Compounds from Natural Products Candidates to Drug for Chikungunya Virus Infection: A Systematic Review.

INTRODUCTION: Chikungunya fever is a disease caused by infection with the Chikungunya virus, transmitted by Aedes aegypti and Aedes albopictus mosquitoes. Despite its self-limited character, more than 60% of patients have chronic recurrent arthralgia with debilitating pain that lasts for years. AIM: The objective of this review was to gather and analyze evidence from the literature on potential therapeutic strategies with molecules from natural products for the treatment of Chikungunya fever. METHODS: A search was performed for clinical trials, observational studies, in vitro or in vivo, without restriction of the year of publication or language in electronic databases (Medline/PubMed, EMBASE, Google Scholar, The Cochrane Library, LILACS (BVS), clinical trial registries (Clinical Trials.gov), digital libraries from CAPES theses and dissertations (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) and conference abstracts. A quality assessment of the selected studies was performed using the SYRCLE, RoB2 and SciRAP tools. RESULTS: 42 studies were included, which showed molecules with potential antiviral pharmacological activity or with activity in reducing the joint complications caused by CHIKV infection. CONCLUSIONS: Among the molecules found in the survey of references, regarding the class of secondary metabolites, flavonoids stood out and for this reason, the molecules may be promising candidates for future clinical trials. Overall, evidence from in vitro studies was of acceptable quality; in vivo and intervention studies showed a high risk of bias, which is a limitation of these studies.

In silico development of adenosine A2B receptor antagonists for sickle cell disease.

Sickle cell disease (SCD) is a disease resulting from mutation in the globin portion of hemoglobin caused by the replacement of adenine for thymine in the codon of the ß globin gene. In Brazil, SCD affects about 0.3% of the black and Caucasian population. Until now, there is no specific treatment and the available drugs have several serious adverse effects which makes the search for new drugs an emergently need. The use of computational techniques can accelerate the drug development process by prioritization of molecules with affinity against essential targets. Adenosine A2b receptor (rA2b) has been studied in SCD due to its relationship with red blood cells concentration of 2,3-diphosphoglycerate which reduces the hemoglobin affinity for oxygen (O2), facilitating its availability for the tissues. Then, development of rA2b antagonists could be helpful for the treatment of SCD. However, there is still no 3D structure of rA2b and to overcome this limitation, homology modeling should be applied. In this scenario, this study aims to build a suitable 3D model of rA2b by SWISS MODEL and to evaluate the structural aspects of rA2b with known antagonists that may be useful for the identification of new potential antagonists by molecular dynamics on a lipid bilayer environment using GROMACS 5.1.4. The complexes with antagonists ZINC223070016 and ZINC17974526 interacted with key residues by hydrophobic contacts and hydrogen bonds which stabilized them at the rA2b binding site. This intermolecular profile can contribute to the development of more potent rA2b antagonists. Communicated by Ramaswamy H. Sarma.

Homology modeling, docking, molecular dynamics and in vitro studies to identify Rhipicephalus microplus acetylcholinesterase inhibitors.

Rhipicephalus microplus is an important ectoparasite of cattle, causing considerable economical losses. Resistance to chemical acaricides has stimulated the search for new antiparasitic drugs, including natural products as an eco-friendly alternative of control. Flavonoids represent a class of natural compounds with many biological activities, such as enzyme inhibitors. Acetylcholinesterase is an essential enzyme for tick survival that stands out as an important target for the development of acaricides. This work aimed to predict this 3D structure by homology modeling and use the model to identify compound with inhibitory activity. The model of R. microplus AChE1 (RmAChE1) was constructed using MODELLER program. The optimization and molecular dynamic investigation were performed in GROMACS program. The model developed was used, by molecular docking, to evaluate the anticholinesterase activity of flavonoids (quercetin, rutin, diosmin, naringin and hesperidin) and an acaricide synthetic (eserine). Additionally, in vitro inhibition of AChE and larval immersion tests were performed. The model of RmAChE1 showed to be sterically and energetically acceptable. In molecular dynamics simulations, the 3D structure remains stable with Root Mean Square Deviation = 3.58 Å and Root Mean Square Fluctuation = 1.43 Å. In molecular docking analyses, only eserine and quercetin show affinity energy to the RmAChE (Gridscore: -52.17 and -39.44 kcal/mol, respectively). Among the flavonoids, quercetin exhibited the best in vitro inhibition of AChE activity (15.8%) and mortality of larvae tick (30.2%). The use of in silico and in vitro techniques has shown that quercetin showed promising anti-tick activity and structural requirements to interact with RmAChE1. Communicated by Ramaswamy H. Sarma.

A novel antiplasmodial compound: integration of in silico and in vitro assays.

