between retroviral intasomes and nucleosomes, and identified drugs that disrupt or prevent their association, inhibiting HIV-1 integration.
Article
Materials Science, Multidisciplinary
Fabio G. Martins, Chanchal Kiran Thakur, Chandrabose Karthikeyan, N. S. Hari Narayana Moorthy, Sergio F. Sousa
Summary: This study used computational models to investigate the pH dependent loading of doxorubicin onto multiwalled carbon nanotubes (MWCNTs). The results showed that systems under acidic conditions had lower adsorption compared to their neutral counterparts, and carbohydrate-modified lysinated MWCNTs had higher adsorption compared to pristine or carboxylated nanotubes. These findings are consistent with previous experimental work and suggest that sugar-tethered multiwalled carbon nanotubes hold promise for doxorubicin delivery to cancer cells.
Article
Chemistry, Multidisciplinary
How Chee Ong, Joao T. S. Coimbra, Maria J. Ramos, Bengang Xing, Pedro A. Fernandes, Felipe Garcia
Summary: Mitochondrial targeting is a promising strategy for treating various diseases, and Triphenylphosphonium (TPP+) moieties have been widely used for this purpose. However, the core structure of TPP+ remains largely unchanged, so this study explored the use of novel phosphorus-nitrogen based frameworks as mitochondrial delivery vectors. The phosphazenylphosphonium (PPN+) moiety was found to be highly effective in delivering cargo to mitochondria, with unique electronic properties and high lipophilicity.
Article
Chemistry, Multidisciplinary
Carola Jerves, Rui P. P. Neves, Saulo L. da Silva, Maria J. Ramos, Pedro A. Fernandes
Summary: The PETase enzyme from Ideonella sakaiensis can degrade PET at room temperature. Computational enzyme optimization can accelerate enzyme engineering. Mutations can stabilize transition states and decrease activation barriers. Rational enzyme engineering on PETase and other enzymes is encouraged.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Tatiana F. Vieira, Nuno M. F. S. A. Cerqueira, Manuel Simoes, Sergio F. Sousa
Summary: PqsD is an enzyme involved in the synthesis of essential secondary metabolites for Pseudomonas quinolone signal (PQS) inducer molecules. Inhibition of PqsD activity can inhibit biofilm formation and can be combined with PqsR inhibition. This study used computational methods to screen and select eight compounds as potential quorum sensing inhibitors.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2024)