Exploring the Potentiality of Natural Products from Essential Oils as Inhibitors of Odorant-Binding Proteins: A Structure- and Ligand-Based Virtual Screening Approach To Find Novel Mosquito Repellents

Development of terpenoid repellents against Aedes albopictus: a combined study of biological activity evaluation and computational modelling

To explore novel terpenoid repellents, 22 candidate terpenoid derivatives were synthesized and tested for their electroantennogram (EAG) responses and repellent activities against Aedes albopictus. The results from the EAG experiments revealed that 5-(2-hydroxypropan-2-yl)-2-methylcyclohex-2-en-1-yl formate (compound 1) induced distinct EAG responses in female Aedes albopictus. At concentrations of 0.1, 1, 10, 100, and 1000 mg/L, the EAG response values for compound 1 were 179.59, 183.99, 190.38, 193.80, and 196.66 mV, demonstrating comparable or superior effectiveness to DEET. Repellent activity analysis indicated significant repellent activity for compound 1, closest to the positive control DEET. The in silico assessment of the ADMET profile of compound 1 indicates that it successfully passed the ADMET evaluation. Molecular docking studies exhibited favourable binding of compound 1 to the active site of the odorant binding protein (OBP) of Aedes albopictus, involving hydrophobic forces and hydrogen bond interactions with residues in the OBP pocket. The QSAR model highlighted the influential role of hydrogen-bonding receptors, positively charged surface area of weighted atoms, polarity parameters of molecules, and maximum nuclear-nuclear repulsion force of carbon-carbon bonds on the relative EAG response values of the tested compounds. This study holds substantial significance for the advancement of new terpenoid repellents.

Essential oils extracted from Citrus macroptera and Homalomena aromatica (Spreng.) Schott. exhibit repellent activities against Aedes aegypti (Diptera: Culicidae)

BACKGROUND OBJECTIVES

Mosquitoes alone transmit diseases to around 700 million individuals annually, killing approximately 0.7 million people every year worldwide. Considering the potential health risks linked with synthetic repellents, it has become vital to identify eco-friendly, natural repellents for mosquito control as well as to understand the underlying mechanism for mosquito repellent activity. To address this, objectives were set to extract essential oils from Citrus macroptera peel and Homalomena aromatica (Spreng.) Schott. rhizomes, evaluate their mosquito repellent activity against Aedes aegypti, and further explore their mosquito odorant receptor inhibition potential.

METHODS

The oils were extracted using Clevenger's apparatus, and properties like specific gravity, refractive index, and boiling point were evaluated and characterised using Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectroscopy (GC-MS). Aedes aegypti mosquito eggs collected from the Indian Council of Medical Research (ICMR), Dibrugarh, were reared in the Department of Pharmaceutical Sciences, Research Laboratory, to obtain adult Aedes aegypti mosquitoes for the mosquito repellent activity evaluation of the essential oils using the Human Bait technique'. Molecular docking studies were performed for the oil components against mosquito odorant binding proteins. Further, toxicity studies of these two oils were evaluated against human dermal fibroblast adult (HDFa) cells.

RESULTS

The results revealed the presence of limonene (86.76%) and linalool (52.35%), respectively, in Citrus macroptera and Homalomena aromatica oils. It was found that the combination of the oils in a ratio of 1:1 showed mosquito repellent activity for up to 6.33 ± 0.23 h. Molecular docking studies showed the presence of major oil components having mosquito odorant receptor blocking potential comparable to N, N-diethyl-meta-toluamide (DEET), indicating a rationale for extended mosquito repellent action. Further, both of these oils were found to be non-cytotoxic against HDFa cells after 24 h.

INTERPRETATION CONCLUSION

The encouraging mosquito repellent activity of these two oils as compared to synthetic mosquito repellent DEET might pave the way for the development of novel herbal mosquito repellent formulations containing these essential oils.

Artificial intelligence: Machine learning approach for screening large database and drug discovery

Recent research in drug discovery dealing with many faces difficulties, including development of new drugs during disease outbreak and drug resistance due to rapidly accumulating mutations. Virtual screening is the most widely used method in computer aided drug discovery. It has a prominent ability in screening drug targets from large molecular databases. Recently, a number of web servers have developed for quickly screening publicly accessible chemical databases. In a nutshell, deep learning algorithms and artificial neural networks have modernised the field. Several drug discovery processes have used machine learning and deep learning algorithms, including peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modelling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity. Although there are presently a wide variety of data-driven AI/ML tools available, the majority of these tools have, up to this point, been developed in the context of non-communicable diseases like cancer, and a number of obstacles have prevented the translation of these tools to the discovery of treatments against infectious diseases. In this review various aspects of AI and ML in virtual screening of large databases were discussed. Here, with an emphasis on antivirals as well as other disease, offers a perspective on the advantages, drawbacks, and hazards of AI/ML techniques in the search for innovative treatments.

Unveiling the Impact of Drying Methods on Phytochemical Composition and Antioxidant Activity of Anthemis palestina

Different drying techniques may alter the chemical composition of plant extracts and consequently affect their bioactivity potential. The current study was designed to reveal the effect of four different drying methods on the phytochemical composition and antioxidant activity of hydrodistilled essential oil (HD-EO) and methanolic (APM) extract obtained from the aerial part of Anthemis palestina from Jordan. Aerial parts of A. palestina in their fresh (FR) form and after drying in shade (ShD), sun (SD), oven at 40 °C (O40D) and 60 °C (O60D), in addition to microwave (MWD), were used to extract their essential oils by hydrodistillation and to prepare the different methanolic extracts (APM). GC/MS analysis of the different HD-EOs revealed qualitative and quantitative differences among the different samples. While FR, O40D, O60D, and MWD EO samples contained mainly sesquiterpene hydrocarbons (35.43%, 29.04%, 53.69%, and 59.38%, respectively), ShD sample was rich in oxygenated monoterpenes (33.57%), and SD-EO contained mainly oxygenated sesquiterpenes (40.36%). Principal component analysis (PCA) and Cluster analysis (CA) grouped the different drying methods based on their impact on the concentration of chemical constituents. SD-EO demonstrated high DPPH and ABTS antioxidant activity (1.31 ± 0.03) × 10-2; (1.66 ± 0.06) × 10-2 μg/mL, respectively). Furthermore, A. paleistina methanolic extracts (APM) obtained after subjecting the plant to different drying methods showed interesting patterns in terms of their TPC, TFC, antioxidant activity, and phytochemical profiling. Of all extracts, SD-APM extract had the highest TPC (105.37 ± 0.19 mg GA/g DE), highest TFC (305.16 ± 3.93 mg Q/g DE) and demonstrated the highest DPPH and ABTS scavenging activities ((4.42 ± 0.02) × 10-2; (3.87 ± 0.02) × 10-2 mg/mL, respectively); all were supported by correlation studies. LC-MS/MS analysis of the different extracts revealed the richness of the SD-APM extract in phenolic acids and flavonoids.

Nonlinear SAR Modelling of Mosquito Repellents for Skin Application

Finding new marketable mosquito repellents is a complex and time-consuming process that can be optimized via modelling. In this context, a SAR (Structure-Activity Relationship) model was designed from a set of 2171 molecules whose actual repellent activity against Aedes aegypti was available. Information-rich descriptors were used as input neurons of a three-layer perceptron (TLP) to compute the models. The most interesting classification model was a 20/6/2 TLP showing 94% and 89% accuracy on the training set and test set, respectively. A total of 57 other artificial neural network models based on the same architecture were also computed. This allowed us to consider all chemicals both as training and test set members in order to better interpret the results obtained with the selected model. Most of the wrong predictions were explainable. The 20/6/2 TLP model was then used for predicting the potential repellent activity of new molecules. Among them, two were successfully evaluated in vivo.

