In Silico Study to Identify New Antituberculosis Molecules from Natural Sources by Hierarchical Virtual Screening and Molecular Dynamics Simulations

The authors acknowledge the Graduate Program in Biotechnology/UEFS for academic support.Tuberculosis (TB) is an infection caused by Mycobacterium tuberculosis, responsible for 1.5 million documented deaths in 2016. The increase in reported cases of M. tuberculosis resistance to the main drugs show the need for the development of new and efficient drugs for better TB control. Based on these facts, this work aimed to use combined in silico techniques for the discovery of potential inhibitors to β-ketoacyl-ACP synthase (MtKasA). Initially compounds from natural sources present in the ZINC database were selected, then filters were sequentially applied by virtual screening, initially with pharmacophoric modeling, and later the selected compounds (based on QFIT scores) were submitted to the DOCK 6.5 program. After recategorization of the variables (QFIT score and GRID score), compounds ZINC35465970 and ZINC31170017 were selected. These compounds showed great hydrophobic contributions and for each established system 100 ns of molecular dynamics simulations were performed and the binding free energy was calculated. ZINC35465970 demonstrated a greater capacity for the KasA enzyme inhibition, with a ΔGbind = −30.90 kcal/mol and ZINC31170017 presented a ΔGbind = −27.49 kcal/mol. These data can be used in other studies that aim at the inhibition of the same biological targets through drugs with a dual action

Volatile Compounds, Chemical Composition and Biological Activities of <em>Apis mellifera</em> Bee Propolis

Propolis is a wax-like resin collected by bees from tree shoots and/or other botanical sources that is used as glue to seal cracks or open spaces in the hive. Its color varies from green to brown and reddish, depending on its botanical origin. Among the substances that can be found in propolis, low molecular weight compounds, such as monoterpenes and sesquiterpenes are the most common. Several biological activities are attributed to these classes of substances, such as antifungal, antibacterial, and others. The objective of this work was to evaluate the chemical composition of volatile compounds present in propolis samples and to analyze their correlation with biological activities

Invasive Species in the Amazon

One of the main reasons for environmental disturbances such as declination in pasture productivity and biodiversity losses is the high infestation of herbaceous weeds, generally referred to as “Juquira” in the Amazon region. If they are not adequately controlled, such infestation might lead to degradation of pasture, resulting in complete loss of productivity and subsequent abandonment of the area. In this sense, this chapter aims to describe the main invasive species present in the Amazon region, as well as to characterize both the old and innovative techniques of use in agriculture, in large and small scale, for the control of agricultural pests

Molecular Modeling Approaches Can Reveal the Molecular Interactions Established between a Biofilm and the Bioactive Compounds of the Essential Oil of Piper divaricatum

Molecular modeling approaches are used in a versatile way to investigate the properties of diverse organic and inorganic structures such as proteins, biomolecules, nanomaterials, functionalized nanoparticles, and membranes. However, more detailed studies are needed to understand the molecular nature of interactions established in gelatin biofilms impregnated with bioactive compounds. Because of this, we used computational methods to evaluate how the major compounds of Piper divaricatum essential oil can interact with the gelatin biofilm structure. For this, we used as inspiration the paper published, where various properties of the essential oil impregnated gelatin biofilm P. divaricatum are reported. After our computer simulations, we related our molecular observations to biofilm&rsquo;s structural and mechanical properties. Our results suggest that the major compounds of the essential oil were able to interrupt intermolecular interactions between the chains of the biofilm matrix. However, the compounds also established interactions with the amino acid residues of these chains. Our molecular analyses also explain changes in the structural and mechanical properties of the essential oil-impregnated biofilm. These results can support the planning of functional packaging impregnated with bioactive compounds that can protect food against microorganisms harmful to human health

Molecular Modeling Approaches Can Reveal the Molecular Interactions Established between a Biofilm and the Bioactive Compounds of the Essential Oil of <em>Piper divaricatum</em>

