Article
Chemistry, Multidisciplinary
Pengwei Fang, Muqing Chen, Nan Yin, Guilin Zhuang, Tianyun Chen, Xinyu Zhang, Pingwu Du
Summary: Supramolecular behavior of rigid macrocycles can be tuned by the synergistic effects of their geometric configurations, sizes, and guests. In this study, two paraphenylene-based macrocycles anchored onto different positions in a triphenylene derivative result in dimeric macrocycles with different shapes and configurations. Interestingly, these dimeric macrocycles show tunable supramolecular interactions with guests.
Article
Multidisciplinary Sciences
Xian-Li Jiang, Rey P. Dimas, Clement T. Y. Chan, Faruck Morcos
Summary: Genetic sensors can be created by mixing and matching DNA-binding modules with ligand-binding modules. This study successfully overcame module incompatibilities using a computational model and restoring function by rescuing key interactions. Predicting which hybrid repressors can be rescued by mutating residues to reinstall relevant module-module interactions is essential for improving gene expression induction.
NATURE COMMUNICATIONS
(2021)
Article
Materials Science, Multidisciplinary
Yipeng Li, Yeping Lin, Dewang Cui, Huiqiu Deng, Guang Ran
Summary: Stacking-fault tetrahedron (SFT) is a three-dimensional vacancy defect that can seriously degrade the mechanical properties of quenched, deformed or irradiated face-centered cubic (FCC) metals. It is generally believed that high stacking fault energy (SFE) is unfavorable for the formation of SFTs. However, this study reveals a new mechanism for the formation of SFTs in Pd with extremely high SFE, where vacancy clusters rearrange directionally to form SFTs due to the ambient stress deviations and compressive stress fields induced by interstitial Frank loops. Continuous hydrogen implantation promotes the growth of the complex, while thermal effects can cause it to disappear.
Article
Multidisciplinary Sciences
Krishnendu Khan, Briana Long, Valentin Gogonea, Gauravi M. Deshpande, Kommireddy Vasu, Paul L. Fox
Summary: Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in the translation process that ligate amino acids to their corresponding transfer RNAs (tRNAs). In mammalian cells, these enzymes, along with AIMPs proteins, form a large multi-tRNA synthetase complex (MSC), whose assembly mechanism and function are still unclear. This study reveals the importance of cotranslational interactions, particularly involving AIMPs proteins, in the assembly process of the MSC. Interestingly, these cotranslational interactions sometimes involve more than two proteins, suggesting a diverse pathway for the ordered assembly of small subcomplexes into larger complexes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Electrical & Electronic
Zhiyun Deng, Jiaxin Fan, Yanjun Shi, Weiming Shen
Summary: This paper proposes a coevolutionary algorithm to optimize longitudinal trajectories of multiple vehicles during the cooperative platoon formation process. The algorithm adopts an adaptive encoding scheme to represent trajectories and decomposes the high-dimensional problem into smaller subproblems. The experimental results indicate the superiority of the proposed approach in optimality and stability for real-life applications.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Motofumi Osaki, Tomoko Sekine, Hiroyasu Yamaguchi, Yoshinori Takashima, Akira Harada
Summary: Combining noncovalent interactions with direct covalent bond formation achieved effective material adhesion. Host-guest interactions and amide bond formation cooperatively led to strong adhesion between materials. The rupture strength between test pieces increased with increasing molar contents of the host and guest units.
ACS APPLIED POLYMER MATERIALS
(2021)
Review
Chemistry, Multidisciplinary
Jiawei Sun, He Yang, Wenjun Tang
Summary: This tutorial review summarizes the total synthesis of complex dimeric natural products and discusses various dimerization strategies. By highlighting selected representative examples, it aims to demonstrate the recent tactics of dimerization and provide insights on structural and chemical properties of related natural products, promoting advancements in organic synthesis and biological studies.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Multidisciplinary Sciences
John C. Zinder, Paul Dominic B. Olinares, Vladimir Svetlov, Martin W. Bush, Evgeny Nudler, Brian T. Chait, Thomas Walz, Titia De lange
Summary: Human shelterin is a six-subunit complex that binds telomeres, protects them from DNA damage, and regulates telomeric DNA maintenance. The study reveals the extensive conformational heterogeneity and dimeric stoichiometry of shelterin subcomplexes, as well as its architectural variability that is beneficial for its functions at telomeres.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Jannick Van Cauwenberghe, Rosa I. Santamaria, Patricia Bustos, Soledad Juarez, Maria Antonella Ducci, Trinidad Figueroa Fleming, Angela Virginia Etcheverry, Victor Gonzalez
Summary: Through the study of four phage-Rhizobium communities in Mexico and Argentina, it was found that both phage and host diversity are spatially structured. Results showed that phage local adaptation and host maladaptation play key roles in shaping phage-host interactions. The study also revealed a nested network of interactions between phages and hosts, with their genetic identity and geographic origin influencing the interactions.