Computational insights of the molecular recognition between volatile molecules and odorant binding proteins from the red palm weevil Rhynchophorus ferrugineus

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most harmful pests for palm trees, causing serious economic damage worldwide. The present work aims to model and study the 3D structures of highly expressed odorant binding proteins from R. ferrugineus (RferOBPs) and identify possible binding modes and ligand release mechanism by docking and molecular dynamics. Highly confident 3D structures of a total of 11 odorant binding proteins (OBPs) were obtained with AlphaFold2. All 3D RferOBPs modeled structures displayed six characteristic α-helices, except for RfeOBP7 and RfeOBP10, which had an extra terminal α-helix. Among the eleven modeled RferOBPs, RferOBP4 was highly expressed in the antennae and subsequently selected for further analyses. Molecular docking analyses demonstrated that ferruginol, α-pinene, DEET, and picaridin can favorably bind the RferOBP4 cavity with low affinity energies. Molecular dynamic simulations of RferOBP4 bound to ferruginol at different pH values showed that low pH environments dictate a structural change into an apo-state that modifies the number of tunnels where the ligand can coexist, further triggering ligand release by a pH-dependent mechanism. This is the first report concerning the modelling and study of ligand binding modes and release mechanism of R. ferrugineus OBPs.Communicated by Ramaswamy H. Sarma.

2D finger-printing and molecular docking studies identified potent mosquito repellents targeting odorant binding protein 1

Personal protection measures against the mosquitoes like the use of repellents constitute valuable tools in the effort to prevent the transmission of vector-borne diseases. Therefore, the discovery of novel repellent molecules which will be effective at lower concentrations and provide a longer duration of protection remains an urgent need. Mosquito Odorant-Binding Proteins (OBPs) involved in the initial steps of the olfactory signal transduction cascade have been recognized not only as passive carriers of odors and pheromones but also as the first molecular filter to discriminate semiochemicals, hence serving as molecular targets for the design of novel pest control agents. Among the three-dimensional structures of mosquito OBPs solved in the last decades, the OBP1 complexes with known repellents have been widely used as reference structures in docking analysis and molecular dynamics simulation studies for the structure-based discovery of new molecules with repellent activity. Herein, ten compounds known to be active against mosquitoes and/or displaying a binding affinity for Anopheles gambiae AgamOBP1 were used as queries in an in silico screening of over 96 million chemical samples in order to detect molecules with structural similarity. Further filtering of the acquired hits on the basis of toxicity, vapor pressure, and commercial availability resulted in 120 unique molecules that were subjected to molecular docking studies against OBP1. For seventeen potential OBP1-binders, the free energy of binding (FEB) and mode of interaction with the protein were further estimated by molecular docking simulations leading to the selection of eight molecules exhibiting the highest similarity with their parental compounds and favorable energy values. The in vitro determination of their binding affinity to AgamOBP1 and the evaluation of their repellent activity against female Aedes albopictus mosquitoes revealed that our combined ligand similarity screening and OBP1 structure-based molecular docking successfully detected three molecules with enhanced repellent properties. A novel DEET-like repellent with lower volatility (8.55 × 10^-4 mmHg) but a higher binding affinity for OBP1 than DEET (1.35 × 10^-3 mmHg). A highly active repellent molecule that is predicted to bind to the secondary Icaridin (sIC)-binding site of OBP1 with higher affinity than to the DEET-site and, therefore, represents a new scaffold to be exploited for the discovery of binders targeting multiple OBP sites. Finally, a third potent repellent exhibiting a high degree of volatility was found to be a strong DEET-site binder of OBP1 that could be used in slow-release formulations.

Design and Identification of Inhibitors for the Spike-ACE2 Target of SARS-CoV-2

When an epidemic started in the Chinese city of Wuhan in December 2019, coronavirus was identified as the cause. Infection by the virus occurs through the interaction of viral S protein with the hosts' angiotensin-converting enzyme 2. By leveraging resources such as the DrugBank database and bioinformatics techniques, ligands with potential activity against the SARS-CoV-2 spike protein were designed and identified in this investigation. The FTMap server and the Molegro software were used to determine the active site of the Spike-ACE2 protein's crystal structure. Virtual screening was performed using a pharmacophore model obtained from antiparasitic drugs, obtaining 2000 molecules from molport^®. The ADME/Tox profiles were used to identify the most promising compounds with desirable drug characteristics. The binding affinity investigation was then conducted with selected candidates. A molecular docking study showed five structures with better binding affinity than hydroxychloroquine. Ligand_003 showed a binding affinity of -8.645 kcal·mol^-1, which was considered an optimal value for the study. The values presented by ligand_033, ligand_013, ligand_044, and ligand_080 meet the profile of novel drugs. To choose compounds with favorable potential for synthesis, synthetic accessibility studies and similarity analyses were carried out. Molecular dynamics and theoretical IC₅₀ values (ranging from 0.459 to 2.371 µM) demonstrate that these candidates are promising for further tests. Chemical descriptors showed that the candidates had strong molecule stability. Theoretical analyses here show that these molecules have potential as SARS-CoV-2 antivirals and therefore warrant further investigation.

Elucidating the molecular mechanisms of essential oils' insecticidal action using a novel cheminformatics protocol

Essential oils (EOs) are a promising source for novel environmentally safe insecticides. However, the structural diversity of their compounds poses challenges to accurately elucidate their biological mechanisms of action. We present a new chemoinformatics methodology aimed at predicting the impact of essential oil (EO) compounds on the molecular targets of commercial insecticides. Our approach merges virtual screening, chemoinformatics, and machine learning to identify custom signatures and reference molecule clusters. By assigning a molecule to a cluster, we can determine its most likely interaction targets. Our findings reveal that the main targets of EOs are juvenile hormone-specific proteins (JHBP and MET) and octopamine receptor agonists (OctpRago). Three of the twenty clusters show strong similarities to the juvenile hormone, steroids, and biogenic amines. For instance, the methodology successfully identified E-Nerolidol, for which literature points indications of disrupting insect metamorphosis and neurochemistry, as a potential insecticide in these pathways. We validated the predictions through experimental bioassays, observing symptoms in blowflies that were consistent with the computational results. This new approach sheds a higher light on the ways of action of EO compounds in nature and biotechnology. It also opens new possibilities for understanding how molecules can interfere with biological systems and has broad implications for areas such as drug design.