Malaria is a disease caused by Plasmodium genus. which P. falciparum is responsible for the most severe form of the disease, cerebral malaria. In 2018, 405,000 people died of malaria. Antimalarial drugs have serious adverse effects and limited efficacy due to multidrug-resistant strains. One way to overcome these limitations is the use of computational approaches for prioritizing candidates to phenotypic assays and/or in vitro assays against validated targets. Plasmodium falciparum Enoyl-ACP reductase (PfENR) is noteworthy because it catalyzes the rate-limiting step of the biosynthetic pathway of fatty acid. Thus, the study aimed to identify potential PfENR inhibitors by ligand (2D molecular similarity and pharmacophore models) and structure-based virtual screening (molecular docking). 2D similarity-based virtual screening using Tanimoto Index (> 0.45) selected 29,236 molecules from natural products subset available in ZINC database (n = 181,603). Next, 10 pharmacophore models for PfENR inhibitors were generated and evaluated based on the internal statistical parameters from GALAHAD™ and ROC/AUC curve. These parameters selected a suitable pharmacophore model with one hydrophobic center and two hydrogen bond acceptors. The alignment of the filtered molecules on best pharmacophore model resulted in the selection of 10,977 molecules. These molecules were directed to the docking-based virtual screening by AutoDock Vina 1.1.2 program. These strategies selected one compound to phenotypic assays against parasite. ZINC630259 showed EC50 = 0.12 ± 0.018 µM in antiplasmodial assays and selective index similar to other antimalarial drugs. Finally, MM/PBSA method showed stability of molecule within PfENR binding site (ΔGbinding=-57.337 kJ/mol).Communicated by Ramaswamy H. Sarma.

Functional annotation and comparative modeling of ligninolytic enzymes from Trametes villosa (SW.) Kreisel for biotechnological applications.

Functional annotation of Trametes villosa genome was performed to search Class II peroxidase proteins in this white-rot fungus, which can be valuable for several biotechnological processes. After sequence identification and manual curation, five proteins were selected to build 3 D models by comparative modeling. Analysis of sequential and structural sequences from selected targets revealed the presence of two putative Lignin Peroxidase and three putative Manganese Peroxidase on this fungal genome. All 3 D models had a similar folding pattern from selected 3 D structure templates. After minimization and validation steps, the best 3 D models were subjected to docking studies and molecular dynamics to identify structural requirements and the interactions required for molecular recognition. Two reliable 3 D models of Class II peroxidases, with typical catalytic site and architecture, and its protein sequences are indicated to recombinant production in biotechnological applications, such as bioenergy.Communicated by Ramaswamy H. Sarma.

Identification of potential modulator of Anopheles gambiae odorant binding protein 1 by hierarchical virtual screening and molecular dynamics.

Malaria is a protozoan infection transmitted by the bite of the infected female mosquito belonging to the genus Anopheles spp., which causes more than 445 million annual deaths worldwide. Available drugs have serious adverse effects (e.g. blurred vision, hypotension and headache) and species-dependent efficacy. An alternative to overcome these problems involve the use of molecules with affinity to the Anopheles gambiae mosquito odor receptors, minimizing the reinfection process as well as reducing the problems related to pharmacological therapy. The vector control can interrupt the epidemiological cycle and, therefore, control the malaria incidence. In the olfactory pathway, odorant binding protein 1 acts on the first level of odor recognition on malarial vector and thus can be used to modulate mosquito behavior and development of new attracts or repellents. Thus, this study applied ligand-based (2D-chemical similarity) and structure-based (docking and molecular dynamics) computational approaches to prioritize potential olfactory modulators on natural products catalogs at ZINC15 database (n = 98,379). Hierarchical virtual screening prioritized a potential olfactory modulator (Z8217) against Anopheles gambiae odorant binding protein 1 (AgOBP1). Next, it was submitted to molecular dynamics routine to identify structural requirements and the interactions profile required for binding-site affinity. This promising natural compound can interact like experimental ligand and will be used in repellency assay to confirm its sensorial behavior.Communicated by Ramaswamy H. Sarma.

Identification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays.

Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergence of drug resistance cases used in monotherapy and combination therapies. Thus, the development of new antimalarial drugs becomes emergency. One way of achieve this goal is to explore essential and/or unique therapeutic targets of the parasite, or at least sufficiently different to ensure selective inhibition. Enoil-ACP reductase (ENR) is a NADH-dependent enzyme responsible for the limiting step of the type II fatty acid biosynthetic pathway (FAS II). Thus, pharmacophore and docking based virtual screening were applied to prioritize molecules for in vitro assays against P. falciparum W2 strain. The application of successive filters at OOCC database (n = 618) resulted in the identification of one molecule (13) (EC50 = 0.098 ± 0.021 µM) with similar biological activity to artemether. The molecule 13 is a typical drug repurposing case due to previous other approved therapeutic uses on Chinese medicine as a non-specific cholinergic antagonist, thus it could be accelerated the drug development process. Additionally, molecular dynamics studies were used to confirm stability of the molecular interactions identified by molecular docking. Thus, representative structures of P. falciparum ENR can be used in a study to propose new derivatives for evaluation of biological activity in vitro and in vivo. Communicated by Ramaswamy H. Sarma.

Virtual screening to identify Leishmania braziliensis N-myristoyltransferase inhibitors: pharmacophore models, docking, and molecular dynamics.