Molecular modeling approaches are used in a versatile way to investigate the properties of diverse organic and inorganic structures such as proteins, biomolecules, nanomaterials, functionalized nanoparticles, and membranes. However, more detailed studies are needed to understand the molecular nature of interactions established in gelatin biofilms impregnated with bioactive compounds. Because of this, we used computational methods to evaluate how the major compounds of Piper divaricatum essential oil can interact with the gelatin biofilm structure. For this, we used as inspiration the paper published, where various properties of the essential oil impregnated gelatin biofilm P. divaricatum are reported. After our computer simulations, we related our molecular observations to biofilm’s structural and mechanical properties. Our results suggest that the major compounds of the essential oil were able to interrupt intermolecular interactions between the chains of the biofilm matrix. However, the compounds also established interactions with the amino acid residues of these chains. Our molecular analyses also explain changes in the structural and mechanical properties of the essential oil-impregnated biofilm. These results can support the planning of functional packaging impregnated with bioactive compounds that can protect food against microorganisms harmful to human health

Naphthoquinones isolated from Eleutherine plicata herb: in vitro antimalarial activity and molecular modeling to investigate their binding modes

CAPES; CNPqUniversidade Federal do Pará. Instituto Ciências da Saúde. Programa de Pós-Graduação em Inovação Farmacêutica. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Tecnologia. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto Ciências da Saúde. Programa de Pós-Graduação em Inovação Farmacêutica. Belém, PA, Brazil / Universidade Federal do Pará. Instituto de Tecnologia. Belém, PA, Brazil.Universidade Federal do Pará. Instituto Ciências da Saúde. Programa de Pós-Graduação em Inovação Farmacêutica. Belém, PA, Brazil.Plasmodium falciparum is the cause of malaria and has become resistant to the drugs used to treat the disease. Therefore, the development for novel compounds with antimalarial activity has become urgent. Plant species, such as naphthoquinone-rich Eleutherine plicata, may provide novel substances that exhibit antimalarial activity and serve as an alternative for the treatment of this disease. From this plant species, ethanol extracts were obtained, fractionated, and the isolated substances eleutherin, and isoleutherin were characterized by nuclear magnetic resonance. There in vitro activity against Plasmodium falciparum was examined using the traditional Microtest method using the extract, fractions, and isolated molecules. Eleutherin and isoleutherin showed the best activity toward the parasite with IC50 values of 10.45 and 8.70 µg/mL, respectively. Characterization of the binding mode of the compounds with a target enzyme and identification of the molecular interactions were revealed via molecular docking results. Eleutherin and isoeleutherin interacted with highly conserved residues from the binding cavity of the cytochrome bc1 complex, a protein found in mitochondria. Therefore, the eleutherin and isoeleutherin naphthoquinones showed antiplasmodial activity with a similar mechanism to that of atovaquone were able to interact with the cytochrome bc1 complex, and showed promise for antimalarial treatments

Effects of Drying Temperature and Solvents on In Vitro Diabetic Wound Healing Potential of <i>Moringa oleifera</i> Leaf Extracts

The delayed healing of wounds among people with diabetes is a severe problem worldwide. Hyperglycemia and increased levels of free radicals are the major inhibiting factors of wound healing in diabetic patients. Plant extracts are a rich source of polyphenols, allowing them to be an effective agent for wound healing. Drying temperature and extraction solvent highly affect the stability of polyphenols in plant materials. However, there is a need to optimize the extraction protocol to ensure the efficacy of the final product. For this purpose, the effects of drying temperature and solvents on the polyphenolic composition and diabetic wound healing activity of Moringa oleifera leaves were examined in the present research. Fresh leaves were oven dried at different temperatures (10 °C, 30 °C, 50 °C, and 100 °C) and extracted in three solvents (acetone, ethanol, and methanol) to obtain twelve extracts in total. The extracts were assessed for free radical scavenging and antihyperglycemic effects using DPPH (2,2-diphenylpicrylhydrazyl) and α- glucosidase inhibition assays. Alongside this, a scratch assay was performed to evaluate the cell migration activity of M. oleifera on the human retinal pigment epithelial cell line. The cytotoxicity of the plant extracts was assessed on human retinal pigment epithelial (RPE) and hepatocellular carcinoma (Huh-7) cell lines. Using high-performance liquid chromatography, phenolic compounds in extracts of M. oleifera were identified. We found that an ethanol-based extract prepared by drying the leaves at 10 °C contained the highest amounts of identified polyphenols. Moringa oleifera extracts showed remarkable antioxidant, antidiabetic, and cell migration properties. The best results were obtained with leaves dried at 10 °C and 30 °C. Decreased activities were observed with drying temperatures of 50 °C and above. Moreover, M. oleifera extracts exhibited no toxicity on RPE cells, and the same extracts were cytotoxic for Huh-7 cells. This study revealed that M. oleifera leaves extracts can enhance wound healing in diabetic conditions due to their antihyperglycemic, antioxidant, and cell migration effects. The leaves of this plant can be an excellent therapeutic option when extracted at optimum conditions

