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Article ; Online: Pepticinnamins N, O, and P, Nonribosomal Peptides from the Soil-Derived

Mohamed, Manar Magdy Mahmoud / Abboud, Maria Mahmoud / Maleckis, Matiss / Souza, Luciano D O / Moreira, José M A / Gotfredsen, Charlotte H / Weber, Tilmann / Ding, Ling

Journal of natural products

2024 Volume 87, Issue 4, Page(s) 1075–1083

Abstract: Cinnamoyl moiety containing nonribosomal peptides represented by pepticinnamin E are a growing family of natural products isolated from ... ...

Abstract	Cinnamoyl moiety containing nonribosomal peptides represented by pepticinnamin E are a growing family of natural products isolated from different
MeSH term(s)	Streptomyces/chemistry ; Soil Microbiology ; Molecular Structure ; Humans ; Multigene Family ; Peptides/chemistry ; Peptides/pharmacology ; Peptides/isolation & purification ; Cell Line, Tumor
Chemical Substances	Peptides
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	304325-3
ISSN	1520-6025 ; 0163-3864
ISSN (online)	1520-6025
ISSN	0163-3864
DOI	10.1021/acs.jnatprod.4c00029
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Book ; Online: Distill n' Explain

Pereira, Tamara / Nasciment, Erik / Resck, Lucas E. / Mesquita, Diego / Souza, Amauri

explaining graph neural networks using simple surrogates

2023

Abstract: ... the question, we propose Distill n' Explain (DnX). First, DnX learns a surrogate GNN via knowledge distillation ...

Abstract	Explaining node predictions in graph neural networks (GNNs) often boils down to finding graph substructures that preserve predictions. Finding these structures usually implies back-propagating through the GNN, bonding the complexity (e.g., number of layers) of the GNN to the cost of explaining it. This naturally begs the question: Can we break this bond by explaining a simpler surrogate GNN? To answer the question, we propose Distill n' Explain (DnX). First, DnX learns a surrogate GNN via knowledge distillation. Then, DnX extracts node or edge-level explanations by solving a simple convex program. We also propose FastDnX, a faster version of DnX that leverages the linear decomposition of our surrogate model. Experiments show that DnX and FastDnX often outperform state-of-the-art GNN explainers while being orders of magnitude faster. Additionally, we support our empirical findings with theoretical results linking the quality of the surrogate model (i.e., distillation error) to the faithfulness of explanations. Comment: To appear in AISTATS 2023
Keywords	Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
Subject code	006
Publishing date	2023-03-17
Publishing country	us
Document type	Book ; Online
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Article ; Online: Near-IR Capturing N-Methylbenzene Sulfonamide-Phenothiazine Incorporating Strong Electron Acceptor Push-Pull Systems: Photochemical Ultrafast Carrier Dynamics.

Kumar Gupta, Pankaj / Das, Somnath / Misra, Rajneesh / D'Souza, Francis

Chemistry (Weinheim an der Bergstrasse, Germany)

2024 Volume 30, Issue 25, Page(s) e202304313

Abstract: Unraveling the intriguing aspects of the intramolecular charge transfer (ICT) phenomenon of multi-modular donor-acceptor-based push-pull systems are of paramount importance considering their promising applications, particularly in solar energy harvesting ...