Article
Crystallography
Huiyeong Ju, Dong Hee Lee, Seulgi Kim, Joon Rae Kim, Yunji Kang, Eunji Lee, In-Hyeok Park
Summary: Two Hg(II) complexes of a NO2S2-macrocycle and its oxidized ligand with different stoichiometries were prepared using different crystallization methods. The structures and binding characteristics of these complexes were studied using NMR titration in solution.
Article
Engineering, Biomedical
Terence W. Gee, Jennifer M. Richards, Ablajan Mahmut, Jonathan T. Butcher
Summary: This study utilized a mechanically stressed 3D culture system to replicate valve interstitial cell-induced matrix calcification and investigated the collaborative interactions between valve endothelial cells and interstitial cells in calcific pathogenesis. Results showed that endothelial cells induce pathological remodeling and calcification of interstitial cells through EndMT and paracrine signaling.
Article
Computer Science, Artificial Intelligence
Honglin Bao, Zachary P. Neal, Wolfgang Banzhaf
Summary: Sparse COevolutionary Open-Ended (SCOOE) model is proposed in this paper to address the limitations of limited information accessibility, sparse interactions, and the coevolution of opinion and an open-ended structure in existing models. The proposed mechanisms effectively reduce conflicts and form lean and fast decision strategies under uncertainty, enhancing a global consensus. The structure evolves towards a small-world network. The paper also studies the influence of structure dynamics and agent heterogeneity.
COMPLEX & INTELLIGENT SYSTEMS
(2023)
Article
Chemistry, Applied
Ehsan Avazverdi, Hamid Mirzadeh, Morteza Ehsani, Shadab Bagheri-Khoulenjani
Summary: The difference between inter-chain and intra-chain electrostatic attractions was investigated in polyelectrolyte and polyampholyte electrostatic complex formation. The study found that the behavior of the polyampholyte complex depended more on the ionic strength rather than the polyelectrolyte one. The inter-chain electrostatic interactions were determined to have an impact on the complex properties.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Multidisciplinary
Zoe Gidden, Curran Oi, Emily J. Johnston, Zuzanna Konieczna, Haresh Bhaskar, Lorena Mendive-Tapia, Fabio de Moliner, Susan J. Rosser, Simon G. J. Mochrie, Marc Vendrell, Mathew H. Horrocks, Lynne Regan
Summary: Fluorescence microscopy is a valuable tool for studying protein subcellular location and function in living cells. However, some proteins exhibit altered localization or function when labeled using direct fusions to fluorescent proteins, which poses challenges for live cell studies. To overcome these challenges, LIVE-PAINT, a live-cell super-resolution approach, has been developed. In this study, LIVE-PAINT successfully images yeast membrane proteins that do not tolerate direct fusion to a fluorescent protein, using short peptide tags. The study also demonstrates the simultaneous resolution of multiple proteins at the nanoscale using orthogonal peptide interaction pairs.
