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Article ; Online: In Silico Study towards Repositioning of FDA-Approved Drug Candidates for Anticoronaviral Therapy: Molecular Docking, Molecular Dynamics and Binding Free Energy Calculations.

Qayed, Wesam S / Ferreira, Rafaela S / Silva, José Rogério A

2022 Volume 27, Issue 18

Abstract: The SARS-CoV-2 targets were evaluated for a set of FDA-approved drugs using a combination of drug repositioning and rigorous computational modeling methodologies such as molecular docking and molecular dynamics (MD) simulations followed by binding free ... ...

Abstract	The SARS-CoV-2 targets were evaluated for a set of FDA-approved drugs using a combination of drug repositioning and rigorous computational modeling methodologies such as molecular docking and molecular dynamics (MD) simulations followed by binding free energy calculations. Six FDA-approved drugs including, Ouabain, Digitoxin, Digoxin, Proscillaridin, Salinomycin and Niclosamide with promising anti-SARS-CoV-2 activity were screened in silico against four SARS-CoV-2 proteins-papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), SARS-CoV-2 main protease (Mpro), and adaptor-associated kinase 1 (AAK1)-in an attempt to define their promising targets. The applied computational techniques suggest that all the tested drugs exhibited excellent binding patterns with higher scores and stable complexes compared to the native protein cocrystallized inhibitors. Ouabain was suggested to act as a dual inhibitor for both PLpro and Mpro enzymes, while Digitoxin bonded perfectly to RdRp. In addition, Salinomycin targeted PLpro. Particularly, Niclosamide was found to target AAK1 with greater affinity compared to the reference drug. Our study provides comprehensive molecular-level insights for identifying or designing novel anti-COVID-19 drugs.
MeSH term(s)	Antiviral Agents/chemistry ; COVID-19 ; Cysteine Endopeptidases/chemistry ; Digitoxin ; Digoxin ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Niclosamide ; Ouabain ; Papain/metabolism ; Proscillaridin ; RNA-Dependent RNA Polymerase ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Ouabain (5ACL011P69) ; Digoxin (73K4184T59) ; Niclosamide (8KK8CQ2K8G) ; Digitoxin (E90NZP2L9U) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Papain (EC 3.4.22.2) ; Proscillaridin (KC6BL281EN)
Language	English
Publishing date	2022-09-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27185988
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Zs.MO 81: Show issues

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Article ; Online: Drug repurposing and computational modeling for discovery of inhibitors of the main protease (M

Silva, José Rogério A / Kruger, Hendrik G / Molfetta, Fábio A

RSC advances

2021 Volume 11, Issue 38, Page(s) 23450–23458

Abstract: The main protease ( ... ...

Abstract	The main protease (M
Language	English
Publishing date	2021-07-02
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra03956c
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Article ; Online: Role of UDP-N-acetylmuramic acid in the regulation of MurA activity revealed by molecular dynamics simulations.

de Oliveira, Maycon Vinicius Damasceno / da Costa, Kauê S / Silva, José Rogério A / Lameira, Jerônimo / Lima, Anderson H

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 4, Page(s) e4969

Abstract: The peptidoglycan biosynthesis pathway plays a vital role in bacterial cells, and facilitates peptidoglycan layer formation, a fundamental structural component of the bacterial cell wall. The enzymes in this pathway are candidates for antibiotic ... ...

Abstract	The peptidoglycan biosynthesis pathway plays a vital role in bacterial cells, and facilitates peptidoglycan layer formation, a fundamental structural component of the bacterial cell wall. The enzymes in this pathway are candidates for antibiotic development, as most do not have mammalian homologues. The UDP-N-acetylglucosamine (UNAG) enolpyruvyl transferase enzyme (MurA) in the peptidoglycan pathway cytoplasmic step is responsible for the phosphoenolpyruvate (PEP)-UNAG catalytic reaction, forming UNAG enolpyruvate and inorganic phosphate. Reportedly, UDP-N-acetylmuramic acid (UNAM) binds tightly to MurA forming a dormant UNAM-PEP-MurA complex and acting as a MurA feedback inhibitor. MurA inhibitors are complex, owing to competitive binding interactions with PEP, UNAM, and UNAG at the MurA active site. We used computational methods to explore UNAM and UNAG binding. UNAM showed stronger hydrogen-bond interactions with the Arg120 and Arg91 residues, which help to stabilize the closed conformation of MurA, than UNAG. Binding free energy calculations using end-point computational methods showed that UNAM has a higher binding affinity than UNAG, when PEP is attached to Cys115. The unbinding process, simulated using τ-random acceleration molecular dynamics, showed that UNAM has a longer relative residence time than UNAG, which is related to several complex dissociation pathways, each with multiple intermediate metastable states. This prevents the loop from opening and exposing the Arg120 residue to accommodate UNAG and potential new ligands. Moreover, we demonstrate the importance of Cys115-linked PEP in closed-state loop stabilization. We provide a basis for evaluating novel UNAM analogues as potential MurA inhibitors. PUBLIC SIGNIFICANCE: MurA is a critical enzyme involved in bacterial cell wall biosynthesis and is involved in antibiotic resistance development. UNAM can remain in the target protein's active site for an extended time compared to its natural substrate, UNAG. The prolonged interaction of this highly stable complex known as the 'dormant complex' comprises UNAM-PEP-MurA and offers insights into antibiotic development, providing potential options against drug-resistant bacteria and advancing our understanding of microbial biology.
MeSH term(s)	Molecular Dynamics Simulation ; Peptidoglycan ; Alkyl and Aryl Transferases/metabolism ; Anti-Bacterial Agents/pharmacology ; Uridine Diphosphate ; Muramic Acids
Chemical Substances	N-acetylmuramic acid (246FXU111L) ; Peptidoglycan ; Alkyl and Aryl Transferases (EC 2.5.-) ; Anti-Bacterial Agents ; Uridine Diphosphate (58-98-0) ; Muramic Acids
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4969
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 1: Show issues