An Updated Review on the Multifaceted Therapeutic Potential of <i>Calendula officinalis</i> L.

Calendula officinalis Linn. (CO) is a popular medicinal plant from the plant kingdom’s Asteraceae family that has been used for millennia. This plant contains flavonoids, triterpenoids, glycosides, saponins, carotenoids, volatile oil, amino acids, steroids, sterols, and quinines. These chemical constituents confer multifaceted biological effects such as anti-inflammatory, anti-cancer, antihelminthic, antidiabetes, wound healing, hepatoprotective, and antioxidant activities. Additionally, it is employed in cases of certain burns and gastrointestinal, gynecological, ocular, and skin conditions. In this review, we have discussed recent research from the last five years on the therapeutic applications of CO and emphasized its myriad capabilities as a traditional medicine. We have also elucidated CO’s molecular mechanisms and recent clinical studies. Overall, this review intends to summarize, fill in the gaps in the existing research, and provide a wealth of possibilities for researchers working to validate traditional claims and advance the safe and effective use of CO in treating various ailments

Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach

The cyclooxygenase-2 receptor is a therapeutic target for planning potential drugs with anti-inflammatory activity. The selective cyclooxygenase-2 (COX-2) inhibitor rofecoxib was selected as a pivot molecule to perform virtual ligand-based screening from six commercial databases. We performed the search for similarly shaped Rapid Overlay of Chemical Structures (ROCS) and electrostatic (EON) compounds. After, we used pharmacokinetic and toxicological parameters to determine the best potential compounds, obtained through the softwares QikProp and Derek, respectively. Then, the compounds proceeded to the molecular anchorage study, which showed promising results of binding affinity with the hCOX-2 receptor: LMQC72 (∆G = &minus;11.0 kcal/mol), LMQC36 (∆G = &minus;10.6 kcal/mol), and LMQC50 (∆G = &minus;10.2 kcal/mol). LMQC72 and LMQC36 showed higher binding affinity compared to rofecoxib (∆G = &minus;10.4 kcal/mol). Finally, molecular dynamics (MD) simulations were used to evaluate the interaction of the compounds with the target hCOX-2 during 150 ns. In all MD simulation trajectories, the ligands remained interacting with the protein until the end of the simulation. The compounds were also complexing with hCOX-2 favorably. The compounds obtained the following affinity energy values: rofecoxib: &Delta;Gbind = &minus;45.31 kcal/mol; LMQC72: &Delta;Gbind = &minus;38.58 kcal/mol; LMQC36: &Delta;Gbind = &minus;36.10 kcal/mol; and LMQC50: &Delta;Gbind = &minus;39.40 kcal/mol. The selected LMQC72, LMQC50, and LMQC36 structures showed satisfactory pharmacokinetic results related to absorption and distribution. The toxicological predictions of these compounds did not display alerts for possible toxic groups and lower risk of cardiotoxicity compared to rofecoxib. Therefore, future in vitro and in vivo studies are needed to confirm the anti-inflammatory potential of the compounds selected here with bioinformatics approaches based on rofecoxib ligand