The structure of AgamOBP5 in complex with the natural insect repellents Carvacrol and Thymol: Crystallographic, fluorescence and thermodynamic binding studies

Among several proteins participating in the olfactory perception process of insects, Odorant Binding Proteins (OBPs) are today considered valid targets for the discovery of compounds that interfere with their host-detection behavior. The 3D structures of Anopheles gambiae mosquito AgamOBP1 in complex with the known synthetic repellents DEET and Icaridin have provided valuable information on the structural characteristics that govern their selective binding. However, no structure of a plant-derived repellent bound to an OBP has been available until now. Herein, we present the novel three-dimensional crystal structures of AgamOBP5 in complex with two natural phenolic monoterpenoid repellents, Carvacrol and Thymol, and the MPD molecule. Structural analysis revealed that both monoterpenoids occupy a binding site (Site-1) by adopting two alternative conformations. An additional Carvacrol was also bound to a secondary site (Site-2) near the central cavity entrance. A protein-ligand hydrogen-bond network supplemented by van der Waals interactions spans the entire binding cavity, bridging α4, α6, and α3 helices and stabilizing the overall structure. Fluorescence competition and Differential Scanning Calorimetry experiments verified the presence of two binding sites and the stabilization effect on AgamOBP5. While Carvacrol and Thymol bind to Site-1 with equal affinity in the submicromolar range, they exhibit a significantly lower and distinct binding capacity for Site-2 with Kd's of ~7 μΜ and ~18 μΜ, respectively. Finally, a comparison of AgamOBP5 complexes with the AgamOBP4-Indole structure revealed that variations of ligand-interacting aminoacids such as A109T, I72M, A112L, and A105T cause two structurally similar and homologous proteins to display different binding specificities.

Antiplasmodial activity of coumarins isolated from Polygala boliviensis: in vitro and in silico studies

Polygala boliviensis is found in the Brazilian semiarid region. This specie is little chemically and biologically studied. Polygala spp. have different metabolites, especially coumarins. Studies indicate that coumarins have antimalarial potential, denoting the importance of researching new active compounds from plants, since the resistance of Plasmodium strains to conventional therapy has increased. The present study aimed to evaluate the antiplasmodial activity of auraptene and poligalen against a chloroquine-resistant strain of Plasmodium falciparum. Coumarins were isolated from P. boliviensis by open column chromatography and identified by Nuclear Magnetic Resonance Spectroscopy. A cytotoxicity assay was carried out using MTT test, and the in vitro antiplasmodial activity was evaluated using the W2 strain. The antiplasmodial activity results found were IC50=0.171 ± 0.016 for auraptene and 0.164 ± 0.012 for poligalen; the selectivity indexes were 78.71 and 609.76, respectively. Inverse virtual screening in the BRAMMT database by OCTOPUS 1.2 was applied to coumarins to find potential P. falciparum targets and showed higher affinity energy of auraptene for purine nucleoside phosphorylase (PfPNP) and of poligalen for dihydroorotate dehydrogenase (PfDHODH). Molecular Dynamics studies (MD and MM-GBSA) approach were applied to calculate binding energies against selected P. falciparum targets and showed that all coumarins were stable at the binding site during simulations. Furthermore, energies were favorable for complexation. This is the first report of auraptene in P. boliviensis species and of in vitro antiplasmodial activity of auraptene and poligalen. In silico studies indicated that the mechanism of action of coumarins is the inhibition of PfPNP and PfDHODH.Communicated by Ramaswamy H. Sarma.

Assessment of host-guest molecular encapsulation of eugenol using β-cyclodextrin

Eugenol is a natural compound with well-known repellent activity. However, its pharmaceutical and cosmetic applications are limited, since this compound is highly volatile and thermolabile. Nanoencapsulation provides protection, stability, conservation, and controlled release for several compounds. Here, eugenol was included in β-cyclodextrin, and the complex was characterized through X-ray diffraction analysis (XRD) and Fourier-transform infrared spectroscopy (FTIR). Additionally, we used molecular dynamics simulations to explore the eugenol-β-cyclodextrin complex stability with temperature increases. Our computational result demonstrates details of the molecular interactions and conformational changes of the eugenol-β-cyclodextrin complex and explains its stability between temperatures 27°C and 48°C, allowing its use in formulations that are subjected to varied temperatures.

In Vitro Antibacterial Activity and in Silico Analysis of the Bioactivity of Major Compounds Obtained from the Essential Oil of Virola surinamensis Warb (Myristicaceae)

Essential oils are well known for their antimicrobial activity and they are used as an effective food preservative. Virola is one of the five genera of Myristicaceae and this genus is native to the American continent, especially in neotropical regions. The largest number of species of this genus is found in the Amazon region and the most important species include Virola surinamensis Warb. and Virola sebifera Aubl. In the present study, we describe the chemical composition of the essential oil of the V. surinamensis obtained at two different periods of the day in two seasons (rainy and dry), as well as their antimicrobial activity against pathogenic bacterial strains of Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. In addition, we investigated, using in silico tools, the antimicrobial activity of the major chemical compounds present in the essential oil of V. surinamensis. The samples collected at different seasons and times showed a similar chemical profile, characterized by the major constituents α-pinene (>33%) and β-pinene (>13%). The essential oil of V. surinamensis showed an interesting antibacterial activity, exhibiting low inhibitory concentrations against the tested bacterial species. The computational investigation indicated that limonene, myrcene, and β-pinene could be related to the antibacterial activity against the tested pathogenic bacterial strains. Our results shed light on the possible constituents of essential oil that could be related to its activity against bacterial species and might be useful for further experimental tests that aim to discover new potential antibacterial agents for food preservation.

Hierarchical Virtual Screening and Binding Free Energy Prediction of Potential Modulators of Aedes Aegypti Odorant-Binding Protein 1

The Aedes aegypti mosquito is the main hematophagous vector responsible for arbovirus transmission in Brazil. The disruption of A. aegypti hematophagy remains one of the most efficient and least toxic methods against these diseases and, therefore, efforts in the research of new chemical entities with repellent activity have advanced due to the elucidation of the functionality of the olfactory receptors and the behavior of mosquitoes. With the growing interest of the pharmaceutical and cosmetic industries in the development of chemical entities with repellent activity, computational studies (e.g., virtual screening and molecular modeling) are a way to prioritize potential modulators with stereoelectronic characteristics (e.g., pharmacophore models) and binding affinity to the AaegOBP1 binding site (e.g., molecular docking) at a lower computational cost. Thus, pharmacophore- and docking-based virtual screening was employed to prioritize compounds from Sigma-Aldrich® (n = 126,851) and biogenic databases (n = 8766). In addition, molecular dynamics (MD) was performed to prioritize the most potential potent compounds compared to DEET according to free binding energy calculations. Two compounds showed adequate stereoelectronic requirements (QFIT > 81.53), AaegOBP1 binding site score (Score > 42.0), volatility and non-toxic properties and better binding free energy value (∆G < −24.13 kcal/mol) compared to DEET ((N,N-diethyl-meta-toluamide)) (∆G = −24.13 kcal/mol).

Molecular insights on ar-turmerone as a structural, functional and pharmacophoric analogue of synthetic mosquito repellent DEET by comprehensive computational assessment

Mosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of skin permeability, N,N-Diethyl-meta-toluamide (DEET) is one of the most extensively used mosquito repellents but a dangerous synthetic chemical. DEET was identified about a decade ago to inhibit mosquito's Odorant Binding Protein 1 (OBP1), impairing the mosquito's ability to recognise the host body odour. OBP1 has been identified as a possible target for the development of new mosquito repellents since its discovery. Essential oils from different plants, on the other hand, have been used to repel mosquitos since antiquity. One essential oil from the Curcuma longa (Zingiberales: Zingiberaceae) rhizome display mosquito repellent properties, according to the literature. Furthermore, one of the phytochemicals found in abundance in C. longa essential oil, ar-turmerone, exhibits mosquito repellency as comparable to synthetic DEET. Till date studies on in-silico interaction of natural ar-turmerone with OBP1, which we depict in our current work are scarce. Further, there exist no published reports demonstrating the literary evidence on detailed insights of interaction of DEET with OBP1 along with Molecular Dynamics (MD) simulation studies. We further performed detailed molecular investigations using pharmacophore analysis of ar-turmerone and compared it with DEET, where our findings in the current manuscript unveils for the first time that ar-turmerone is a functional, structural and pharmacophoric analogue of DEET.