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Article ; Online: Nutritional performance, hepatic and renal function in goats fed diets containing detoxified castor cake at different stages of pregnancy.

Araújo, Ricardo A DE / Neiva, José N M / Cândido, Magno José D / Rogério, Marcos Cláudio P / Silva, Luiza DE N C DA / Pompeu, Roberto Cláudio F F

Anais da Academia Brasileira de Ciencias

2022 Volume 94, Issue 4, Page(s) e20201775

Abstract: We evaluated the influence of the substitution of soybean meal by detoxified castor cake on performance, digestibility of nutrients, nitrogen balance, hepatic and renal functions of pregnant goats fed with diets containing detoxified castor cake by ... ...

Abstract	We evaluated the influence of the substitution of soybean meal by detoxified castor cake on performance, digestibility of nutrients, nitrogen balance, hepatic and renal functions of pregnant goats fed with diets containing detoxified castor cake by alkaline solutions during the stages (first two-thirds and final third) of pregnancy. Three diets were provided: one based on soybean meal and the other two based on castor cake detoxified with whit calcium hydroxide or sodium hydroxide. Goats fed detoxified castor cake sodium hydroxide had lower consumption. Was no effect (P>0.05) of diets or stages on the digestibility of dry matter and nutrients. The goats that received the diets based on soybean meal and detoxified castor cake calcium hydroxide consumed larger amounts of nitrogen. The goats fed with diet the basis of SM had greater weight in the parturition day. The average levels of enzymes for hepatic and renal functions were within normal patterns. Of enzymes related to liver metabolism, only the gamma-glutamyl transferase increased in the final third of pregnancy. The present study demonstrated that detoxified castor by sodium hydroxide reduces the consumption of goats during gestation, but did not affect negatively the renal and hepatic parameters.
MeSH term(s)	Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Calcium Hydroxide ; Castor Oil ; Diet/veterinary ; Digestion ; Female ; Goats ; Kidney/physiology ; Liver ; Nitrogen ; Pregnancy ; Sodium Hydroxide ; Glycine max ; Transferases
Chemical Substances	Sodium Hydroxide (55X04QC32I) ; Castor Oil (8001-79-4) ; Transferases (EC 2.-) ; Nitrogen (N762921K75) ; Calcium Hydroxide (PF5DZW74VN)
Language	English
Publishing date	2022-10-10
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	2046885-4
ISSN	1678-2690 ; 0001-3765
ISSN (online)	1678-2690
ISSN	0001-3765
DOI	10.1590/0001-3765202220201775
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Article ; Online: Novel Azine Linked Hybrids of 2-Indolinone and Thiazolodinone Scaffolds as CDK2 Inhibitors with Potential Anticancer Activity: In Silico Design, Synthesis, Biological, Molecular Dynamics and Binding Free Energy Studies.

Qayed, Wesam S / Hassan, Mostafa A / El-Sayed, Wael M / Rogério A Silva, José / Aboul-Fadl, Tarek

Bioorganic chemistry

2022 Volume 126, Page(s) 105884

Abstract: Molecular hybrid of 2-indolinone-thiazolidinone is a well known scaffold for variable biological activities including anticancer activity. Accordingly, in the current work aided with structure-based molecular modeling studies, a library of novel twenty- ... ...