Abstract	Unraveling the intriguing aspects of the intramolecular charge transfer (ICT) phenomenon of multi-modular donor-acceptor-based push-pull systems are of paramount importance considering their promising applications, particularly in solar energy harvesting and light-emitting devices. Herein, a series of symmetrical and unsymmetrical donor-acceptor chromophores 1-6, are designed and synthesized by the Corey-Fuchs reaction via Evano's condition followed by [2+2] cycloaddition retroelectrocyclic ring-opening reaction with strong electron acceptors TCNE and TCNQ in good yields (~60-85 %). The photophysical, electrochemical, and computational studies are investigated to explore the effect of incorporation of strong electron acceptors 1,1,4,4-tetracyanobuta-1,3-diene (TCBD) and dicyanoquinodimethane (DCNQ) with phenothiazine (PTZ) donor. An additional low-lying broad absorption band extended towards the near-infrared (NIR) region suggests charge polarization after the introduction of the electron acceptors in both symmetrical and asymmetrical systems, leading to such strong ICT bands. The electrochemical properties reveal that reduction potentials of 3 and 6 are lower than those of 2 and 5, suggesting DCNQ imparts more on the electronic properties and hence largely contributes to the stabilization of LUMO energy levels than TCBD, in line with theoretical observations. Relative positions of the frontier orbitals on geometry-optimized structures further support accessing donor-acceptor sites responsible for the ICT transitions. Eventually, ultrafast carrier dynamics of the photoinduced species are investigated by femtosecond transient absorption studies to identify their spectral characteristics and target analysis further provides information about different excited states photophysical events including ICT and their associated time profiles. The key findings obtained here related to excited state dynamical processes of these newly synthesized systems are believed to be significant in advancing their prospect of utilization in solar energy conversion and related photonic applications.
Language	English
Publishing date	2024-03-14
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202304313
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Article ; Online: Structure-based design of new N-benzyl-piperidine derivatives as multitarget-directed AChE/BuChE inhibitors for Alzheimer's disease.

Conceição, Raissa Alves da / von Ranke, Natalia / Azevedo, Luciana / Franco, Daiana / Nadur, Nathalia Fonseca / Kummerle, Arthur Eugen / Barbosa, Maria Letícia de C / Souza, Alessandra M T

Journal of cellular biochemistry

2023 Volume 124, Issue 11, Page(s) 1734–1748

Abstract: ... for the design of new N-benzyl-piperidine derivatives (4a-d) as potential multitarget-direct AChE and BuChE ... methods. ADMET predictions showed that 4a-d are anticipated to be orally bioavailable, able to cross ... molecular dynamics indicated the formation of favorable complexes between 4a-d and both cholinesterases. Derivative ...

Abstract	The pathogenic complexity of Alzheimer's disease (AD) demands the development of multitarget-directed agents aiming at improving actual pharmacotherapy. Based on the cholinergic hypothesis and considering the well-established role of butyrylcholinesterase (BuChE) in advanced stages of AD, the chemical structure of the acetylcholinesterase (AChE) inhibitor drug donepezil (1) was rationally modified for the design of new N-benzyl-piperidine derivatives (4a-d) as potential multitarget-direct AChE and BuChE inhibitors. The designed analogues were further studied through the integration of in silico and in vitro methods. ADMET predictions showed that 4a-d are anticipated to be orally bioavailable, able to cross the blood-brain barrier and be retained in the brain, and to have low toxicity. Computational docking and molecular dynamics indicated the formation of favorable complexes between 4a-d and both cholinesterases. Derivative 4a presented the lowest binding free energy estimation due to interaction with key residues from both target enzymes (-36.69 ± 4.47 and -32.23 ± 3.99 kcal/mol with AChE and BuChE, respectively). The in vitro enzymatic assay demonstrated that 4a was the most potent inhibitor of AChE (IC
MeSH term(s)	Humans ; Butyrylcholinesterase/metabolism ; Butyrylcholinesterase/therapeutic use ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/chemistry ; Cholinesterase Inhibitors/therapeutic use ; Acetylcholinesterase/metabolism ; Alzheimer Disease/drug therapy ; Alzheimer Disease/metabolism ; Piperidines/pharmacology ; Piperidines/therapeutic use ; Structure-Activity Relationship ; Molecular Docking Simulation
Chemical Substances	Butyrylcholinesterase (EC 3.1.1.8) ; Cholinesterase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; Piperidines
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.30483
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Article: A mechanism-based pathway toward administering highly active N-phage cocktails.

