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Alzheimer's disease (AD) is a common brain disease associated with cognitive impairment and dementia. donepezil, an acetylcholinesterase (AChE) inhibitor drug as a commercial AD drug represents a non-cost-effective treatment with the toxic effects reported. As the prevalence of AD increases, the development of effective therapeutic treatments is urgently required. Laminaria digitata is a brown seaweed claimed to be able to prevent and treat neurodegenerative diseases. Therefore, this study measured and compared the binding affinity and toxicity of seven common phytoconstituents in Laminaria digitata against acetylcholinesterase (AChE) with those of donepezil using a molecular docking approach. The binding free energy values of donepezil, dieckol, eckol, fucodiphlorethol G, 7-Phloroecol, laminaran, alginic acid, and fucoidan with acetylcholinesterase (AChE) were −12.3, −13.5, −10.5, −8,7, −9.7, −8.0, −10.3, and −7.4 kcal/mol. All ligands constantly interacted with the AChE amino acid residues, namely Tyr124. Dieckol, with the strongest and most stable interaction, is classified as class IV toxicity, with an LD50 value of 866 mg/kg. It has aryl hydrocarbon receptor (AhR) and mitochondrial membrane potential (MMP) toxicity at certain doses. Theoretically, based on Lipinski's rule, dieckol is likely to have poor absorption and permeation properties; therefore, several considerations during the drug discovery process are needed. [ABSTRACT FROM AUTHOR]

Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.

As infecções bacterianas e a resistência antimicrobiana, particularmente de Klebsiella pneumoniae, continuam sendo algumas das questões mais desafiadoras que ameaçam a saúde das pessoas em todo o mundo. Compostos naturais derivados de plantas têm recebido atenção considerável por seu papel como potencial antibacteriano e para mitigar a resistência a antibióticos. Entre esses compostos, identificou-se o linalol, importante metabólito secundário, encontrado em grande variedade de plantas, e que apresenta diversas propriedades farmacológicas, incluindo atividade antibacteriana. Portanto, este estudo teve como objetivo investigar, por meio do docking molecular, a atividade antibacteriana do linalol contra Klebsiella pneumoniae e suas interações com a ATP sintase. Neste trabalho, foram realizados ensaios in vitro, aplicando-se a técnica de microdiluição em caldo, obtendo-se a concentração inibitória e bactericida mínima (CIM e CBM). O procedimento adotado para o docking molecular foi o de ancoramento com a proteína rígida e os ligantes flexíveis. As análises in vitro mostraram que o linalol teve efeito bactericida contra K. pneumoniae na concentração de 256 µg/mL. O docking molecular revelou que o linalol interage com o centro ativo da subunidade B da ATP sintase, com energia de ligação ΔΕ = -3,63 kcal/mol. Neste estudo foi demonstrado que o linalol é uma molécula capaz de induzir a morte bacteriana e que, preditivamente, esse efeito possivelmente ocorre por interrupção na síntese de ATP.

Herein, a Cs2CO3‐promoted N‐alkylation of 3‐cyano‐2(1H)‐pyridones containing alkyl groups with diverse alkyl halides to synthesize N‐alkyl‐2‐pyridones over O‐alkylpyridines is reported. The use of alkyl dihalides resulted in complex mixtures of N‐ and O‐alkylated products. The primary factor influencing regioselectivity in these reactions is the electronic effects of substituents on the 2(1H)‐pyridone ring, as evidenced by the preferential formation of O‐alkylpyridines upon the introduction of aryl groups. Remarkably, we efficiently employed CuAAC and Ti(Oi‐Pr)4‐catalyzed amidation reactions to functionalize N‐alkyl‐2‐pyridones containing propargyl and ester groups, leading to the synthesis of 1,2,3‐triazoles and amides, respectively. Moreover, O‐alkylpyridines 10 b and 10 d displayed remarkable selectivity toward the A‐498 renal cancer cell line with growth inhibition percentages (%GI) of 54.75 and 67.64, respectively. The binding modes of compounds 10 b and 10 d to the PIM‐1 kinase enzyme were determined through molecular docking studies. [ABSTRACT FROM AUTHOR]

Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies. [ABSTRACT FROM AUTHOR]