Abstract	Molecular hybrid of 2-indolinone-thiazolidinone is a well known scaffold for variable biological activities including anticancer activity. Accordingly, in the current work aided with structure-based molecular modeling studies, a library of novel twenty-six hybrids, 4(a-z), was designed and synthesized. Docking studies in the active site of CDK2, one of the key checkpoints enzymes, revealed that the binding scores of the designed molecules are comparable to the reference enzyme's inhibitors Sunitinib, Nintedanib, and Semaxanib. Variable antiproliferative activities are shown for these molecules against human liver (HepG2), breast (MCF7), and colon (HCT-29) cell lines considering Doxrubacin as a refrence drug. Compared to cytotoxic activities on the normal fibroblasts (WI-38), the tested molecules had better selectivity against the cancerous cells, expressed by their selectivity index (SI), than Doxrubacin and compound 4i was the safest compound. CDK2 inhibitory results of compounds 4f, 4g, 4h, and 4w showed IC
MeSH term(s)	Antineoplastic Agents/chemistry ; Cell Line, Tumor ; Cell Proliferation ; Cyclin-Dependent Kinase 2/metabolism ; Drug Design ; Drug Screening Assays, Antitumor ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Oxindoles ; Structure-Activity Relationship ; Sunitinib/pharmacology
Chemical Substances	Antineoplastic Agents ; Oxindoles ; 2-oxindole (0S9338U62H) ; CDK2 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 2 (EC 2.7.11.22) ; Sunitinib (V99T50803M)
Language	English
Publishing date	2022-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2022.105884
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Zs.A 4207: Show issues

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Jg. 1995 - 2021: Lesesall (2.OG)
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Article ; Online: Computational Analysis of Triazole-Based Kojic Acid Analogs as Tyrosinase Inhibitors by Molecular Dynamics and Free Energy Calculations.

Martins, Lucas Sousa / Gonçalves, Reinaldo W A / Moraes, Joana J S / Alves, Cláudio Nahum / Silva, José Rogério A

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 23

Abstract: Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key ... ...

Abstract	Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key metalloenzyme of the melanogenesis process. Initially, molecular docking calculations satisfactorily predicted the binding mode of evaluated KA analogs, where the KA part overlays the crystal conformation of the KA inhibitor into the catalytic site of TYR. The MD simulations were followed by the LIE method, which reproduced the experimental binding free energies for KA analogs with an
Language	English
Publishing date	2022-11-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27238141
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Article ; Online: QM/MM Study of the Fosfomycin Resistance Mechanism Involving FosB Enzyme.

Lima, Anderson H / Silva, José Rogério A / Alves, Cláudio Nahum / Lameira, Jerônimo

ACS omega

2021 Volume 6, Issue 19, Page(s) 12507–12512

Abstract: Multidrug-resistant organisms contain antibiotic-modifying enzymes that facilitate resistance to a variety of antimicrobial compounds. Particularly, the fosfomycin (FOF) drug can be structurally modified by several FOF-modifying enzymes before it reaches ...

Abstract	Multidrug-resistant organisms contain antibiotic-modifying enzymes that facilitate resistance to a variety of antimicrobial compounds. Particularly, the fosfomycin (FOF) drug can be structurally modified by several FOF-modifying enzymes before it reaches the biological target. Among them, FosB is an enzyme that utilizes l-cysteine or bacillithiol in the presence of a divalent metal to open the epoxide ring of FOF and, consequently, inactivate the drug. Here, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of the reaction involving FosB and FOF. The calculated free-energy profiles show that the cost to open the epoxide ring of FOF at the C2 atom is ∼3.0 kcal/mol higher than that at the C1 atom. Besides, our QM/MM MD results revealed the critical role of conformation change of Cys9 and Asn50 to release the drug from the active site. Overall, the present study provides insights into the mechanism of FOF-resistant proteins.
Language	English
Publishing date	2021-05-03
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c00096
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Article ; Online: Computational Analysis of SAM Analogs as Methyltransferase Inhibitors of nsp16/nsp10 Complex from SARS-CoV-2.

Balieiro, Alessandra M / Anunciação, Eduarda L S / Costa, Clauber H S / Qayed, Wesam S / Silva, José Rogério A

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: Methyltransferases (MTases) enzymes, responsible for RNA capping into severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are emerging important targets for the design of new anti-SARS-CoV-2 agents. Here, analogs of S-adenosylmethionine (SAM), ... ...

Abstract	Methyltransferases (MTases) enzymes, responsible for RNA capping into severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are emerging important targets for the design of new anti-SARS-CoV-2 agents. Here, analogs of S-adenosylmethionine (SAM), obtained from the bioisosteric substitution of the sulfonium and amino acid groups, were evaluated by rigorous computational modeling techniques such as molecular dynamics (MD) simulations followed by relative binding free analysis against nsp16/nsp10 complex from SARS-CoV-2. The most potent inhibitor (
MeSH term(s)	Humans ; S-Adenosylmethionine/pharmacology ; S-Adenosylmethionine/metabolism ; SARS-CoV-2 ; Viral Nonstructural Proteins/metabolism ; COVID-19/drug therapy ; Methyltransferases/metabolism
Chemical Substances	S-Adenosylmethionine (7LP2MPO46S) ; Viral Nonstructural Proteins ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2022-11-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232213972
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Article ; Online: Are there differences in the adaptive profile of hair sheep and their crosses with wool breeds?

