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Article ; Online: In silico study of the interaction of phenazines with tuberculostatic activity with known molecular targets of Mycobacterium tuberculosis

Raphael S.F. Silva / Joyce S.F.D. de Almeida / Tanos C.C. França

Results in Chemistry, Vol 6, Iss , Pp 101094- (2023)

2023

Abstract: Phenazines derived from β-lapachone had tuberculostatic activity reported in the literature. However, very little is known about their mechanism of action or molecular targets. In order to investigate this, we performed an in silico study through ... ...

Abstract	Phenazines derived from β-lapachone had tuberculostatic activity reported in the literature. However, very little is known about their mechanism of action or molecular targets. In order to investigate this, we performed an in silico study through molecular docking and molecular dynamics simulations, meant to evaluate the interactions of ten phenazines (active or not) with the molecular targets for rifampicin, isoniazid and ethambutol, three drugs used in the treatment of tuberculosis. The results showed that these phenazines might bind to the enzyme arabinosyltransferase from Mycobacterium tuberculosis, the same molecular target of ethambutol. The results obtained in this work open the perspective to design and synthesis of new phenazinic inhibitors of arabinosyltransferase from M. tuberculosis.
Keywords	Phenazines ; Ethambutol ; Tuberculosis ; Arabinosyltransferase ; Molecular docking ; Molecular dynamics ; Chemistry ; QD1-999
Subject code	541
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Molecular modeling of Mannich phenols as reactivators of human acetylcholinesterase inhibited by A-series nerve agents.

Vieira, Leandro A / Almeida, Joyce S F D / De Koning, Martijn C / LaPlante, Steven R / Borges, Itamar / França, Tanos C C

Chemico-biological interactions

2023 Volume 382, Page(s) 110622

Abstract: The A-series is the most recent generation of chemical warfare nerve agents (CWA) which act directly on the inhibition of the human acetylcholinesterase (HssAChE) enzyme. These compounds lack accurate experimental data on their physicochemical properties, ...

Abstract	The A-series is the most recent generation of chemical warfare nerve agents (CWA) which act directly on the inhibition of the human acetylcholinesterase (HssAChE) enzyme. These compounds lack accurate experimental data on their physicochemical properties, and there is no evidence that traditional antidotes effectively reactivate HssAChE inhibited by them. In the search for potential antidotes, we employed virtual screening, molecular docking, and molecular dynamics (MD) simulations for the theoretical assessment of the performance of a library of Mannich phenols as potential reactivators of HssAChE inhibited by the Novichok agents A-230, A-232, and A-234, in comparison with the commercial oximes pralidoxime (2-PAM), asoxime (HI-6), trimedoxime (TMB-4), and obidoxime. Following the near-attack conformation (NAC) approach, our results suggest that the compounds assessed would face difficulties in triggering the proposed nucleophilic in-line displacement mechanism. Despite this, it was observed that certain Mannich phenols presented similar or superior results to those obtained by reference oximes against A-232 and A-234 model, suggesting that these compounds can adopt more favourable conformations. Additional binding energy calculations confirmed the stability of the model/ligands complexes and the reactivating potential observed in the molecular docking and MD studies. Our findings indicate that the Mannich phenols could be alternative antidotes and that their efficacy should be evaluated experimentally against the A-series CWA.
MeSH term(s)	Humans ; Antidotes/pharmacology ; Cholinesterase Reactivators/pharmacology ; Acetylcholinesterase/metabolism ; Nerve Agents ; Molecular Docking Simulation ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/chemistry ; Oximes/pharmacology ; Oximes/chemistry ; Trimedoxime/chemistry ; Trimedoxime/pharmacology ; Chemical Warfare Agents/pharmacology ; Pyridinium Compounds/pharmacology
Chemical Substances	Antidotes ; Cholinesterase Reactivators ; Acetylcholinesterase (EC 3.1.1.7) ; Nerve Agents ; Cholinesterase Inhibitors ; pralidoxime (P7MU9UTP52) ; Oximes ; Trimedoxime (56-97-3) ; Chemical Warfare Agents ; Pyridinium Compounds
Language	English
Publishing date	2023-07-12
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	218799-1
ISSN	1872-7786 ; 0009-2797
ISSN (online)	1872-7786
ISSN	0009-2797
DOI	10.1016/j.cbi.2023.110622
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Article ; Online: Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2.