Article
Multidisciplinary Sciences
Kazutoshi Tani, Ryo Kanno, Riku Kikuchi, Saki Kawamura, Kenji V. P. Nagashima, Malgorzata Hall, Ai Takahashi, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Zheng-Yu Wang-Otomo
Summary: In this study, the authors used cryo-EM to analyze the structure of the light-harvesting-reaction center complex in Rhodobacter sphaeroides. They found asymmetric features and altered shape in the complex, and also identified the critical role of protein-U in assembly and stability.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Fabio S. Fernandes, Hugo Santos, Samia R. Lima, Caroline Conti, Manoel T. Rodrigues Jr, Lucas A. Zeoly, Leonardo L. G. Ferreira, Renata Krogh, Adriano D. Andricopulo, Fernando Coelho
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Plant Sciences
Airton Damasceno Silva, Alessandra Regina Pepe Ambrozin, Ana Flavia S. de Camargo, Felipe De Paula Nogueira Cruz, Leonardo Luiz Gomes Ferreira, Renata Krogh, Taynara Lopes Silva, Ilana Lopes Baratella da Cunha Camargo, Adriano Defini Andricopulo, Paulo Cezar Vieira
Summary: Fungal cocultivation increases the biological activity of extracts, with some extracts obtained from cocultivation showing activity against Gram-positive and Gram-negative bacteria, as well as Trypanosoma cruzi and Leishmania infantum. Co-cultures containing Fusarium guttiforme produce extracts with the highest activity against Leishmania infantum.
Article
Oncology
Wanessa F. Altei, Bianca C. Pachane, Lucimara J. Martins, Ralph C. Gomes, Ricardo N. Santos, Daniara C. Fernandes, Heloisa S. Selistre-de-Araujo, Fernando Coelho, Adriano D. Andricopulo
Summary: The study evaluated the potential of eight synthetic spirocyclohexadienones as cell migration inhibitors, with four compounds significantly inhibiting cell migration and highlighting a potential binding at the colchicine binding site in tubulin. The most potent analogs induced apoptosis of tumor cells, suggesting a different mechanism of action for inhibiting cell migration.
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY
(2021)
Review
Plant Sciences
Marilia Valli, Leticia Cristina Vieira Atanazio, Gustavo Claro Monteiro, Roberta Ramos Coelho, Daniel Pecoraro Demarque, Adriano Defini Andricopulo, Laila Salmen Espindola, Vanderlan da Silva Bolzani
Summary: Natural products from Brazilian biodiversity, particularly from the Cerrado region, are highlighted as potential sources of active compounds for mosquito control due to the emergence of resistant mosquito populations. Scientific reviews on bioactive natural products are important for providing molecular models and effective measures to reduce the incidence of arboviruses diseases worldwide.
Article
Biochemistry & Molecular Biology
Humberto E. Ortega, Vitor B. Lourenzon, Marc G. Chevrette, Leonardo L. G. Ferreira, Rene F. Ramos Alvarenga, Weilan G. P. Melo, Tiago Venancio, Cameron R. Currie, Adriano D. Andricopulo, Tim S. Bugni, Monica T. Pupo
Summary: Three antifungal macrolides were isolated from Streptomyces sp. ISID311, showing high antagonism against Escovopsis sp. and potent activity against Leishmania donovani. The planar structures were determined by NMR and MS analysis, with stereochemical assignments confirmed by bioinformatic analysis.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mariana Bastos dos Santos, Beatriz Carvalho Marques, Gabriela Miranda Ayusso, Mayara Aparecida Rocha Garcia, Luana Chiquetto Paracatu, Ivani Pauli, Vanderlan Silva Bolzani, Adriano Defini Andricopulo, Valdecir Farias Ximenes, Maria Luiza Zeraik, Luis Octavio Regasini
Summary: A series of chalcones and their B-aryl analogues were synthesized and evaluated for their inhibitory effects on MPO chlorinating activity. B-thiophenyl chalcone showed inhibition of MPO activity with low toxicity, making it a potential candidate for new non-steroidal anti-inflammatory compounds.