Decoding molecular recognition of inhibitors targeting HDAC2 via molecular dynamics simulations and configurational entropy estimation

Molecular recognition by enzymes is a complicated process involving thermodynamic energies governing protein-ligand interactions. In order to aid the estimation of inhibitory activity of compounds targeting an enzyme, several computational methods can be employed to dissect this intermolecular contact. Herein, we report a structural dynamics investigation of an epigenetic enzyme HDAC2 in differentiating its binding to various inhibitors within the sub-sites of its active site. Molecular dynamics (MD) simulation was employed to elucidate the intermolecular interactions as well as the dynamics behavior of ligand binding. MD trajectories of five distinct HDAC2-inhibitor complexes reveal that compounds lacking adequate contacts with the opening rim of the active site possess high fluctuation along the cap portion, thus weakening the overall affinity. Key intermolecular interactions determining the effective binding of inhibitors include hydrogen bonds with Gly154, Asp181, and Tyr308; hydrophobic interactions between Phe155/Phe210 and the linker region; and a pi-stacking with Arg39 at the foot pocket. Decomposition of the binding free energy calculated per-residue by MM/PBSA also indicates that the interactions within the internal foot pocket, especially with residues Met35, Leu144, Gly305, and Gly306, can contribute significantly to the ligand binding. Additionally, configurational entropy of the binding was estimated and compared to the scale of the binding free energy in order to assess its contribution to the binding and to differentiate various ligand partners. It was found that the levels of entropic contribution are comparable among a set of structurally similar carbamide ligands, while it is greatly different for the set of unrelated ligands, ranging from 2.75 to 16.38 kcal/mol for the five inhibitors examined. These findings exemplify the importance of assessing molecular dynamics as well as estimating the entropic contribution in evaluating the ligand binding mechanism.

In Silico Study and Excito-Repellent Activity of Vitex negundo L. Essential Oil against Anopheles gambiae

(1) Background: Essential oil from Vitex negundo is known to have repellent and insecticidal properties toward the Anopheles gambiae and this is linked to its monoterpene and sesquiterpene content. In this work, an effort is made to delineate the constitution of V. negundo essential oil (VNEO) and their interaction with odorant-binding proteins (OBPs) of A. gambiae and hence access its repellent efficiency as cost-effective and safer malaria vector control alternatives. (2) Methods: Anopheles species authentication was performed by genomic DNA analysis and was subjected to behavioral analysis. GC-MS profiling was used to identify individual components of VNEO. Anopheles OBPs were obtained from the RCSB protein data bank and used for docking studies. Determination of ligand efficiency metrics and QSAR studies were performed using Hyper Chem Professional 8.0.3, and molecular dynamics simulations were performed using the Desmond module. (3) Results: GC-MS analysis of VNEO showed 28 compounds (monoterpenes, 80.16%; sesquiterpenes, 7.63%; and unknown constituents, 10.88%). The ligand efficiency metrics of all four ligands against the OBP 7 were within acceptable ranges. β-selinene (−12.2 kcal/mol), β-caryophellene (−9.5 kcal/mol), sulcatone (−10.9 kcal/mol), and α-ylangene (−9.3 kcal/mol) showed the strongest binding affinities for the target proteins. The most stable hydrophobic interactions were observed between β-selinene (Phe111 and Phe120), Sulcatone (Phe54 and Phe120), and α-ylangene (Phe111), while only sulcatone (Tyr49) presented H-bond interactions in the simulated environment. (4) Conclusions: Sulcatone and β-caryophyllene presented the best log p values, 6.45 and 5.20, respectively. These lead phytocompounds can be used in their purest as repellent supplement or as a natural anti-mosquito agent in product formulations.

A Combined Computational Methodology for the Discovery of Hit Compounds with Putative Insect Repellency Properties

Mosquitoes and other hematophagous arthropods, the primary vectors of multiple parasites and viruses, are responsible for the transmission of serious diseases to humans. Nowadays, the interest is focused on the development of novel repellents to the existing ones with advanced properties. The present study attempts the discovery of novel hit compounds which may evolve as insect repellents using a combined computational methodology targeting the Odorant Binding Protein 1 (OBP1). The in silico results indicated two compounds, namely coniferyl alcohol and 1,2-diphenyl-2-propanol, which were further evaluated (a) in vitro for their binding affinity to AgamOBP1 and (b) in vivo using dose-depended repellence tests against the aggressive-day biting Aedes albopictus. The combination of in vitro and in vivo results pointed that coniferyl alcohol and 1,2-diphenyl-2-propanol exhibited high binding affinity over OBP1 with 69.4 and 84.7 nM, respectively as well as efficient repellent activity. Compounds were also tested for their dose-depended repellency activity in vivo against Aedes albopictus. Overall, the selected compounds can serve as scaffolds for the development of novel repellents.

Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from Eleusine indica (EiEPSPS) as a starting point. First, ligand-based pharmacophore screening was performed to select compounds with a similar pharmacophore to glyphosate. Then, structure-based pharmacophore modeling was applied to build a model which represents the molecular features of glyphosate. Then, consensus docking was performed to rank the best poses of the natural compounds against the PEP binding site, and then molecular dynamics simulations were performed to analyze the stability of EPSPS complexed with the selected ligands. Finally, we have investigated the binding affinity of the complexes using free energy calculations. The selected hit compound, namely AG332841, showed a stable conformation and binding affinity to the EPSPS structure and showed no structural similarity to the already known weed EPSPS inhibitors. Our computational study aims to clarify the inhibition of the mutant EiEPSPS, which is resistant to glyphosate, and identify new potential herbicides from natural products.

Host-Guest Inclusion Complexes of Natural Products and Nanosystems: Applications in the Development of Repellents

Repellents are compounds that prevent direct contact between the hosts and the arthropods that are vectors of diseases. Several studies have described the repellent activities of natural compounds obtained from essential oils. In addition, these chemical constituents have been pointed out as alternatives to conventional synthetic repellents due to their interesting residual protection and low toxicity to the environment. However, these compounds have been reported with short shelf life, in part, due to their volatile nature. Nanoencapsulation provides protection, stability, conservation, and controlled release for several compounds. Here, we review the most commonly used polymeric/lipid nanosystems applied in the encapsulation of small organic molecules obtained from essential oils that possess repellent activity, and we also explore the theoretical aspects related to the intermolecular interactions, thermal stability, and controlled release of the nanoencapsulated bioactive compounds.

Behavioural response of Culex pipiens biotype molestus to oviposition pheromone

Insect behaviour relies on an olfactory sensory system that controls a range of activities, from food choice and mating to oviposition, where pheromones play a central role. In Culex mosquitoes, egg-laying is accompanied by the release of mosquito oviposition pheromone (MOP), which has been shown to affect the oviposition behaviour of conspecifics. Here, we investigated for the first time the effect of MOP on the oviposition rate of Culex pipiens biotype molestus, examining separately males and females, before and after mating and oviposition. Our results demonstrate that MOP is more likely to act as an oviposition stimulant rather than an attractant, since more gravid females laid eggs in its presence, while the number of male or female mosquitoes (virgin or mated) captured on pheromone-treated pots was similar to those treated with control water.