Alzheimer’s disease (AD) is a common brain disease associated with cognitive impairment and dementia. donepezil, an acetylcholinesterase (AChE) inhibitor drug as a commercial AD drug represents a non-cost-effective treatment with the toxic effects reported. As the prevalence of AD increases, the development of effective therapeutic treatments is urgently required. Laminaria digitata is a brown seaweed claimed to be able to prevent and treat neurodegenerative diseases. Therefore, this study measured and compared the binding affinity and toxicity of seven common phytoconstituents in Laminaria digitata against acetylcholinesterase (AChE) with those of donepezil using a molecular docking approach. The binding free energy values of donepezil, dieckol, eckol, fucodiphlorethol G, 7-Phloroecol, laminaran, alginic acid, and fucoidan with acetylcholinesterase (AChE) were −12.3, −13.5, −10.5, −8,7, −9.7, −8.0, −10.3, and −7.4 kcal/mol. All ligands constantly interacted with the AChE amino acid residues, namely Tyr124. Dieckol, with the strongest and most stable interaction, is classified as class IV toxicity, with an LD50 value of 866 mg/kg. It has aryl hydrocarbon receptor (AhR) and mitochondrial membrane potential (MMP) toxicity at certain doses. Theoretically, based on Lipinski’s rule, dieckol is likely to have poor absorption and permeation properties; therefore, several considerations during the drug discovery process are needed.

Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival. [ABSTRACT FROM AUTHOR]

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The global surge in Alzheimer's disease poses a significant public health concern. In response, we study the efficacy of carnosic acid and related abietane-type diterpenes extracted from rosemary as acetylcholinesterase (AChE) inhibitors. Our analyses, using in silico techniques, encompassed all the compounds within this extract. Through molecular docking, we explored how these compounds interact with the active site of the AChE protein. The docking scores, ranging from −5.560 Kcal/mol to −7.270 Kcal/mol, indicate robust binding affinities. Assessment of the ADME/T (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) properties and pharmacokinetics of these compounds reveal favorable profiles for all the tested substances. These encouraging results suggest the potential of these compounds as candidates for further development to prevent and/or treat Alzheimer's disease. Among these compounds, we find rosmanol as the most likely candidate for further research and clinical trials to validate their efficacy.

Acetylcholinesterase (AChE) is a cholinergic enzyme that plays an essential role in the autonomic nervous system. This enzyme is often the target of many nerve agents. When this enzyme is inhibited, its function to hydrolyze acetylcholine is stopped, accumulating the acetylcholine in the tissue and causing prolonged stimulation. Some of the significant nerve agents include sarin (GB), soman (GD), tabun (GA), and venomous agent (VX). In order to determine which compound is the most stable and has the best affinity, the nerve agent venomous agent (VX), sarin (GB), soman (GD), and tabun (GA) are docked to the acetylcholinesterase (AChE) enzyme. After that, toxicity tests will be performed on 17 targets for the compound that was chosen. Autodock Vina 1.2.0 is the software used for the docking procedure. should use the Pymol program version 2.5.4 for analysis and the Ligplot software version 2.2 for visualization of the docking findings. The 'Tox Prediction' algorithm from Insilico was used to determine the toxicity of various substances. Based on the results of molecular docking, the free binding energy of Donepezil, sarin (GB), soman (GD), tabun (GA), and venomous agent (VX) in kcal/mol are −12,3, −4.8, −6.0, −5,1, and −6.3 respectively. Finally, four ligands bind strongly to the receptor Donepezil at RMSD 0.327 Å, and the venomous agent (VX) compound binds the most strongly compared to the other test ligands. Furthermore, in the toxicity test of Compound VX, which exhibits neurotoxic activity, no toxic activity was observed on specific organs and targets. [ABSTRACT FROM AUTHOR]

Copyright of Nativa is the property of Revista Nativa and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The protease 3CLpro of the SARS-CoV-2 is a crucial enzyme for viral replication, becoming a highly important therapeutic target. Thymol (2-isopropyl-5-methylphenol), a naturally occurring compound found in thyme, exhibits potential antiviral activity against the 3CLpro protease. In this study, using molecular docking with AutoDockTools-1.5.6, the molecular interaction energies between thymol and amino acid residues in the active site of the protein protease 3CLpro were evaluated. Then, with the Atoms in Molecules (QTAIM) and Non-covalent Interactions (NCI) theories, the types of molecular interactions between identifi ed amino acid residues and thymol were analyzed. Quantum calculations were carried out with the Orca-5.0.3 software using the DFT method with the M06-2X functional and the aug-cc-pVDZ basis set in the gas phase. The molecular docking results indicate that thymol is linked to the 3CL protein with an interaction energy equal to -3.784 kcal/mol. QTAIM analysis indicates the presence of critical binding sites between thymol and residues HIS41 and CYS145. In addition, the formation of a hydrogen bond between the OH group of thymol and the CYS145 residue is observed, which is corroborated by the ELF and NCI analyses. Finally, the NCI method confi rms the presence of Van der Waals interactions with the HIS41 residue. The results suggest that the mechanism of inhibition of the activity of the 3CLpro protein is controlled by molecular interactions such as hydrogen bonding and weak interactions. [ABSTRACT FROM AUTHOR]