BIOORGANIC CHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Hugo Passos Vicari, Keli Lima, Ralph da Costa Gomes, Daniara Cristina Fernandes, Jean Carlos Lipreri da Silva, Manoel Trindade Rodrigues Junior, Aline Silva Barroso de Oliveira, Ricardo Nascimento dos Santos, Adriano Defini Andricopulo, Fernando Coelho, Leticia Veras Costa-Lotufo, Joao Agostinho Machado-Neto
Summary: The study identified a novel synthetic cyclopenta[b]indole compound that exhibited anti-leukemic effects by disrupting microtubule dynamics, presenting a potential therapeutic option for ATRA-resistant APL. This compound showed significant cytotoxic activity in APL cells, decreased clonogenicity, increased apoptosis, and induced cell cycle arrest, indicating its potential as a new antineoplastic agent. In addition, molecular analyses revealed the impact of the compound on gene expression and molecular pathways involved in cell proliferation, apoptosis, and DNA damage.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Infectious Diseases
Rafael Augusto Alves Ferreira, Celso de Oliveira Rezende Junior, Pablo David Grigol Martinez, Paul John Koovits, Bruna Miranda Soares, Leonardo L. G. Ferreira, Simone Michelan-Duarte, Rafael Consolin Chelucci, Adriano D. Andricopulo, Mariana K. Galuppo, Silvia R. B. Uliana, An Matheeussen, Guy Caljon, Louis Maes, Simon Campbell, Jadel M. Kratz, Charles E. Mowbray, Luiz Carlos Dias
Summary: Leishmaniasis is a neglected tropical disease that affects millions of people worldwide. The current drugs for treating this disease have drawbacks such as toxicity and long treatment regimens. Research has identified a promising target molecule, but in vivo tests showed poor efficacy.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Maria Luiza Zeraik, Ivani Pauli, Luiz A. Dutra, Raquel S. Cruz, Marilia Valli, Luana C. Paracatu, Carolina M. Q. G. de Faria, Valdecir F. Ximenes, Luis O. Regasini, Adriano D. Andricopulo, Vanderlan S. Bolzani
Summary: Two prenyl chalcones were identified as potent inhibitors of LOX-1, with the most active compound showing competitive LOX-1 inhibitory properties. Molecular modeling studies indicated the importance of prenyl moieties for the binding of the inhibitors to the LOX binding site, related to their pharmacological properties.
Article
Biochemistry & Molecular Biology
Alex R. Medeiros, Leonardo L. G. Ferreira, Mariana L. de Souza, Celso de Oliveira Rezende Junior, Rocio Marisol Espinoza-Chavez, Luiz Carlos Dias, Adriano D. Andricopulo
Summary: The study explored the design of cruzain inhibitors based on imidazole scaffolds through molecular docking and quantitative structure-activity relationship analysis. Models were built and key structural properties determining cruzain inhibition were identified, revealing novel insights for the design of improved inhibitors.
Article
Engineering, Electrical & Electronic
Ricardo N. Santos, Sami Yamouni, Beatriz Albiero, Renato Vicente, Juliano A. Silva, Tales F. B. Souza, Mario C. M. Freitas Souza, Zhili Lei
Summary: The article describes an efficient and scalable system to predict fraudulent behavior in electrical energy consumption and guide on-site inspections. By comparing machine learning algorithms and performing proper feature engineering, patterns related to fraud occurrence can be extracted to achieve practical predictive power, with the help of SHAP values for user-friendly explanations.
INTERNATIONAL TRANSACTIONS ON ELECTRICAL ENERGY SYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Henrique R. Teles, Leonardo L. G. Ferreira, Marilia Valli, Fernando Coelho, Adriano D. Andricopulo
Summary: In this study, 2D- and 4D-quantitative structure-activity relationship (QSAR) models were developed to investigate the activity of a series of oxazole and oxadiazole derivatives against Leishmania infantum, the causative agent of visceral leishmaniasis. A clustering strategy based on structural similarity was used to divide the compounds into two groups, followed by the development of 2D- (R-2 = 0.90, R(2)pred = 0.82) and 4D-QSAR models (R-2 = 0.80, R(2)pred = 0.64) with improved statistical robustness and predictive ability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Infectious Diseases
Gabriela Marinho Righetto, Jose Luiz de Souza Lopes, Paulo Jose Martins Bispo, Camille Andre, Julia Medeiros Souza, Adriano Defini Andricopulo, Leila Maria Beltramini, Ilana Lopes Baratella da Cunha Camargo
Summary: Antimicrobial resistance is a major public health concern and there is a need for novel antimicrobial therapies. This study designed a new antimicrobial peptide Pln149-PEP20 and tested its activity against 60 different species of bacteria. The results showed that Pln149-PEP20 had excellent bactericidal activity and its target was likely genes associated with membrane metabolism.