Newly Identified COVID-19 Drug Candidates Based on Computational Strategies

The COVID-19 has raised a public health catastrophe in early 2020 worldwide. Despite several approved vaccines that have repressed the pandemic and decreased the mortality rate since then, attempts to discover an effective antiviral drug have not indicated reliable results. In this research, in silico studies (virtual screening and molecular docking) were performed based on quinoline structure to identify novel drug candidates against SARS-CoV-2 before laboratory evaluations. A chemical library consisting of 548 compounds was collected from literature mining of five databases to select the best ligands interacting with three target proteins of SARS-CoV-2, including the main protease, spike protein, and chimeric receptor-binding domain in a complex of human angiotensin-converting enzyme 2. The top five compounds that presented suitable binding energy against each target protein are reported in detail for the first time. Notably, new compound N-4-(6-methyl-3-pyridinyl) phenyl)-9-acridinamine showed high affinity to all selected proteins. These identified compounds will help in speeding up the drug development against COVID-19.

New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation

New compounds with potential insecticide activity were synthesized by structural modifications performed in the monoterpenoid phenolic moieties of carvacrol and thymol, resulting in a set of derivatives with the ether function containing the propyl, chloropropyl or hydroxypropyl chains, as well as a bicyclic ether with an unsaturated chain containing a carboxylic acid terminal. In addition, an analogue of carvacrol and thymol isomers bearing methoxyl, 1-hydroxyethyl and (3-chlorobenzoyl)oxy, instead of the three original methyl groups, was also synthesized. Several structural changes that resulted in diminished insecticide activity have been identified, but two significantly active molecules have been synthesized, one of them being less toxic to human cells than the naturally-derived starting materials. Structure-based inverted virtual screening and molecular dynamics simulations demonstrate that these active molecules likely target the insect odorant binding proteins and/or acetylcholinesterase and are able to form stable complexes. For the most promising compounds, nanoencapsulation assays were carried out in liposomes of egg phosphatidylcholine/cholesterol (7 : 3) prepared by both thin film hydration and ethanolic injection methods. The compound-loaded liposomes were generally monodisperse and with sizes smaller than or around 200 nm. The thin film hydration method allowed high encapsulation efficiencies (above 85%) for both compounds and a delayed release, while for the systems prepared by ethanolic injection the encapsulation efficiency is lower than 50%, but the release is almost complete in two days.

Gonçalves Vianez JL, Santana da Costa K, de Molfetta FA, Nahum Alves C. Analysis of Kojic Acid Derivatives as Competitive Inhibitors of Tyrosinase: A Molecular Modeling Approach

Tyrosinases belong to the functional copper-containing proteins family, and their structure contains two copper atoms, in the active site, which are coordinated by three histidine residues. The biosynthesis of melanin in melanocytes has two stages depending on the actions of the natural substrates L-DOPA and L-tyrosine. The dysregulation of tyrosinase is involved in skin cancer initiation. In the present study, using molecular modeling tools, we analyzed the inhibition activity of tyrosinase activity using kojic acid (KA) derivatives designed from aromatic aldehydes and malononitrile. All derivatives showed conformational affinity to the enzyme active site, and a favorable distance to chelate the copper ion, which is essential for enzyme function. Molecular dynamics simulations revealed that the derivatives formed promising complexes, presenting stable conformations with deviations between 0.2 and 0.35 Å. In addition, the investigated KA derivatives showed favorable binding free energies. The most stable KA derivatives showed the following binding free energies: -17.65 kcal mol-1 (D6), -18.07 kcal mol-1 (D2), -18.13 (D5) kcal mol-1, and -10.31 kcal mol-1 (D4). Our results suggest that these derivatives could be potent competitive inhibitors of the natural substrates of L-DOPA (-12.84 kcal mol-1) and L-tyrosine (-9.04 kcal mol-1) in melanogenesis.

Drying Effects on Chemical Composition and Antioxidant Activity of Lippia thymoides Essential Oil, a Natural Source of Thymol

Leaves of Lippia thymoides (Verbenaceae) were dried in an oven at 40, 50 and 60 °C and the kinetic of drying and the influence of the drying process on the chemical composition, yield, and DPPH radical scavenging activity of the obtained essential oils were evaluated. The composition of the essential oils was determined with gas chromatography-mass spectrometry and gas chromatography-flame ionization detection analyses. The influence of drying on the chemical composition of the essential oils of L. thymoides was evaluated by multivariate analysis, and their antioxidant activity was investigated via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. The Midilli model was the most appropriate to describe the behavior of drying kinetic data of L. thymoides leaves. Thymol was the major compound for all analyzed conditions; the maximum content was obtained from fresh leaves (62.78 ± 0.63%). The essential oils showed DPPH radical scavenging activity with an average of 73.10 ± 12.08%, and the fresh leaves showed higher inhibition (89.97 ± 0.31%). This is the first study to evaluate the influence of drying on the chemical composition and antioxidant activity of L. thymoides essential oils rich in thymol.

Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products

Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.

Predicting cell-penetrating peptides using machine learning algorithms and navigating in their chemical space

Cell-penetrating peptides (CPPs) are naturally able to cross the lipid bilayer membrane that protects cells. These peptides share common structural and physicochemical properties and show different pharmaceutical applications, among which drug delivery is the most important. Due to their ability to cross the membranes by pulling high-molecular-weight polar molecules, they are termed Trojan horses. In this study, we proposed a machine learning (ML)-based framework named BChemRF-CPPred (beyond chemical rules-based framework for CPP prediction) that uses an artificial neural network, a support vector machine, and a Gaussian process classifier to differentiate CPPs from non-CPPs, using structure- and sequence-based descriptors extracted from PDB and FASTA formats. The performance of our algorithm was evaluated by tenfold cross-validation and compared with those of previously reported prediction tools using an independent dataset. The BChemRF-CPPred satisfactorily identified CPP-like structures using natural and synthetic modified peptide libraries and also obtained better performance than those of previously reported ML-based algorithms, reaching the independent test accuracy of 90.66% (AUC = 0.9365) for PDB, and an accuracy of 86.5% (AUC = 0.9216) for FASTA input. Moreover, our analyses of the CPP chemical space demonstrated that these peptides break some molecular rules related to the prediction of permeability of therapeutic molecules in cell membranes. This is the first comprehensive analysis to predict synthetic and natural CPP structures and to evaluate their chemical space using an ML-based framework. Our algorithm is freely available for academic use at http://comptools.linc.ufpa.br/BChemRF-CPPred .

Analyses of structural dynamics revealed flexible binding mechanism for the Agrilus mali odorant binding protein 8 towards plant volatiles

BACKGROUND

Volatiles from host plants are an important source of insect pest attractants and repellents. Insect odorant binding proteins (OBPs) have been widely characterized, but the molecular binding dynamics and underlying mechanisms are still not well understood. Thus, we characterized binding characteristics of AmalOBP8 from the apple buprestid beetle (Agrilus mali Matsumura), an unprecedented serious threat to rare apple germplasm resources and local ecosystems.