Background: the significant role of glutamate-cysteine ligase (GCL) towards the synthesis of glutathione for the sequestration of reactive species as a regulatory point is second to none. However, much still need to be known about the enzyme molecular characterization. Thus, the homology modeling of GCL was carried out using different modeling webserver tools. The quality of the predicted crystal structures of human and mouse GCLs with inhibition were further assessed on molecular interaction with naphthalene and its metabolites. Results: the predicted human GCL and mouse GCL model structures have respective 89.8% and 89.6% residues in the most favored region of the Ramachandran plot. However, the molecular docking interaction study with the assessed ligands revealed two different binding pockets with pi-interactions as major non-covalent bond and better binding scores than glutathione. Conclusion: the predicted model could provide better mechanism of GCL catalysis to preserve its essential residues for reasonable GSH synthesis. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Revista de la Sociedad Química del Perú is the property of Sociedad Quimica del Peru and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

• Magnoflorine, a natural isoquinoline alkaloid was experimentally analyzed by different spectroscopies techniques. • The optimized structural and electronic properties of the molecule were predicted by DFT calculations. • Vibrational frequencies assignments were performed based on PED calculations. • The reactivity sites were evaluated by theoretical calculation. • The preference of anxiolytic activity toward the extracellular in comparison with intracellular domains of GABAA receptor was predicted. Magnoflorine (MGF), an isoquinoline alkaloid, emerges as a quaternary aporphine alkaloid derived from L-tyrosine amino acid, found in families Magnoliaceae plants and it presents important biological activity being noted for its effect on the nervous system. In this work, a deep study of structural, vibrational and electronic properties has been carried out for the MGF. From Potential Energy Surface (PES) scan the most stable conformer of alkaloid was identified and geometrical parameters were determined by Density Functional Theory (DFT) using B3LYP/6–311++G** method. A complete vibrational assignment of the normal modes was theoretical and experimentally achieved from FT-IR and Raman spectroscopies and scaled SQM methodology. Electronic transitions observed in UV–visible spectrum in aqueous medium were identified using TD-DFT methodology, with the π→π* transition being the most probable UV signal. The MEPs, the electric charge distribution along with the HOMO and LUMO frontier orbitals were analyzed and the GAP energy values justified the stability of the molecule in aqueous medium. The molecular electrostatic potential map reveals the most favourable region for electrophilic attack on MGF. Molecular docking was used to analyze the anxiolytic biological activity of the title molecule on the GABA A receptor. The results suggest an intermolecular binding capability of MFG toward both intracellular and extracellular domains of GABA A receptor, and the extracellular domain presents a higher affinity by alkaloid. Finally, the biological study infers that MGF could be used as a potential anxiolytic compound. [Display omitted] [ABSTRACT FROM AUTHOR]

This study concerns the molecular docking of dopamine family compounds in the β-cyclodextrin (β-CD) to establish the most critical driving forces in complexation. Our method is called "Determination of driving forces of inclusion complexes using generated surfaces" since it is based on the contact between host and guest molecules observed on distinct generated surfaces. These surfaces allow us to examine hydrophobic interactions, hydrogen interactions, electrostatic potential and dipole moment. The results found in this article confirm the experimental results. Finally, we suggest a number of molecules that can form stable inclusion complexes. [ABSTRACT FROM AUTHOR]

As doenças cardiovasculares são extensivamente estudadas devido aos seus riscos e prevalência mundial. Sendo assim, a pesquisa por novos tratamentos é um processo contínuo e as substâncias isoladas de plantas são uma promissora fonte de fármacos. Atualmente, análises de modelagem molecular são realizadas para compreender a relação entre estrutura-função de um alvo farmacológico e suas interações proteína-ligante, e assim o mecanismo exato da ação farmacológica. Diante disso, este trabalho pretende comparar o bloqueio do canal de cálcio dependente de voltagem promovido por verapamil e nifedipina com análises de modelagem molecular. Os experimentos de docking molecular foram realizados usando o portal Dockthor e análises com o programa Chimera. As energias de afinidade foram comparadas utilizando o programa GraphPad Prism, com o teste “t”, onde valores de p < 0,05 foram considerados significantes. Os resultados mostram que verapamil teve uma afinidade melhor do que nifedipina (p < 0,0001). As simulações de configuração no canal foram diferentes, ambos bloqueando o poro do canal, o que impede o influxo de cálcio na célula. Estes dados serão úteis para comparar com a prospecção de novas drogas que possam bloquear o canal de cálcio.