Ribeiro, Rayssa / Botelho, Fernanda D / Pinto, Amanda M V / La Torre, Antonia M A / Almeida, Joyce S F D / LaPlante, Steven R / Franca, Tanos C C / Veiga-Junior, Valdir F / Dos Santos, Marcelo C

Journal of molecular modeling

2023 Volume 29, Issue 6, Page(s) 183

Abstract: Context: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of ... ...

Abstract	Context: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. Methods: The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.
MeSH term(s)	Humans ; SARS-CoV-2 ; Biological Products/pharmacology ; COVID-19 ; Molecular Dynamics Simulation ; Databases, Protein ; Molecular Docking Simulation ; Antiviral Agents/pharmacology
Chemical Substances	Biological Products ; Antiviral Agents
Language	English
Publishing date	2023-05-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05586-5
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Article ; Online: Identification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach.

Botelho, Fernanda D / Santos, Marcelo C / Gonçalves, Arlan S / França, Tanos C C / LaPlante, Steven R / de Almeida, Joyce S F D

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 12, Page(s) 5309–5319

Abstract: Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and ...

Abstract	Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and high toxicity turns ricin into a potential weapon for terrorist attacks, urging the need of discovering effective antidotes. On this context, we used computational techniques, in order to identify potential ricin inhibitors among approved drugs. Two libraries were screened by two different docking algorithms, followed by molecular dynamics simulations and MM-PBSA calculations in order to corroborate the docking results. Three drugs were identified as potential ricin inhibitors: deferoxamine, leucovorin and plazomicin. Our calculations showed that these compounds were able to, simultaneously, form hydrogen bonds with residues of the catalytic site and the secondary binding site of RTA, qualifying as potential antidotes against intoxication by ricin.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Antidotes ; Drug Repositioning ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Ricin/chemistry ; Ricin/metabolism ; Ricin/pharmacology
Chemical Substances	Antidotes ; Ricin (9009-86-3)
Language	English
Publishing date	2021-01-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1870154
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Article ; Online: 1

Correia, Banny S B / Ferreira, Vinicius G / Piagge, Priscila M F D / Almeida, Mariana B / Assunção, Nilson A / Raimundo, Joyce R S / Fonseca, Fernando L A / Carrilho, Emanuel / Cardoso, Daniel R

Journal of proteome research

2022 Volume 21, Issue 7, Page(s) 1640–1653

Abstract: The coronavirus disease 2019 (Covid-19), which caused respiratory problems in many patients worldwide, led to more than 5 million deaths by the end of 2021. Experienced symptoms vary from mild to severe illness. Understanding the infection severity to ... ...

Abstract	The coronavirus disease 2019 (Covid-19), which caused respiratory problems in many patients worldwide, led to more than 5 million deaths by the end of 2021. Experienced symptoms vary from mild to severe illness. Understanding the infection severity to reach a better prognosis could be useful to the clinics, and one study area to fulfill one piece of this biological puzzle is metabolomics. The metabolite profile and/or levels being monitored can help predict phenotype properties. Therefore, this study evaluated plasma metabolomes of 110 individual samples, 57 from control patients and 53 from recent positive cases of Covid-19 (IgM 98% reagent), representing mild to severe symptoms, before any clinical intervention. Polar metabolites from plasma samples were analyzed by quantitative
MeSH term(s)	Amino Acids ; COVID-19/diagnosis ; Formates ; Glucuronates ; Glycerol ; Humans ; Lactates ; Metabolomics ; SARS-CoV-2
Chemical Substances	Amino Acids ; Formates ; Glucuronates ; Lactates ; Glycerol (PDC6A3C0OX)
Language	English
Publishing date	2022-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00977
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Article ; Online: COMPARAÇÃO ENTRE MÉTODOS PARA DETERMINAÇÃO DE CARGAS ATÔMICAS EM SISTEMAS MOLECULARES

Fernanda Diniz Botelho / Roberta Siqueira Soldaini de Oliveira / Joyce S. F. D. de Almeida / Tanos C. C. França / Itamar Borges Jr.

Química Nova, Vol 44, Iss 2, Pp 161-

A MOLÉCULA N-{N-(PTERINA-7-IL)CARBONILGLICIL}-L-TIROSINA (NNPT)

2021 Volume 171

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Sociedade Brasileira de Química
Document type	Article ; Online
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Article ; Online: Discovery Science highlights from the 17th International Conference on Malignant Lymphoma.