Smith, Nicholas M / Nguyen, Thomas D / Chin, Wai Hoe / Sanborn, Jacob T / de Souza, Harriet / Ho, Brian M / Luong, Tiffany / Roach, Dwayne R

Frontiers in microbiology

2023 Volume 14, Page(s) 1292618

Abstract: Bacteriophage (phage) therapy is being explored as a possible response to the antimicrobial resistance public health emergency. Administering a mixture of different phage types as a cocktail is one proposed strategy for therapeutic applications, but the ... ...

Abstract	Bacteriophage (phage) therapy is being explored as a possible response to the antimicrobial resistance public health emergency. Administering a mixture of different phage types as a cocktail is one proposed strategy for therapeutic applications, but the optimal method for formulating phage cocktails remains a major challenge. Each phage strain has complex pharmacokinetic/pharmacodynamic (PK/PD) properties which depend on the nano-scale size, target-mediated, self-dosing nature of each phage strain, and rapid selection of resistant subpopulations. The objective of this study was to explore the pharmacodynamics (PD) of three unique and clinically relevant anti-
Language	English
Publishing date	2023-11-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1292618
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Article ; Online: N-acetylcysteine absorption and its potential dual effect improve fitness and fruit yield in Xylella fastidiosa infected plants.

Picchi, Simone C / Rebelatto, Daniele / Martins, Paula M M / Blumer, Silvia / Mesquita, Geisa L / Hippler, Franz W R / Mattos, Dirceu / Boaretto, Rodrigo M / Machado, Marco A / Takita, Marco A / Coletta-Filho, Helvécio D / de Souza, Alessandra A

Pest management science

2024

Abstract: ... to control not only the insect but also the bacteria and plant health. We demonstrated that N-acetylcysteine ...

Abstract	Background: Xylella fastidiosa is a multi-host bacterium that can be detected in hundreds of plant species including several crops. Diseases caused by X. fastidiosa are considered a threat to global food production. The primary method for managing diseases caused by X. fastidiosa involves using insecticides to control the vector. Hence, it is necessary to adopt new and sustainable disease management technologies to control not only the insect but also the bacteria and plant health. We demonstrated that N-acetylcysteine (NAC), a low-cost cysteine analogue, is a sustainable molecule that can be used in agriculture to decrease the damage caused by X. fastidiosa and improve plant health. Results: Using Conclusion: Our research not only advances the understanding of NAC absorption in plants, but also indicates its dual effect as an antimicrobial and antioxidant molecule. This, in turn, negatively affects bacterial survival while improving plant health by decreasing oxidative stress. Overall, the positive field-based evidence supports the viability of NAC as a sustainable agricultural application. © 2024 Society of Chemical Industry.
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2001705-4
ISSN	1526-4998 ; 1526-498X
ISSN (online)	1526-4998
ISSN	1526-498X
DOI	10.1002/ps.8137
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Article: N-Doped graphene/C

Barrejón, Myriam / Arellano, Luis M / Gobeze, Habtom B / Gómez-Escalonilla, María J / Fierro, Jose Luis G / D'Souza, Francis / Langa, Fernando

Chemical science

2018 Volume 9, Issue 43, Page(s) 8221–8227

Abstract: N-Doped graphene (N-G) was chemically functionalized by ...

Abstract	N-Doped graphene (N-G) was chemically functionalized by
Language	English
Publishing date	2018-08-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/c8sc02013b
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Article ; Online: Rock n' Seeds: A database of seed functional traits and germination experiments from Brazilian rock outcrop vegetation.

Ordóñez-Parra, Carlos A / Dayrell, Roberta L C / Negreiros, Daniel / Andrade, Antônio C S / Andrade, Letícia G / Antonini, Yasmine / Barreto, Leilane C / Barros, Fernanda de V / Carvalho, Vanessa da Cruz / Corredor, Blanca Auxiliadora Dugarte / Davide, Antônio Cláudio / Duarte, Alexandre A / Feitosa, Selma Dos Santos / Fernandes, Alessandra F / Fernandes, G Wilson / Figueiredo, Maurílio Assis / Fidelis, Alessandra / Garcia, Letícia Couto / Garcia, Queila Souza /

