Article
Chemistry, Multidisciplinary
Mohamed M. Aboelnga, Subha Kalyaanamoorthy
Summary: Polyethylene terephthalate (PET), a widely used plastic, is a significant contributor to global plastic pollution. This study investigates the enzymatic biodegradation of PET and identifies key factors for efficient PET hydrolysis. The results provide insights into the reaction mechanism and molecular features of PETase and cutinase enzymes, which can be useful for designing more efficient enzymes for PET hydrolysis.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
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
Biochemistry & Molecular Biology
Ana Lucia Leitao, Francisco J. Enguita
Summary: This study analyzed the structure-activity relationships in microbial esterases, focusing on plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. The analysis revealed specific characteristics of some polyester hydrolases that may be related to their efficiency in degrading aromatic polyesters, such as phthalates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Li Yang, Jie Gao, Ying Liu, Guoqiang Zhuang, Xiawei Peng, Wei-Min Wu, Xuliang Zhuang
Summary: Yellow mealworms are capable of biodegrading polystyrene and low-density polyethylene, forming new oxygen-containing functional groups and causing changes in physical and chemical properties. The biodegradation of PS is gut microbe-dependent, while LDPE biodegradation is less dependent on gut microbes. Gut microbial community significantly shift under different dietary conditions associated with the biodegradation of EPS and LDPE.
Article
Biochemistry & Molecular Biology
Zekeriya Duzgun, Zuhal Eroglu
Summary: This study examined the interactions of statins, ACE inhibitors, antiarrhythmic drugs, and flavonoids with IRE1, ASK1, and JNK1 on a molecular level, finding that statins had the best affinity with ASK1 and JNK1, while flavonoid norizalpinine and antiarrhythmic drug amiodarone showed strong binding interactions with IRE1. Atorvastatin, pitavastatin, norizalpinine, and amiodarone were identified as potential compounds for preventing cardiac dysfunctions caused by ER stress, suggesting avenues for further research in vitro and in vivo.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Chemistry, Multidisciplinary
William Dawson, Augustin Degomme, Martina Stella, Takahito Nakajima, Laura E. Ratcliff, Luigi Genovese
Summary: In the past decade, advancements in computational technology have allowed for larger system sizes to be simulated using density functional theory. This has enabled computational physicists and chemists to collaborate with experimentalists and consider portions of systems as building blocks for analysis. It has also highlighted the need to bridge knowledge gaps in order to simulate increasingly realistic systems.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Environmental Sciences
Ayyasamy Gowthami, Mohammed Syed Marjuk, Piliyan Raju, Karuppaiya Nanthini Devi, Perumal Santhanam, Sundarraj Dinesh Kumar, Pachiappan Perumal
Summary: The present study investigated the degradation ability of five marine microalgae strains on low-density polyethylene (LDPE). The results showed that Picochlorum maculatum was the most effective strain in degrading LDPE, with significant weight loss, high reduction rate, and short half-life. SEM images revealed surface erosion and ATR-FTIR spectra showed functional group peaks and new peaks, indicating the degradation of LDPE by microalgae.
MARINE POLLUTION BULLETIN
(2023)
Article
Engineering, Environmental
Gajendra Joshi, Prasun Goswami, Pankaj Verma, Gopika Prakash, Priya Simon, Nambali Valsalan Vinithkumar, Gopal Dharani
Summary: This study isolated 97 bacteria with LDPE degradation potential from macroplastic debris collected from Andaman Island, and formulated a bacterial consortium that efficiently degrades plastics. Incubation experiments confirmed significant increase in LDPE degradation by the consortium, demonstrating its potential as an eco-friendly solution for plastic waste mitigation.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Wenyuan Zhang, Eric A. C. Bushnell
Summary: In this study, the QM/MM approach was used to investigate the impact of the second environmental shell of the active site on the catalytic conversion of acetylene to acetaldehyde by acetylene hydratase (AH). Results indicated that the presence of the second shell environment significantly affected the reaction, and substitutions of sulfur atoms with selenium atoms had a notable impact on the Gibbs energy for acetylene binding. The study suggested that substituting key W-coordinating sulfur atoms with selenium atoms may enhance the catalytic mechanism of AH.