Introduction: HIV, whose viral multiplication is associated with three enzymes. Reverse transcriptase is responsible for synthesizing vital DNA based on its RNA; integrase is responsible for integrating viral DNA into human DNA; and protease is responsible for cleaving the genetic code into smaller, functional units. Many research groups around the world are motivated by the proposal of a new bioactive against HIV. Objectives: To propose natural diterpenes or synthetic products from the Pau-Brasil plant species against HIV through in silico techniques. Methods: Diterpenes found in the ethanolic extract of Pau-Brasil (Paubrasilia echinata Lam.) were used, as well as some of their products that were known by computational means. The work was developed through a hybrid screening (ligand-based and structure-based) for a possible biological activity of these phytoconstituents against the main enzymes of HIV-1 multiplication. Results: Computational assays showed that the compounds ALX04 and ALX07 showed possible activity against HIV-integrase and reverse transcriptase proteins, respectively. No compound was simultaneously active against the two enzymes (HIV-integrase and reverse transcriptase), and all other compounds proved inactive. Discussion: Diterpenes found in the ethanolic extract of Pau-Brasil (Paubrasilia echinata Lam.) were used, and some results were obtained through computational methods. The work was developed to achieve a viable observable activity to the tested prediction models. Conclusions: Computational assays showed that the diterpenes ALX04 and ALX07 had promising assays of retroviral activity. [ABSTRACT FROM AUTHOR]

COVID-19 is a zoonotic viral disease caused by the SARS-CoV-2 virus. Its abrupt outbreak has caused a tremendous challenge to public health systems due to the rapid spread of the virus. In this sense, a great deal of work has been focused on finding substances from herbal plants to be used against this virus. In order to investigate the molecular interactions between natural metabolites from Algerian herbal plants and the SARS-CoV-2 protease Mpro, computational docking and molecular dynamics were used, also the drug likeness degree and in silico ADMET prediction were carried out in this study. warfarin and catalponol preferentially binds to a pocket of the SARS-Cov-2 Mpro active site that is made up of residues His 41 to Glu 166 and Leu 27 to His 163 with a relatively low binding energy of -7.1 and -6.6 kcal/mol respectively. Dynamic molecular assay further established that only warfarin managed to stay in the active site. The results suggest that warfarin may be an interesting candidate for development as a medical treatment of COVID-19 and more research is proposed, without disregarding its toxicity which deserves to be well studied. [ABSTRACT FROM AUTHOR]

The p53 is a tumor suppressor protein that adjusts cell cycle and growth arrest as well as genes that restore DNA damage and apoptosis. Murine double minute 2 (MDM2) is a main p53 antagonist. We created a novel QSAR model using a series of highly active spiro [pyrrolidin-3,2-oxindoles] that consisted of 29 compounds that were experimentally validated to inhibit the MDM2-p53 interaction. Three optimal models have been developed CoMFA/E + S, CoMSIA/S + H + A, and HQSAR have revealed good statistical results, but the CoMSIA mode only which validates all the external validation tests applied successfully. Based on the CoMSIA/S + H + A model was carefully chosen to design four compounds with values of inhibitory activity greater than the highly active compound in the data set. The newly designed compounds were docked in the target receptor binding site (ID: 4LWU). The newly designed compound Pred 01 showed the highest affinity with a value of − 9.4 kcal/mol, while compound No. 04 which represents the data set and control compound (Nutlin-3) showed binding energies of the order of − 8.8 kcal/mol and − 8.2 kcal/mol, respectively. In addition, ADME/toxicity prediction and the drug-likeness predicted out of Lipinski's rule and Veber's rule were estimated; the results obtained demonstrate that the proposed molecules involve good oral bioavailability and an ability to diffuse through different biological barriers. For in-depth study, The Pred01/receptor, No. 04/receptor, and Nutlin-3/receptor complexes were selected via dynamic simulation analyzes with a simulation time of 100 ns and, also, their free binding energy was examined operating the MM-GBSA approach. The molecular docking results obtained accentuate the crucial residues responsible for the ligand/protein interaction, providing insight into the mode of interaction. The MD simulation analysis confirms the conformational stability of the selected complexes during the MD trajectory, and the fluctuations recorded are insignificant. The results of MM-GBSA reveal that the new compound Pred 01 exhibits the lowest free energy, which confirms the result of molecular docking. [ABSTRACT FROM AUTHOR]