Silveira, Robson Mateus Freitas / Garcia, Paulo Rogério / de Castro Júnior, Sérgio Luís / Arno, Alessandra / da Silva, Iran José Oliveira

International journal of biometeorology

2023 Volume 68, Issue 2, Page(s) 229–236

Abstract: This study aimed to evaluate and compare the physiological performance of different genetic groups of sheep, by physiological variables and serum hormone levels, in a hot weather environment. Thirty sheep from five genetic groups were used: Santa Inês ( ... ...

Abstract	This study aimed to evaluate and compare the physiological performance of different genetic groups of sheep, by physiological variables and serum hormone levels, in a hot weather environment. Thirty sheep from five genetic groups were used: Santa Inês (SI), ½ Dorper + ½ Santa Inês (DO), ½ Ilê de France + ½ Santa Inês (IF), ½ Suffolk + ½ Santa Inês (SK), and ½ Texel + ½ Santa Inês (TX). The readings and records of physiological parameters (respiratory rate (RR), rectal temperature (RT), auricular cavity temperature (ACT), and surface temperature (ST)) were carried out at 7:00 am, 1:00 pm, and 7:00 pm, in 12 non-consecutive days. The collections of blood samples for hormone analysis (triiodothyronine (T
MeSH term(s)	Sheep/genetics ; Animals ; Wool ; Body Temperature Regulation ; Body Temperature ; Thyroid Hormones ; Triiodothyronine
Chemical Substances	Thyroid Hormones ; Triiodothyronine (06LU7C9H1V)
Language	English
Publishing date	2023-11-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	280324-0
ISSN	1432-1254 ; 0020-7128
ISSN (online)	1432-1254
ISSN	0020-7128
DOI	10.1007/s00484-023-02585-2
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Zs.A 998: Show issues

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Article ; Online: Piroplasmid Infections Among Domestic Dogs in the Mountain City of Rio de Janeiro, Brazil.

Palmer, João Pedro Siqueira / Gazêta, Gilberto Salles / André, Marcos Rogério / Fialho, Priscila Alves / Corrêa, Laís Lisboa / Damasceno, José André Lessa / Israel, Carolina Bistritschan / Pereira, Rafael Rempto / da Silva Barbosa, Alynne

Acta parasitologica

2024

Abstract: Purpose: The aim of the present study was to analyze the frequency of the piroplasmids in blood from dogs and ticks recovered from these animals in Teresópolis city, located in the mountain region of Rio de Janeiro state, Brazil. In addition to the ... ...

Abstract	Purpose: The aim of the present study was to analyze the frequency of the piroplasmids in blood from dogs and ticks recovered from these animals in Teresópolis city, located in the mountain region of Rio de Janeiro state, Brazil. In addition to the clinical and hematological profile. Methods: A total of 400 dogs attended in a veterinary clinic in this city between 2020 and 2021 were included. The blood was collected from the dogs, along with ticks and information on these dogs was obtained through a questionnaire applied to the owners. Thin-smear analyses and complete blood counts were performed. All forms characteristic of piroplasmids were measured and classified morphologically. The blood was also subjected to PCR assays based on the genes 18S rRNA and hsp70. In addition, the ixodid ticks were classified morphologically and subjected to PCR for piroplasmids research. The amplified products were sent for gene sequencing. Results: Piroplasmids were detected in 2.3% of the dogs. The variables statistically associated with infections in these animals were hemorrhage/bleeding, jaundice, anisocytosis, activated monocytes and macroplatelets (p ≤ 0.05). Piriform, ring-shaped, oval and aberrant structures were viewed in erythrocytes, neutrophils and monocytes, with lengths greater than and less than 2.5 µm. The nine positive samples from these dogs were characterized as due to Rangelia vitalii. However, one sequence from B. vogeli was detected in a single adult specimen of R. sanguineus. Conclusion: Although circulation of two species of piroplasmids potentially infective for domestic dogs has been observed in the mountain city of Rio de Janeiro, infection due to R. vitalii was mostly seen in the dogs of the present study.
Language	English
Publishing date	2024-04-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1132735-2
ISSN	1896-1851 ; 0065-1478 ; 1230-2821
ISSN (online)	1896-1851
ISSN	0065-1478 ; 1230-2821
DOI	10.1007/s11686-024-00843-w
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