Forestieri, Gabriela / de Almeida, Joyce Marques / Napoli, Sara / Piffaretti, Deborah / Tarantelli, Chiara / Zhang, Fangwen / Mensah, Afua Adjeiwaa

Hematological oncology

2024 Volume 42, Issue 3, Page(s) e3275

Language	English
Publishing date	2024-04-23
Publishing country	England
Document type	Journal Article
ZDB-ID	604884-5
ISSN	1099-1069 ; 0278-0232
ISSN (online)	1099-1069
ISSN	0278-0232
DOI	10.1002/hon.3275
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Article: ¹H qNMR-Based Metabolomics Discrimination of Covid-19 Severity

Correia, Banny S. B. / Ferreira, Vinicius G. / Piagge, Priscila M. F. D. / Almeida, Mariana B. / Assunção, Nilson A. / Raimundo, Joyce R. S. / Fonseca, Fernando L. A. / Carrilho, Emanuel / Cardoso, Daniel R.

Journal of proteome research. 2022 June 08, v. 21, no. 7

2022

Abstract: ... to those in the control group (Tukey’s HSD p-value cutoff = 0.05), affecting the lactate, phenylalanine, tyrosine, and ... tryptophan biosynthesis and d-glutamine, d-glutamate, and glycerolipid metabolisms. These metabolic ...

Abstract	The coronavirus disease 2019 (Covid-19), which caused respiratory problems in many patients worldwide, led to more than 5 million deaths by the end of 2021. Experienced symptoms vary from mild to severe illness. Understanding the infection severity to reach a better prognosis could be useful to the clinics, and one study area to fulfill one piece of this biological puzzle is metabolomics. The metabolite profile and/or levels being monitored can help predict phenotype properties. Therefore, this study evaluated plasma metabolomes of 110 individual samples, 57 from control patients and 53 from recent positive cases of Covid-19 (IgM 98% reagent), representing mild to severe symptoms, before any clinical intervention. Polar metabolites from plasma samples were analyzed by quantitative ¹H NMR. Glycerol, 3-aminoisobutyrate, formate, and glucuronate levels showed alterations in Covid-19 patients compared to those in the control group (Tukey’s HSD p-value cutoff = 0.05), affecting the lactate, phenylalanine, tyrosine, and tryptophan biosynthesis and d-glutamine, d-glutamate, and glycerolipid metabolisms. These metabolic alterations show that SARS-CoV-2 infection led to disturbance in the energetic system, supporting the viral replication and corroborating with the severe clinical conditions of patients. Six polar metabolites (glycerol, acetate, 3-aminoisobutyrate, formate, glucuronate, and lactate) were revealed by PLS-DA and predicted by ROC curves and ANOVA to be potential prognostic metabolite panels for Covid-19 and considered clinically relevant for predicting infection severity due to their straight roles in the lipid and energy metabolism. Thus, metabolomics from samples of Covid-19 patients is a powerful tool for a better understanding of the disease mechanism of action and metabolic consequences of the infection in the human body and may corroborate allowing clinicians to intervene quickly according to the needs of Covid-19 patients.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; acetates ; biosynthesis ; disease severity ; energy metabolism ; formates ; glutamic acid ; glycerol ; humans ; lactic acid ; lipids ; mechanism of action ; metabolites ; metabolome ; metabolomics ; phenotype ; phenylalanine ; prognosis ; proteome ; research ; tryptophan ; tyrosine ; virus replication
Language	English
Dates of publication	2022-0608
Size	p. 1640-1653.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00977
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Surface screening, molecular modeling and in vitro studies on the interactions of aflatoxin M1 and human enzymes acetyl- and butyrylcholinesterase.

de Almeida, Joyce S F D / Cavalcante, Samir F de A / Dolezal, Rafael / Kuca, Kamil / Musilek, Kamil / Jun, Daniel / França, Tanos C C

Chemico-biological interactions

2019 Volume 308, Page(s) 113–119

Abstract: Aflatoxin M1 (AFM1) is a mycotoxin produced by Aspergillus fungi and found in contaminated milk, breastfeed and dairy products, being highly toxic and carcinogenic to humans and other mammalian species. It is also produced in the human body as a ... ...