[Display omitted] Human Rotavirus (HRV) is the causative pathogen of severe acute enteric infections that cause mortality among children worldwide. This study focuses on developing a new and effective treatment for rotavirus infection using an extract from Saccharomyces cerevisiae, aiming to make this treatment easily accessible to everyone. 15 antigens and 26 antibodies were detected in serum and stool using ELISA. The titers of HRVq1, HRVq2, HRVC1, and HRVC2 on Vero cells were determined to be 1.2x106, 3.0x106, 4.2x106, and 7.5x105 (Plaque forming unit, PFU/ml) four days after infection, respectively. The HRVq1 isolate induced cytopathic effects, i.e., forming multinucleated, rounded, enlarged, and expanding gigantic cells. RT-PCR identified this isolate, and the accession number 2691714 was assigned to GeneBank. The molecular docking analysis revealed that nonstructural proteins (NSPs) NSP1, NSP2, NSP3, NSP4, NSP5, and NSP6 exhibited significant binding with RNA. NSP2 demonstrated the highest binding affinity and the lowest binding energy (−8.9 kcal/mol). This affinity was maintained via hydrophobic interactions and hydrogen bonds spanning in length from 1.12 Å to 3.11 Å. The ADMET and bioactivity predictions indicated that the yeast extract possessed ideal solubility, was nontoxic, and did not cause cancer. The inhibitory constant values predicted for the S. cerevisiae extract in the presence of HRV vital proteins varied from 5.32 to 7.45 mM, indicating its potential as a viable drug candidate. Saccharomyces cerevisiae extract could be utilized as a dietary supplement to combat HRV as an alternative dietary supplement. [ABSTRACT FROM AUTHOR]

Recently, Zanubrutinib, as a novel, selective covalent and potent inhibitor Bruton's tyrosine kinase (BTK), has been used to treat COVID-19 patients. In this regard, the interaction of Zanubrutinib with Bruton's tyrosine kinase (BTK) inhibitor studied. The docking molecular and ONIOM2 (B3LYP/6-311G: UFF) methods were conducted to investigate the binding properties of Zanubrutinib with Bruton's tyrosine kinase (BTK) inhibitor. The active sites of the Bruton's tyrosine kinase (BTK) inhibitor is evaluated by docking molecular and is used for ONIOM2 calculations. The binding between Zanubrutinib and the BTK receptor is strong because values of the free binding energy are negative. The hydrogen bonds are formed between Zanubrutinib and three residues of the active amino acids Asn484, Arg 525, and Asn 526 at 2.69, 3.15, and 2.75 Å, respectively, which create through the Oatom, and the N-atom of Zanubrutinib. ONIOM2 calculation was displayed that the stability system in the solvent phase is higher than the gas-phase, which can occur due to the solvation of the species. Our results display the first mechanistic study of BTK inactivation by Zanubrutinib. This study can be helpful in the design of covalent drugs that target BTK and other similar targets. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Zika fever is a viral infection of great relevance in public health, especially in tropic regions, in which there is a predominance of mosquitoes of the genus Aedes, vectors of the disease. Microcephaly in neonatal children and Guillain-Barré syndrome in adults can be caused by the action of the Zika virus (ZIKV). Non-structural proteins, such as NS2B, NS3 and NS5, are important pharmacological targets, due to their action in the life cycle. The absence of anti-Zika drugs raises new research, including prospecting for natural products. This work investigated the in silico antiviral activity of bixin and six other derived molecules against the Zika viral proteins NS2B-NS3 and NS5. The optimized structure was subjected to molecular docking to characterize the interaction between bixinoids and ZIKV non-structural proteins, where significant interactions were observed with amino acid residues in the catalytic site in each enzyme. These results suggest that bixin and ethyl bixin has the potential to interfere with the enzymatic activity of NS2B, NS3 and NS5, thus being an indication of being a promising anti-Zika agent.

Herein, a Cs 2 CO 3 -promoted N-alkylation of 3-cyano-2(1H)-pyridones containing alkyl groups with diverse alkyl halides to synthesize N-alkyl-2-pyridones over O-alkylpyridines is reported. The use of alkyl dihalides resulted in complex mixtures of N- and O-alkylated products. The primary factor influencing regioselectivity in these reactions is the electronic effects of substituents on the 2(1H)-pyridone ring, as evidenced by the preferential formation of O-alkylpyridines upon the introduction of aryl groups. Remarkably, we efficiently employed CuAAC and Ti(Oi-Pr) 4 -catalyzed amidation reactions to functionalize N-alkyl-2-pyridones containing propargyl and ester groups, leading to the synthesis of 1,2,3-triazoles and amides, respectively. Moreover, O-alkylpyridines 10 b and 10 d displayed remarkable selectivity toward the A-498 renal cancer cell line with growth inhibition percentages (%GI) of 54.75 and 67.64, respectively. The binding modes of compounds 10 b and 10 d to the PIM-1 kinase enzyme were determined through molecular docking studies., (© 2024 Wiley-VCH GmbH.)