RESULTS

Fluorescence studies demonstrated that the quenching mechanism was clearly static. AmalOBP8 was found to bind with both volatiles at single independent sites. Negative thermodynamic parameters suggested that binding interactions between AmalOBP8 and both volatiles could occur spontaneously. Hydrogen bonding was the key force in AmalOBP8's binding to geranyl formate, for which the amino acid residue Trp106 played a critical role in the binding pocket. Multiple Leu residues in AmalOBP8 created a strong hydrophobic environment, and formed the binding pocket for (Z)-3-hexenyl hexanoate. Compared to classic OBPs, in addition to lack of one disulfide bridge, AmalOBP8 had a small α-helix (α7) at the C-terminus, resulting in greater flexibility and adaptability for this protein to bind with different compound molecules.

CONCLUSION

Key residues of AmalOBP8 in binding interactions with plant volatiles were clarified. AmalOPB8 had a large ligand binding spectrum and great flexibility in binding with plant volatiles, providing good molecular targets for screening insect attractants and repellents. Our results can promote understanding of insects' perception of various odorants, and establish a foundation for discovery of new pest control agents. © 2020 Society of Chemical Industry.

First report on the Annona exsucca DC. Essential oil and in silico identification of potential biological targets of its major compounds

In the present study, the essential oil (EO) of Annona exsucca DC. or Rollinia exsucca was extracted by hydrodistillation, and the identification and quantification of volatile compounds were performed by GC-MS and GC-FID. A. exsucca leaves were collected from the Magalhães Barata, northeast of the State of Pará (Brazil) in March and September of 2019. Moreover, we used computational approaches to evaluate possible biological targets for the major compounds of the EO. In the sample obtained in March, 50 compounds were identified, with hydrocarbon sesquiterpenes being the predominant ones with the content of 80.52%. In the sample collected in September, 58 compounds were identified, and the chemical class of hydrocarbon monoterpenes and sesquiterpenes were the dominant ones with contents of 43.36 and 31.29%, respectively. Computational methods demonstrated that some major compounds have potential biological activity against some strains of pathogenic bacteria, as well as against molecular targets involved in cancer development.

In silico analyses of toxicity of the major constituents of essential oils from two Ipomoea L. species

Convolvulaceae Juss. is a family of vines and shrubs composed of species of ecological and economic importance. Ipomoea asarifolia (Desr.) Roem. & Schult. and I. setifera Poir. are ruderal and evergreen weeds that invade pastures and cause intoxication in cattle during the dry season. In the present study, the essential oils (EOs) of the leaves from I. setifera (dry season) and I. asarifolia (dry and wet seasons) were obtained by steam distillation for 3h. The chemical composition of the EOs was determined using gas chromatography coupled to gas spectrometry (CG/MS) and gas chromatography with flame ionization detector (CG-FID). To correlate the toxicity of the major chemical constituents of I. setifera and I. asarifolia EOs, we predicted the inhibition activity against the cytochrome P450 (CYP450) and P-glycoprotein 1 (P-gp) using a machine learning-based (ML-based) algorithm. In silico analyses were also applied to evaluate the pharmacokinetics properties related to the penetration in the blood-brain barrier (BBB) and gastrointestinal absorption. The chemical composition of the EO of I. setifera was characterized by high levels of (E)-caryophyllene (36.7%) and β-elemene (20.49%). The I. asarifolia EO showed a phytol derivative as the main chemical constituent in the dry season (35.49%), and its content was reduced in the sample collected during the wet season (10.67%). The constituent (E)-caryophyllene was also present in the leaves of I. asarifolia, but at lower levels (15.93-19.93%) when compared to the EOs of I. setifera. Our computational analyses indicated that the constituents caryophyllene oxide, cedroxyde, pentadecanal, and phytol can be related to the toxicity of these weeds. This is the first study to report the chemical composition of I. asarifolia and I. setifera EOs and correlate their molecular mechanism of toxicity using in silico approaches.

Insight into the Dual inhibitory Mechanism of verbascoside targeting serine/threonine phosphatase Stp1 against Staphylococcus aureus

The eukaryotic-like serine/threonine phosphatase (Stp1) is an enzyme-dependent protein phosphatase involved in regulating various virulence factors of Staphylococcus aureus. Owing to its role in S. aureus infections, Stp1 has become a potential target for antibiotic development. Unfortunately, there are very few reports describing Stp1 inhibitors. Using virtual screening, we have identified a potent and effective Stp1 inhibitor, verbascoside (VBS). Interestingly, the kinetics of the enzymatic reaction revealed that this natural inhibitor acts via both competitive and allosteric mechanisms. To explore the mechanism of interaction between VBS and Stp1, standard molecular dynamics (MD) simulations were performed for the Stp1-VBS complex. Consistent with the experimental results, competitive and allosteric binding sites for VBS were identified in Stp1. Met39, Gly41, His42, Arg161, and Asn162 residues were involved in the competitive binding of VBS, while Arg122, Ser136, Asp137, Asn142, and Val145 residues were associated with the allosteric binding of VBS. The contributions of these residues were confirmed by amino acid site-directed mutagenesis and fluorescence quenching experiments. This work demonstrates that VBS is a potent anti-virulence compound against S. aureus infection, laying the foundation for the further development of novel anti-virulence agents.

Isolation, Identification, and Bioinformatic Analysis of Antibacterial Proteins and Peptides from Immunized Hemolymph of Red Palm Weevil Rhynchophorus ferrugineus

Red palm weevil (Rhynchophorus ferrugineus Olivier, 1791, Coleoptera: Curculionidae) is a destructive pest of palms, rapidly extending its native geographical range and causing large economic losses worldwide. The present work describes isolation, identification, and bioinformatic analysis of antibacterial proteins and peptides from the immunized hemolymph of this beetle. In total, 17 different bactericidal or bacteriostatic compounds were isolated via a series of high-pressure liquid chromatography steps, and their partial amino acid sequences were determined by N-terminal sequencing or by mass spectrometry. The bioinformatic analysis of the results facilitated identification and description of corresponding nucleotide coding sequences for each peptide and protein, based on the recently published R. ferrugineus transcriptome database. The identified compounds are represented by several well-known bactericidal factors: two peptides similar to defensins, one cecropin-A1-like peptide, and one attacin-B-like protein. Interestingly, we have also identified some unexpected compounds comprising five isoforms of pheromone-binding proteins as well as seven isoforms of odorant-binding proteins. The particular role of these factors in insect response to bacterial infection needs further investigation.

In silico design and analysis of NS4B inhibitors against hepatitis C virus

The hepatitis C virus is a communicable disease that gradually harms the liver leading to cirrhosis and hepatocellular carcinoma. Important therapeutic interventions have been reached since the discovery of the disease. However, its resurgence urges the need for new approaches against this malady. The NS4B receptor is one of the important proteins for Hepatitis C Virus RNA replication that acts by mediating different viral properties. In this work, we opt to explore the relationships between the molecular structures of biologically tested NS4B inhibitors and their corresponding inhibitory activities to assist the design of novel and potent NS4B inhibitors. For that, a set of 115 indol-2-ylpyridine-3-sulfonamides (IPSA) compounds with inhibitory activity against NS4B is used. A hybrid genetic algorithm combined with multiple linear regressions (GA-MLR) was implemented to construct a predictive model. This model was further used and applied to a set of compounds that were generated based on a pharmacophore modeling study combined with virtual screening to identify structurally similar lead compounds. Multiple filtrations were implemented for selecting potent hits. The selected hits exhibited advantageous molecular features, allowing for favorable inhibitory activity against HCV. The results showed that 7 out of 1285 screened compounds, were selected as potent candidate hits where Zinc14822482 exhibits the best predicted potency and pharmacophore features. The predictive pharmacokinetic analysis further justified the compounds as potential hit molecules, prompting their recommendation for a confirmatory biological evaluation. We believe that our strategy could help in the design and screening of potential inhibitors in drug discovery.Communicated by Ramaswamy H. Sarma.