CANADIAN JOURNAL OF CHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Naike Ye, Zekai Yang, Yuchen Liu
Summary: This article reviews the recent advances in using density functional theory (DFT) in molecular modeling studies of COVID-19 pharmaceuticals. It provides an overview of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) drugs and targets, introduces the basic principles and application methods of DFT, discusses different approaches of applying DFT, and highlights important factors to consider when incorporating DFT in future drug modeling research.
DRUG DISCOVERY TODAY
(2022)
Article
Chemistry, Multidisciplinary
Hans Georg Gallmetzer, Thomas S. Hofer
Summary: Optimized link bond parameters for the C-alpha-C-beta bond have been determined and compared to reference data. The results suggest that the optimized parameters are more suitable for QM/MM link bonds compared to a single global setting, and virtually identical parameters were obtained in calculations using different levels of theory. The provided collection of link atoms parameters is valuable for QM/MM studies of biomacromolecules.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Physics, Condensed Matter
P. Aghdasi, R. Ansari, S. Rouhi, Sh Yousefi, M. Goli, H. R. Soleimani
Summary: The elastic and plastic properties of monolayer phosphorene with atomic adsorption were studied using density functional theory. Different atoms were selected and it was found that adsorption with most atoms increased the elastic modulus of armchair phosphorene while decreasing that of zigzag phosphorene. Additionally, adsorption changed the width of different regions in the nanosheet.
PHYSICA B-CONDENSED MATTER
(2021)
Article
Engineering, Environmental
Tamer Elsamahy, Jianzhong Sun, Sobhy E. Elsilk, Sameh S. Ali
Summary: A newly discovered yeast consortium isolated from termite guts has shown great potential for degrading LDPE, a common type of plastic. The consortium, made up of three yeast species, displayed a high growth rate on UV-sterilized LDPE and produced enzymes that can break down the plastic. This study highlights the use of wood-feeding termite yeasts as a novel approach for LDPE biodegradation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Green & Sustainable Science & Technology
Bo-Yu Peng, Ying Sun, Zeyu Wu, Jiabin Chen, Zheng Shen, Xuefei Zhou, Wei-Min Wu, Yalei Zhang
Summary: This study characterized the biodegradation of polystyrene (PS) and low-density polyethylene (LDPE) by Zophobas atratus larvae over a 28-day test period. The larvae were able to degrade PS and LDPE into microplastic particles, providing new insights into insect-mediated biodegradation of persistent plastics.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Chemistry, Physical
Maysa Yusef Buey, Tzonka Mineva, Mathias Rapacioli
Summary: QM/MM hybrid methods are popular schemes to calculate molecular properties with environmental effects. This paper presents a new implementation of a hybrid QM/MM scheme using density functional based tight binding and class 1 force fields within the deMonNano code.
THEORETICAL CHEMISTRY ACCOUNTS
(2022)
Review
Biochemistry & Molecular Biology
Rafaela Diniz-Sousa, Cleopatra A. da S. Caldeira, Soraya S. Pereira, Saulo L. Da Silva, Pedro A. Fernandes, Luis M. C. Teixeira, Juliana P. Zuliani, Andreimar M. Soares
Summary: Animal venoms and their chemical compounds have attracted attention for their potential applications in biotechnology, diagnosis, and therapy. Snake venoms, containing proteins and peptides, offer opportunities for drug development in various fields, such as cancer, cardiovascular diseases, and infectious-parasitic diseases. This minireview provides an overview of the biotechnological potential of animal venoms, particularly snakes, and highlights the fascinating world of Applied Toxinology, where animal biodiversity can be harnessed for therapeutic and diagnostic applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
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
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
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
Sudip Das, Umberto Raucci, Rui P. P. Neves, Maria J. J. Ramos, Michele Parrinello
Summary: In this study, an enhanced sampling and machine learning-based approach was used to explore the catalytic reaction space and characterize the transformation from reactive to non-reactive conformations. By studying the rate-determining step of the glycolysis reaction, we unraveled the complexity of enzymatic reaction, revealed three binding modes of the substrate, and highlighted the role of water in the catalytic process and in the stepwise conversion of reaction-ready to non-reactive conformations.
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
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
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
Biochemistry & Molecular Biology
Ana Novo de Oliveira, Andreimar Martins Soares, Saulo Luis Da Silva
Summary: This review provides a detailed overview of venom peptides present in various animal groups and highlights their therapeutic potential against a wide variety of diseases. Venom and poison peptides have proven to be powerful biological weapons with immense pharmacological potential.
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
(2023)
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)