Giorni, Victor T / Gomes, Vanessa G N / Gonçalves-Magalhães, Carollayne / Kozovits, Alessandra R / Lemos-Filho, José P / Le Stradic, Soizig / Machado, Isabel Cristina / Maia, Fabiano Rodrigo / Marques, Andréa R / Mendes-Rodrigues, Clesnan / Messias, Maria Cristina T B / Morellato, Leonor Patrícia Cerdeira / de Moraes, Moemy Gomes / Moreira, Bruno / Nunes, Flávia Peres / Oliveira, Ademir K M / Oki, Yumi / Rodrigues, Alba R P / Pietczak, Carolina / Pina, José Carlos / Ramos, Silvio Junio / Ranal, Marli A / Ribeiro-Oliveira, João Paulo / Rodrigues, Flávio H / Santana, Denise G / Santos, Fernando M G / Senhuk, Ana Paula M S / Silveira, Rodrigo A / Soares, Natalia Costa / Tonetti, Olívia Alvina Oliveira / Vieira, Vinícius Augusto da Silveira / Viana, Letícia Cristiane de Sena / Zanetti, Marcílio / Zirondi, Heloiza L / Silveira, Fernando A O

Ecology

2022 Volume 104, Issue 1, Page(s) e3852

Abstract: ... to temperate areas and vegetative traits such as leaf and wood traits. Here, we present Rock n' Seeds ...

Abstract	Advancing functional ecology depends fundamentally on the availability of data on reproductive traits, including those from tropical plants, which have been historically underrepresented in global trait databases. Although some valuable databases have been created recently, they are mainly restricted to temperate areas and vegetative traits such as leaf and wood traits. Here, we present Rock n' Seeds, a database of seed functional traits and germination experiments from Brazilian rock outcrop vegetation, recognized as outstanding centers of diversity and endemism. Data were compiled through a systematic literature search, resulting in 103 publications from which seed functional traits were extracted. The database includes information on 16 functional traits for 383 taxa from 148 genera, 50 families, and 25 orders. These 16 traits include two dispersal, six production, four morphological, two biophysical, and two germination traits-the major axes of the seed ecological spectrum. The database also provides raw data for 48 germination experiments, for a total of 10,187 records for 281 taxa. Germination experiments in the database assessed the effect of a wide range of abiotic and biotic factors on germination and different dormancy-breaking treatments. Notably, 8255 of these records include daily germination counts. This input will facilitate synthesizing germination data and using this database for a myriad of ecological questions. Given the variety of seed traits and the extensive germination information made available by this database, we expect it to be a valuable resource advancing comparative functional ecology and guiding seed-based restoration and biodiversity conservation in tropical megadiverse ecosystems. There are no copyright restrictions on the data; please cite this paper when using the current data in publications; also the authors would appreciate notification of how the data are used in publications.
MeSH term(s)	Humans ; Germination ; Ecosystem ; Brazil ; Seeds ; Plants
Language	English
Publishing date	2022-12-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010140-5
ISSN	1939-9170 ; 0012-9658
ISSN (online)	1939-9170
ISSN	0012-9658
DOI	10.1002/ecy.3852
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Article ; Online: Effect of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide in combination with antibacterial drugs against Klebsiella pneumoniae.

Cordeiro, Laísa V / Souza, Helivaldo D S / Sousa, Aleson P / Andrade Júnior, Francisco P DE / Figueiredo, Pedro T R DE / Oliveira, Rafael F DE / Athayde Filho, Petrônio F DE / Oliveira-Filho, Abrahão A / Lima, Edeltrudes DE O

Anais da Academia Brasileira de Ciencias

2023 Volume 95, Issue 2, Page(s) e20210141

Abstract: ... infections. Recently, the antibacterial activity of of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide has been ... on this, this research aimed to analyze the effects of the association of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide ...