The (5α,6α)-7,8-didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol (morphine)molecule has been studied using the density functional theory and molecular docking methods and non covalent interactions. The conformational analysis of the molecule at the B3LYP/6−311++G** and HF/6−311++G** levels has been made. The comparison of the structural parameters computed using the B3LYP function with the experimental data has revealed their good agreement. The weak intermolecular interactions in the morphine structure have been analyzed using several techniques. The Hirshfeld surface study has been carried out to identify the diverse intermolecular interactions (mainly hydrogen bonds) and the … π stacking interactions. The analysis of the topological (AIM, ELF, LOL) and non covalent (RDG, IRI, DORI) interactions has revealed different categories of inter- and intramolecular contacts on the basis of the electron localization density and color scale indicator, respectively. The molecular docking study has been carried out to examine the possibility of biological application of the title conformer using the 1DLO (cancerous), 2BK3 (Parkinson), 3LN1 (inflammatory), 4HOE (microbial), and 5 K95 (schizophrenia) enzymes. The analysis has shown that the morphine structure can be used not only in analgesia, but also in the treatment of diseases. The investigated compound has shown good results with monoamine oxidase B (MOAB) at a score of −105.04 kcal/mol.

Introduction: Chagas disease is endemic to the tropical areas of Latin America and has an important prevalence, however, there are few treatments available in the market, so the search for molecules with pharmacological potential that can act in the same way as the disease, it is necessary considering the serious complications. Aim: to evaluate the possible target proteins available in the PDB database, considering the similarity with human proteins as an initial parameter and identify potential inhibitors of the chosen target using molecular docking. Methodology: an evaluation of the parasite proteins was carried out by means of sequence alignment and subsequently a virtual molecular coupling screening was performed with databases and computer resources available at Centro de Cómputo Avanzado de Universidad de Texas (TACC), and the best results were evaluated based on affinity, pharmacokinetics, and toxicity. Results: the molecular target chosen was the dUTPase. After virtual screening, 12 moles showing inhibitory potential were selected of these, 4- {3- [3- (trifluoromethyl) phenyl] isoxazole-5-yl} pyrimidine-2-amine is one of the molecules with the best profile to become a candidate in the treatment of Chagas disease. [ABSTRACT FROM AUTHOR]

Candidemia, one of the most common invasive fungal infections in hospitalized patients, can lead to death and huge financial losses. Candida albicans is the main causative agent of this disorder and Candida glabrata occupies the second or third place, for which new therapeutic alternatives must be found. The objective of the present study was to evaluate the inhibitory effect of etoposide and camptothecin (inhibitors of deoxyribonucleic acid (DNA) topoisomerase) on the C. glabrata CBS138 strain. Etoposide and camptothecin showed better or similar MIC (minimum inhibitory concentration) (5 and 2.5 μg/mL, respectively), with respect to fluconazole (8 μg/mL) and itraconazole (4 μg/mL). They also suppressed colony formation during the 12-h test. On the other hand, petite colonies were less formed by exposing C. glabrata to etoposide or camptothecin (indicating low toxicity), with respect fluconazole and itraconazole. Such colonies are phenotypically observed as limited growth in medium containing a non-fermentable carbon source, and are genotypically characterized by a partial or total loss of mitochondrial DNA (mtDNA) fragments. Using PCR techniques and cell staining with 4′,6-diamidino-2-phenylindole (DAPI), loss of mtDNA was detected only in yeast cells treated with fluconazole. Additionally, molecular docking studies with etoposide and camptothecin showed recognition in the active site of the Topo I and II enzymes from C. glabrata. Since etoposide and camptothecin showed good inhibitory activity and low toxicity on C. glabrata; they should certainly be of interest for the treatment of C. glabrata infections and the design and development of new antifungal compounds derived from these drugs. [ABSTRACT FROM AUTHOR]