Abstract	Aflatoxin M1 (AFM1) is a mycotoxin produced by Aspergillus fungi and found in contaminated milk, breastfeed and dairy products, being highly toxic and carcinogenic to humans and other mammalian species. It is also produced in the human body as a metabolite of aflatoxin B1 (AFB1), one of the most toxic natural products known. Previous studies have shown that AFM1 is a potential inhibitor of the enzyme acetylcholinesterase (AChE), and therefore, a potential neurotoxic agent. In this work, surface screening (SS) and molecular dynamics (MD) simulation on human acetylcholinesterase AChE (HssAChE) were performed to corroborate literature data regarding preferential binding sites and type of inhibition. Also, an inedited theoretical study on the interactions of AFM1 with human butyrylcholinesterase (HssBChE) was performed. In vitro inhibition tests on both enzymes were done to support theoretical results. MD simulations suggested the catalytic anionic site of HssAChE as the preferential binding site for AFM1 and also that this metabolite is not a good inhibitor of HssBChE, corroborating previous studies. In vitro assays also corroborated molecular modeling studies by showing that AFM1 did not inhibit BChE and was able to inhibit AChE, although not as much as AFB1.
MeSH term(s)	Acetylcholinesterase/chemistry ; Acetylcholinesterase/metabolism ; Aflatoxin B1/chemistry ; Aflatoxin B1/metabolism ; Aflatoxin M1/chemistry ; Aflatoxin M1/metabolism ; Aspergillus/metabolism ; Binding Sites ; Butyrylcholinesterase/chemistry ; Butyrylcholinesterase/metabolism ; Catalytic Domain ; Humans ; Molecular Dynamics Simulation ; Surface Properties ; Thermodynamics
Chemical Substances	Aflatoxin M1 (6795-23-9) ; Aflatoxin B1 (9N2N2Y55MH) ; Acetylcholinesterase (EC 3.1.1.7) ; Butyrylcholinesterase (EC 3.1.1.8)
Language	English
Publishing date	2019-05-14
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	218799-1
ISSN	1872-7786 ; 0009-2797
ISSN (online)	1872-7786
ISSN	0009-2797
DOI	10.1016/j.cbi.2019.05.022
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Article ; Online: Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors.

Botelho, Fernanda D / Dos Santos, Marcelo C / Gonçalves, Arlan da S / Kuca, Kamil / Valis, Martin / LaPlante, Steven R / França, Tanos C C / de Almeida, Joyce S F D

Toxins

2020 Volume 12, Issue 12

Abstract: Ricin is a toxin found in the castor seeds and listed as a chemical weapon by the Chemical Weapons Convention (CWC) due to its high toxicity combined with the easiness of obtention and lack of available antidotes. The relatively frequent episodes of ... ...

Abstract	Ricin is a toxin found in the castor seeds and listed as a chemical weapon by the Chemical Weapons Convention (CWC) due to its high toxicity combined with the easiness of obtention and lack of available antidotes. The relatively frequent episodes of usage or attempting to use ricin in terrorist attacks reinforce the urge to develop an antidote for this toxin. In this sense, we selected in this work the current RTA (ricin catalytic subunit) inhibitor with the best experimental performance, as a reference molecule for virtual screening in the PubChem database. The selected molecules were then evaluated through docking studies, followed by drug-likeness investigation, molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations. In every step, the selection of molecules was mainly based on their ability to occupy both the active and secondary sites of RTA, which are located right next to each other, but are not simultaneously occupied by the current RTA inhibitors. Results show that the three PubChem compounds 18309602, 18498053, and 136023163 presented better overall results than the reference molecule itself, showing up as new hits for the RTA inhibition, and encouraging further experimental evaluation.
MeSH term(s)	Algorithms ; Binding Sites ; Chemical Warfare Agents/chemistry ; Drug Discovery ; Hydrogen Bonding ; Ligands ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Ricin/antagonists & inhibitors ; Ricin/chemistry
Chemical Substances	Chemical Warfare Agents ; Ligands ; Ricin (9009-86-3)
Language	English
Publishing date	2020-11-26
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518395-3
ISSN	2072-6651 ; 2072-6651
ISSN (online)	2072-6651
ISSN	2072-6651
DOI	10.3390/toxins12120746
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