In silico improvement of the cyanobacterial lectin microvirin and mannose interaction

Lectins that bind to HIV envelope glycoprotein can inhibit virus-cell fusion and be used for rational drug design. This paper presents the results of an in silico approach to improve affinity interaction between the cyanobacterial lectin microvirin and its ligand Manα(1-2)Man. Comparative modeling and molecular dynamics tools were used. Additionally, the alanine scanning webserver was used to study the importance of protein residues in the binding site and to guide mutant production. The model obtained presented two homologous domains designated as domains A and B, each consisting of a single strand with triple and antiparallel β-sheets of (β1-β3 and β6-β8). Disulfide bonds between the cysteines (Cys60-Cys80, Cys63-Cys78 and Cys8-Cys24) were also found. The highly conserved binding site, including residues Asn44, Ile45, Asp46, Gln54, Asn55, Glu58, Thr59, Gln81, Thr82 and Met83. The RMSD values of the di-mannose and the interaction site were very stable during the molecular dynamics. Calculations of the occupation time of the hydrogen bonds were made for the residues that showed interaction in the complex lectin and ligand. The residue that contributed most to the interaction with Manα(1-2)Man was Asn55. After validation, the model generated remained stable during the entire simulation. Despite its structural similarity with the template we used, our mutant (Thr82Arg) showed a higher affinity interaction with Manα(1-2)Man. Communicated by Ramaswamy H. Sarma.

Identification of Potential COX-2 Inhibitors for the Treatment of Inflammatory Diseases Using Molecular Modeling Approaches

Non-steroidal anti-inflammatory drugs are inhibitors of cyclooxygenase-2 (COX-2) that were developed in order to avoid the side effects of non-selective inhibitors of COX-1. Thus, the present study aims to identify new selective chemical entities for the COX-2 enzyme via molecular modeling approaches. The best pharmacophore model was used to identify compounds within the ZINC database. The molecular properties were determined and selected with Pearson’s correlation for the construction of quantitative structure–activity relationship (QSAR) models to predict the biological activities of the compounds obtained with virtual screening. The pharmacokinetic/toxicological profiles of the compounds were determined, as well as the binding modes through molecular docking compared to commercial compounds (rofecoxib and celecoxib). The QSAR analysis showed a fit with R = 0.9617, R² = 0.9250, standard error of estimate (SEE) = 0.2238, and F = 46.2739, with the tetra-parametric regression model. After the analysis, only three promising inhibitors were selected, Z-964, Z-627, and Z-814, with their predicted pIC₅₀ (−log IC₅₀) values, Z-814 = 7.9484, Z-627 = 9.3458, and Z-964 = 9.5272. All candidates inhibitors complied with Lipinski’s rule of five, which predicts a good oral availability and can be used in in vitro and in vivo tests in the zebrafish model in order to confirm the obtained in silico data.

Current and potential biotechnological applications of odorant-binding proteins

Odorant-binding proteins (OBPs) are small soluble proteins whose biological function is believed to be facilitating olfaction by assisting the transport of volatile chemicals in both vertebrate and insect sensory organs, where they are secreted. Their capability to interact with a broad range of hydrophobic compounds combined with interesting features such as being small, stable, and easy to produce and modify, makes them suitable targets for applied research in various industrial segments, including textile, cosmetic, pesticide, and pharmaceutical, as well as for military, environmental, health, and security field applications. In addition to reviewing already established biotechnological applications of OBPs, this paper also discusses their potential use in prospecting of new technologies. The development of new products for insect population management is currently the most prevailing use for OBPs, followed by biosensor technology, an area that has recently seen a significant increase in studies evaluating their incorporation into sensing devices. Finally, less typical approaches include applications in anchorage systems and analytical tools. KEY POINTS: • Odorant-binding proteins (OBPs) present desired characteristics for applied research. • OBPs are mainly used for developing new products for insect population control. • Incorporation of OBPs into chemosensory devices is a growing area of study. • Less conventional uses for OBPs include anchorage systems and analytical purposes. Graphical Abstract.

Targeting shikimate pathway: In silico analysis of phosphoenolpyruvate derivatives as inhibitors of EPSP synthase and DAHP synthase

The shikimate pathway consists of seven enzymatic steps involved in the conversion of erythrose-4-phosphate and phosphoenolpyruvate to chorismate and also responsible to the production of aromatic amino acids, such as phenylalanine, tyrosine, and tryptophan which are essential to the bacterial metabolism. The 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) catalyze important steps in the shikimate pathway using as substrate the phosphoenolpyruvate (PEP). Due to the importance of PEP in shikimate pathway, its structure has been investigated to develop new bioinspired competitive inhibitors against DAHPS and EPSPS. In the present study, we perform a literature survey of 28 PEP derivatives, then we analyzed the selectivity and affinity of these compounds against the EPSPS and DAHPS structures using consensual molecular docking, pharmacophore prediction, molecular dynamics (MD) simulations, and binding free energy calculations. Here, we propose consistent binding modes of the selected ligands and indicate that their structures show interesting pharmacophoric properties related to multi-targets inhibitors for both enzymes. Our computational results are supported by previous experimental findings related to the interactions of PEP derivatives with DAHPS and EPSPS structures.

Chemometric methods in antimalarial drug design from 1,2,4,5-tetraoxanes analogues

A set of 23 steroidal 1,2,4,5-tetraoxane analogues were studied using quantum-chemical method (B3LYP/6-31 G*) and multivariate analyses (PCA, HCA, KNN and SIMCA) in order to calculate the properties and correlate them with antimalarial activity (log RA) against Plasmodium falciparum clone D-6 from Sierra Leone. PCA results indicated 99.94% of the total variance and it was possible to divide the compounds into two classes: less and more active. Descriptors responsible for separating were: highest occupied molecular orbital energy (HOMO), bond length (O1-O2), Mulliken electronegativity (χ) and Bond information content (BIC0). We use HCA, KNN and SIMCA to explain relationships between molecular properties and biological activity of a training set and to predict antimalarial activity (log RA) of 13 compounds (#24-36) with unknown biological activity. We apply molecular docking simulations to identify intermolecular interactions with a selected biological target. The results obtained in multivariate analysis aided in the understanding of the activity of the new compound's design (#24-36). Thus, through chemometric analyses and docking molecular study, we propose theoretical synthetic routes for the most promising compounds 28, 30, 32 and 36 that can proceed to synthesis steps and in vitro and in vivo assays.

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 = -11.0 kcal/mol), LMQC36 (∆G = -10.6 kcal/mol), and LMQC50 (∆G = -10.2 kcal/mol). LMQC72 and LMQC36 showed higher binding affinity compared to rofecoxib (∆G = -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: ΔGbind = -45.31 kcal/mol; LMQC72: ΔGbind = -38.58 kcal/mol; LMQC36: ΔGbind = -36.10 kcal/mol; and LMQC50: ΔGbind = -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.