Geraniol is a very valuable aroma chemical and has commonly been used in fragrances and aroma compound. Geraniol biotransformation by Aspergillus niger has been studied. The main bioconversion products obtained from geraniol and liquid culture of A. niger are linalool and alpha-terpineol. Linalool plays a major role in anti-inflammatory, antibacterial and antioxidant activities. This study aims to know the interaction of geraniol in Aspergillus niger enzyme with docking molecular. Comparative modeling of Aspergillus niger enzyme was conducted by means of one of the crystal structure of Linalool Dehydratase – Idomerase (LDI) as a template. The best model of this comparative modeling was then used in docking molecular to investigate geraniol binding mode inactive site enzyme of Aspergillus niger. Inactive site enzyme of Aspergillus niger, geraniol is located with hydrophobic and hydrogen bonds: Amino acid – the amino acids are Asn 105, Arg 96, Lys 112 inactive site - OH with hydrogen bond, Arg 97 inactive site – CH3 with hydrophobic bond and Leu54 inactive site – CH3 with the hydrophobic bond. The distances among pharmacophore respectively are 3,603 A, 6,768 A, and 7,345A. It has higher score (ΔGbind: -3.4 kcal/mol) compared to linalool (ΔGbind: -3.6 kcal/mol). Virtual tethering of linalool with LDI Aspergillus niger enzyme in amino acid Leu120 and Glu118 had been done. The pharmacophore is - OH and methyl C8 group. The distances among pharmacophore respectively are 5,835 Å, 2,52 Å, and 5,32 Å. Virtual tethering of LDI Aspergillus niger enzyme with geraniol has a higher score (ΔGbind: -3.4 kcal/mol) compared to linalool (ΔGbind: -3.6 kcal/mol). It shows that interaction between linalool and LDI Aspergillus niger enzyme is easier to occur than the interaction between geraniol and LDI Aspergillus niger enzyme, geraniol reaction to linalool that occurs is rearrangement reaction.

The purpose of this study was to analyze the inhibitory action of ursolic acid (UA) as an antitubercular agent by computational docking studies and molecular dynamics simulations. The effect of UA on the cell wall of Mycobacterium tuberculosis (MTB) was evaluated by using Scanning Electron Microscopy (SEM). UA was used as a ligand for molecular interaction and investigate its binding activities to a group of proteins involved in the growth of MTB and the biosynthesis of the cell wall. Computational docking analysis was performed by using autodock 4.2.6 based on scoring functions. UA binding was confirmed by 30 ns molecular dynamics simulation using gromacs 5.1.1. H37Rv sensitive strain and isoniazid-resistant strain were used in the SEM study. UA showed to have the optimum binding affinity to inhA (Two-trans-enoyl-ACP reductase enzyme involved in elongation of fatty acid) with the binding energy of -9.2 kcal/mol. The dynamic simulation showed that the UA-inhA complex relatively stable and found to establish hydrogen bond with Thr196 and Ile194. SEM analysis confirms that UA treatment in both sensitive strain and resistant strain affected the morphology cell wall of MTB. This result indicated that UA could be one of the potential ligands for the development of new antituberculosis drugs.

The genus Artemisia has recognized medicinal value and its use by humans Dates back to centuries ago. With the appearance of the new coronavirus, end of 2019, several countries have recommended the use of herbal teas consisting mainly of Artemisia. The individual analysis of the constituents of this species is crucial to characterize and optimize its antiSARS-Cov-2 action. We evaluated by molecular docking the inhibitory action of major compounds of the Artemisia genus (Artemisinin, Arteannuin B, Alpha Thujone, P-Hydroxyacetophenone, Fisetin, Cirsimaritin, Capillin, β-Sitosterol, and Quercetin) against three targets namely SARS-CoV-2 main protease (Mp), SARS-CoV-2 receptor binding domain (RBD) and human furin protease (HF protease). The two flavonols, quercetin and fisetin, have the best binding energies with the three targets. Quercetin/Fisetin possesses binding energy of -7.17/-6.9, -6.3/-6.15 and -- 5.98/- 5.49 kcal/mol with MP, RBD and HF protease respectively. Their physicochemical properties meet the requirements of an oral active principle and are not toxic according to predictive simulations. Thereby DFT calculation has been used to analyze the electronic and geometric characteristics of these two compounds. The gap energies were also deduced for the stable structure and their reactivity. The abundance of Quercetin in different plants may be another advantage in the use of this bio-compound in the treatment of coronavirus. [ABSTRACT FROM AUTHOR]