Abstract	Klebsiella pneumoniae is a species of Gram-negative bacteria related to a wide range of infections and high rates of drug resistance. The combined use of antibacterial agents is one of the strategies that has been analyzed in recent years as part of the alternatives in the treatment of drug-resistant infections. Recently, the antibacterial activity of of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide has been demonstrated against K. pneumoniae, also indicating that this acetamide did not show significant cytotoxic potential in preliminary tests. Thus, it becomes an interesting substance for future studies that explore its antimicrobial capacity, including investigating its association with antibacterial drugs. Based on this, this research aimed to analyze the effects of the association of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide (CFA) with ciprofloxacin, cefepime, ceftazidime, meropenem and imipenem against K. pneumoniae strains. The results showed additivity when the substance was combined with ciprofloxacin and cefepime, indifference when associated with ceftazidime and synergistic effect when combined with meropenem and imipenem. Thus, the acetamide was able to optimize the effects of antibacterial drugs, reducing the concentrations necessary to cause bacterial death. These data indicate a potential future clinical use of these combinations, and further studies are needed to analyze this viability.
MeSH term(s)	Meropenem/pharmacology ; Ceftazidime/pharmacology ; Klebsiella pneumoniae ; Cefepime/pharmacology ; Anti-Bacterial Agents/pharmacology ; Imipenem/pharmacology ; Anti-Infective Agents/pharmacology ; Ciprofloxacin/pharmacology ; Acetamides/pharmacology ; Microbial Sensitivity Tests
Chemical Substances	Meropenem (FV9J3JU8B1) ; Ceftazidime (9M416Z9QNR) ; Cefepime (807PW4VQE3) ; Anti-Bacterial Agents ; Imipenem (71OTZ9ZE0A) ; Anti-Infective Agents ; Ciprofloxacin (5E8K9I0O4U) ; Acetamides
Language	English
Publishing date	2023-03-13
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	2046885-4
ISSN	1678-2690 ; 0001-3765
ISSN (online)	1678-2690
ISSN	0001-3765
DOI	10.1590/0001-3765202320210141
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Article ; Online: Formation and Photoinduced Electron Transfer in Porphyrin- and Phthalocyanine-Bearing N-Doped Graphene Hybrids Synthesized by Click Chemistry.

Arellano, Luis M / Gobeze, Habtom B / Jang, Youngwoo / Barrejón, Myriam / Parejo, Concepción / Álvarez, Julio C / Gómez-Escalonilla, María J / Sastre-Santos, Ángela / D'Souza, Francis / Langa, Fernando

Chemistry (Weinheim an der Bergstrasse, Germany)

2022 Volume 28, Issue 22, Page(s) e202200254

Abstract: ... for light-induced applications. Herein, we report the covalent functionalization of N-doped graphene (NG ... ZnPc), using the simple click chemistry approach. Covalent attachment of ZnP and ZnPc at the N-sites ...

Abstract	Graphene doped with heteroatoms such as nitrogen, boron, and phosphorous by replacing some of the skeletal carbon atoms is emerging as an important class of two-dimensional materials as it offers the much-needed bandgap for optoelectronic applications and provides better access for chemical functionalization at the heteroatom sites. Covalent grafting of photosensitizers onto such doped graphenes makes them extremely useful for light-induced applications. Herein, we report the covalent functionalization of N-doped graphene (NG) with two well-known electron donor photosensitizers, namely, zinc porphyrin (ZnP) and zinc phthalocyanine (ZnPc), using the simple click chemistry approach. Covalent attachment of ZnP and ZnPc at the N-sites of NG in NG-ZnP and NG-ZnPc hybrids was confirmed by using a range of spectroscopic, thermogravimetric and imaging techniques. Ground- and excited-state interactions in NG-ZnP and NG-ZnPc were monitored by using spectral and electrochemical techniques. Efficient quenching of photosensitizer fluorescence in these hybrids was observed, and the relatively easier oxidations of ZnP and ZnPc supported excited-state charge-separation events. Photoinduced charge separation in NG-ZnP and NG-ZnPc hybrids was confirmed by using the ultrafast pump-probe technique. The measured rate constants were of the order of 10
Language	English
Publishing date	2022-03-28
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202200254
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