Identification of novel Aedes aegypti odorant-binding protein 1 modulators by ligand and structure-based approaches and bioassays

Arboviruses are a group of viruses (e.g. Dengue, Chikungunya and Yellow fever virus) that are transmitted by arthropod vectors, which Aedes aegipty is the vector of main viruses in Americas. This vector is responsible to 2.4 millions of arboviruses cases in Brazil with less than a thousand deaths annually. Despite of epidemiological data, arboviruses treatment is symptomatic and the vaccine control is not effective, which makes the vector control against A. aegipty a promising strategy to diseases control. One way to achieve this goal is to development of A. aegipty sensitive olfactory modulators. Odorant binding protein 1 from A. aegypti (AaegOBP1) is essential in sensory communication, and is the first filter in odorant selection, which makes this target promising to development of new repellents. For this reason, hierarchical virtual screening (ligand-based pharmacophore model and molecular docking) together volatility filter was applied at Sigma-Aldrich database (n = 126.851) to prioritize potential molecules to repellency assays. Three compounds showed adequate stereo-electronic requirements (QFIT> 81.53), score to AaegOBP1 binding site (Score > 36.0) and volatile properties and it was chosen for repellency assays. ZINC00170981 and ZINC00131924 showed a dose-response behavior, while ZINC01621824 did not showed activity in repellency assays. Finally, Molecular Dynamics (MD) was employed to hypothesize the stability of protein-ligand complexes. According to RMSD, RMSF and binding free energy data, ZINC00170981 and ZINC00131924 were able to stabilize AaegOBP1 binding-site during the trajectory by interactions with key residues such as His77, Leu89 and Trp114). Communicated by Ramaswamy H. Sarma.

An in-silico evaluation of dietary components for structural inhibition of SARS-Cov-2 main protease

The main protease (M^pro) of SARS-CoV-2 is responsible for the cleavage of viral replicase polyproteins 1a and 1ab into their mature form and is highly specific and exclusive in its activity. Many studies have targeted this enzyme by small molecule inhibitors to develop therapeutics against the highly infectious disease Covid-19. Our diet contains many natural antioxidants which along with providing support for proper growth and functioning of the body, pose additional health benefits. Present in-silico analysis depicted that natural antioxidants like sesamin, ellagic acid, capsaisin, and epicatechin along with galangin, exhibited significant binding at the catalytic site of the M^pro enzyme. They interacted with excellent efficiency with the chief active site residue Cys145 and thus seem to possess the remarkable potential to act as drug candidates for the treatment of Covid-19. Such dietary compounds can be easily administered orally with least toxicity related concern and thus yell for urgent exhaustive research to develop into efficient therapies.

Communicated by Ramaswamy H. Sarma

In silico analysis of polyphenols and flavonoids for design of human Nav1.7 inhibitors

Neuropathic pain is commonly associated with lesion or disease of the somatosensory system and often reflected as indicator of impaired life. Although the central nervous system is main regulator of pain but for initiation and maintenance of the neuropathic pain is regulated by peripheral nervous system. Sodium channels particularly Nav1.7, Nav1.8, Nav 1.9 are key stake holders in the peripheral neuropathy, activation of these sodium channels might lead to genesis and propagation. Flavonoids and polyphenols showed promising effects in neuropathic pain. Here we are reporting In silico analysis of some selected flavonoids and polyphenols on sodium activated voltage channel 1.7 to explore the structural fragments required for binding. Results indicated Baicalin, Butrin, Dihydromonospermoside, Icariin, Isocoreopsin and Isosaponarin are showing promising docking score with sodium activated voltage channel 1.7 than other compounds. Structural modification of these promising leads keeping pharamcophoric requirement intact may yield potent Nav1.7 inhibitors for peripheral pain management.Communicated by Ramaswamy H. Sarma.

Molecular basis of the beta-lactamase protein using comparative modelling, drug screening and molecular dynamics studies to understand the resistance of β-lactam antibiotics

Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human population in overexpressing resistance against β-lactam antibiotics. These β-lactam antibiotics being experimentally well studied still lack the key information and mechanism for their resistance. The structural information of the ampC protein is unknown and poorly studied; hence, it is the need of the hour to find effective inhibitors against it. In our study, the prediction of the three-dimensional structure of ampC protein from Morganella morganii was performed using a comparative modelling approach. The predicted structure was energetically stabilized and functional conformations were mapped through 100-ns molecular dynamics simulation runs. Also, Ramachandran plot shows the model to be stereo-chemically stable with most residues found under core allowed regions. Drug screening with several experimentally tested inhibitors was then confirmed to check the activity against ampC protein using an AutoDock tool. The results suggested OncoglabrinolC molecule as the best inhibitor (out of 21 drug molecules) with a binding affinity of - 11.44 kcal/mol. Anti-bacterial/anti-parasitic inhibitors have not only been used against bacterial infections, but later reports have also shown them to work against deadly viruses such as SARS-CoV2. This key structural and inhibitory information is certain to help in the discovery of specific and potent substitute therapeutic drugs and the development of experimental procedures against human infection.

Bioactive Natural Compounds and Antioxidant Activity of Essential Oils from Spice Plants: New Findings and Potential Applications

Spice plants have a great influence on world history. For centuries, different civilizations have used them to condiment the foods of kings and nobles and applied them as embalming preservatives, perfumes, cosmetics, and medicines in different regions of the world. In general, these plants have formed the basis of traditional medicine and some of their derived substances have been utilized to treat different human diseases. Essential oils (EOs) obtained from these plants have been also used as therapeutic agents and have shown supportive uses in remedial practices. The discovery and development of bioactive compounds from these natural products, based on their traditional uses, play an important role in developing the scientific evidence of their potential pharmaceutical, cosmetic, and food applications. In the present review, using recent studies, we exhibit a general overview of the main aspects related to the importance of spice plants widely used in traditional medicine: Cinnamomum zeylanicum (true cinnamon), Mentha piperita (peppermint), Ocimum basilicum (basil), Origanum vulgare (oregano), Piper nigrum (black pepper), Rosmarinus officinalis (rosemary), and Thymus vulgaris (thyme); and we discuss new findings of the bioactive compounds obtained from their EOs, their potential applications, as well as their molecular mechanisms of action, focusing on their antioxidant activity. We also exhibit the main in vitro methods applied to determine the antioxidant activities of these natural products.

Insilico analysis of marine indole alkaloids for design of adenosine A2A receptor antagonist

Neurological disease is the disease associated with most of geriatric population in the world. The diseases like Alzheimer's disease and Parkinson's disease are associated with the change in the life style in current era. Treatment of these diseases normally focused on the agents which can able to manipulate the neurotransmitter release, so it is associated with severe side effects. Adenosine receptors are the upcoming targets for the inflammatory as well as neurological diseases as agents like istradefylline are in the clinical use. Marine natural products are the rich source of the valuable drug like substances, number marine alkaloids are known for their ability to pass blood brain barrier (BBB) which is major hurdle in the neurological drug discovery. Here, we report the virtual screening of some marine alkaloids for adenosine 2 receptor binding potential. Results indicated topsentin C, 6'-debromohamacanthin, 6-hydroxydiscodermindole and discodermindole are having excellent binding affinity towards the adenosine 2A receptor than other selected alkaloids.Communicated by Ramaswamy H. Sarma.