Himatanthus sucuuba, also known as “Bellaco caspi”, is a medicinal plant whose latex, stem bark, and leaves possess phenolic acids, lupeol, β-dihydro-plumbericinic acid, plumericin, and plumeride, among other components. Some of these have been linked to such biological activities as antiulcer, anti-inflammatory, and wound healing. The aim of this study was to determine the phytochemical compounds of H. sucuuba latex, as well as its in vitro cytotoxicity and wound healing effect in mice. Latex was collected in the province of Iquitos, Peru. Phytochemical analysis was carried out with UPLC-ESI-MS/MS. The cytotoxicity was evaluated on two colon tumor cell lines (SW480 and SW620) and non-malignant cells (human keratinocytes, HaCaT, and Chinese hamster ovary, CHO-K1). The mice were distributed into two groups, as follows: Group I—control (n = 10; without treatment); II—(n = 10) H. sucuuba latex; wounds were induced with a scalpel in the dorsal–cervical area and treatments were applied topically twice a day on the incision for 10 days. Molecular docking was carried out on the glycogen synthase kinase 3β protein. Twenty-four chemical compounds were determined, mainly flavonoid-type compounds. Latex did not have a cytotoxic effect on tumor cells with IC50 values of more than 500 µg/mL. The latex had a regenerative effect on wounds in mice. Acacetin-7-O-neohesperidoside had the best docking score of −9.9 kcal/mol. In conclusion, H. sucuuba latex had a wound healing effect in mice, as confirmed by histological study. However, a non-cytotoxic effect was observed on colon tumor cells SW480 and SW620.

Introduction: Epilepsy is one of the most common brain conditions. 1,3,4-oxadiazole and N-phenylacetamide, are found in anticonvulsant agents that acted via benzodiazepine (BZD) receptor. In this study we evaluated the anticonvulsant properties of some new 2-phenoxyphenyl-1,3,4-oxadiazole-N-phenylacetamid derivatives. Methods and Materials: A new series of 2-phenoxyphenyl-1,3,4-oxadiazole-N-phenylacetamid derivatives C1- 13 have been designed based on reported BZD receptor agonists and synthesized by simple chemical reactions. These compounds evaluated for their anticonvulsant activity against pentylenetetrazole (PTZ) and maximal electroshock (MES)-induced seizures in mice. Flumazenil as a standard antagonist against BZD receptor was used for understanding the possible mechanism of the most potent compound. For further investigation of interaction of the most potent compounds in BZD receptor, molecular modeling was performed by Autodock (1.5.6) software. Also neurotoxicity was evaluated by rotarod test. Results: The results of pharmacological studies showed that target compounds especially were active in MES seizure. The most potent compounds were nitro derivatives C5 and C4. Whereas in PTZ model the majority of them were inactive except 4-nitro derivative C4 and 4-bromo derivative C1 with mild protection. Flumazenil test on C5 demonstrated that anticonvulsant activity of the latter compound was completely reversed. In docking analysis, C5 and C4 showed important interactions at the BZD-binding site of GABAA receptor compared with diazepam. Furthermore, neurotoxicity of the latter compounds was lower than positive control diazepam. Conclusion: The designed compounds have good potential for further evaluations as new anticonvulsant agents. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The global surge in Alzheimer's disease poses a significant public health concern. In response, we study the efficacy of carnosic acid and related abietane-type diterpenes extracted from rosemary as acetylcholinesterase (AChE) inhibitors. Our analyses, using in silico techniques, encompassed all the compounds within this extract. Through molecular docking, we explored how these compounds interact with the active site of the AChE protein. The docking scores, ranging from -5.560 Kcal/mol to -7.270 Kcal/mol, indicate robust binding affinities. Assessment of the ADME/T (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) properties and pharmacokinetics of these compounds reveal favorable profiles for all the tested substances. These encouraging results suggest the potential of these compounds as candidates for further development to prevent and/or treat Alzheimer's disease. Among these compounds, we find rosmanol as the most likely candidate for further research and clinical trials to validate their efficacy., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Author(s).)

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Abstract The aqua theophyllinate complexes of general formula [M(II)(Th) 2 (H 2 O) 4 ] M(II) = Cd(II), Ni(II), Mn(II) and Cu(II), Th: theophyllinate, were prepared and characterized by the X-Ray diffraction analysis using the Fox program, infrared, UV–visible and TGA/DTA. These complexes were crystallized in the monoclinic system (P 2 1 /C). Moreover, the asymmetric unit of complexes contains one-half metal ion, one theophillinate anion and two coordinated water molecules. The intermolecular hydrogen bonds: O H⋯O, O H⋯N interactions are together playing a vital role in the stabilization of the crystal packing of all theophyllinate complexes. Additionally, molecular modelings of prepared complexes were investigated to study the expected anticancer activities of the prepared complexes. The results of molecular docking show that the complexes have a good affinity towards the protein kinase CK2. Graphical abstract Image 1096 Highlights • The complexes of general formula [M(II)(Th)2(H2O)4] M(II) = Cd(II), Ni(II), Mn(II) and Cu(II) were prepared and characterized. • The Metal cations have a slightly distorted octahedral geometry. • The structure of complexes was determined by X-Ray diffraction analysis using the Fox program. • Docking study was performed using receptor (protein kinase CK2) as a target for anticancer activity. [ABSTRACT FROM AUTHOR]