Leishmaniasis is caused by several protozoa species belonging to genus Leishmania that are hosted by humans and other mammals. Millions of new cases are recorded every year and the drugs available on the market do not show satisfactory efficacy and safety. A hierarchical virtual screening approach based on the pharmacophore model, molecular docking, and molecular dynamics was conducted to identify possible Leishmania braziliensis N-misristoyltransferase (LbNMT) inhibitors. The adopted pharmacophore model had three main features: four hydrophobic centers, four hydrogen-bond acceptor atoms, and one positive nitrogen center. The molecules (n=15,000) were submitted to alignment with the pharmacophore model and only 27 molecules aligned to model. Six molecules were submitted to molecular docking, using receptor PDB ID 5A27. After docking, the ZINC35426134 was a top-ranked molecule (- 64.61 kcal/mol). The molecule ZINC35426134 shows hydrophobic interactions with Phe82, Tyr209, Val370, and Leu391 and hydrogen bonds with Asn159, Tyr318, and Val370. Molecular dynamics simulations were performed with the protein in its APO and HOLO forms for 37 ns in order to assess the stability of the protein-ligand complex. Results showed that the HOLO form was more stable than the APO one, and it suggests that the ZINC35426134 binding stabilizes the enzyme. Therefore, the selected molecule has the potential to meet the herein proposed target.

Pharmacophore modeling, docking and molecular dynamics to identify Leishmania major farnesyl pyrophosphate synthase inhibitors.

Leishmaniasis is caused by protozoa of the genus Leishmania spp. and is considered the second most important protozoa in the world due to the number of cases and mortality. Despite its importance in terms of public health, the treatment of patients is limited and has mostly low levels of efficacy and safety. Farnesyl pyrophosphate synthase (FPPS) acts in the early stages of isoprenoid synthesis, and is important for maintaining the integrity of the lipid bilayer of the parasite that causes the disease. The aim of this work was to identify one potential inhibitor of the FPPS of Leishmania major through virtual screening by pharmacophore modeling and docking. A total of 85,000 compounds from a natural products database (ZINC15) was submitted for virtual hierarchical screening, and the top ranked molecule in both methods was analyzed by intermolecular interaction profile and 20 ns molecular dynamics simulations. These results showed a promising compound from natural products that mimic the major interactions present in the substrate/inhibitor.

Identification of new promising Plasmodium falciparum superoxide dismutase allosteric inhibitors through hierarchical pharmacophore-based virtual screening and molecular dynamics.

Malaria is the world's most widespread protozoan infection, being responsible for more than 445,000 annual deaths. Among the malaria parasites, Plasmodium falciparum is the most prevalent and lethal. In this context, the search for new antimalarial drugs is urgently needed. P. falciparum superoxide dismutase (PfSOD) is an important enzyme involved in the defense mechanism against oxidative stress. The goal of this study was to identify through hierarchical screening on pharmacophore models and molecular dynamics (MD), promising allosteric PfSOD inhibitors that do not show structural requirements for human inhibition. MD simulations of 1000 ps were performed on PfSOD using GROMACS 5.1.2. For this, the AMBER99SB-ILDN force field was adapted to describe the metal-containing system. The simulations indicated stability in the developed system. Therefore, a covariance matrix was generated, in which it was possible to identify residues with correlated and anticorrelated movements with the active site. These results were associated with the results found in the predictor of allosteric sites, AlloSitePro, which affirmed the ability of these residues to delimit an allosteric site. Then, after successive filtering of the Sigma-Aldrich® compounds database for HsSOD1 and PfSOD pharmacophores, 152 compounds were selected, also obeying Lipinski's rule of 5. Further filtering of those compounds based on molecular docking results, toxicity essays, availability, and price filtering led to the selection of a best compound, which was then submitted to MD simulations of 20,000 ps on the allosteric site. The study concludes that the ZINC00626080 compound could be assayed against SODs. Graphical Abstract Plasmodium falciparum superoxide dismutase.

Promoção do uso racional de medicamentos: uma experiência na estratégia saúde da família / Promotion of rational use of drugs: An experience in the Family Health Strategy

Descrever as experiências sobre o uso racional de medicamentos provenientes dasatividades de um programa de extensão universitária. Síntese dos dados: Desenvolveramseatividades em uma Unidade de Saúde da Família de um município baiano, no períodode agosto de 2010 a agosto de 2013, com a equipe de saúde da família, usuários (adultos,idosos e gestantes), discentes e docentes de uma universidade estadual. Realizaram-seobservação sistemática, visitas domiciliares, oficinas temáticas, salas de espera, eventoscientíficos e colaboração em pesquisa. As atividades foram desenvolvidas de modoarticulado e tiveram quatro objetos: uso racional de medicamentos por idosos, dispensaçãoracional de medicamentos na atenção básica, uso racional de medicamentos psicotrópicos, eprescrição racional de medicamentos. Conclusão: As experiências revelaram que a questãodos medicamentos não está inserida no processo de trabalho da equipe, contudo, as açõesextensionistas podem ter contribuído para a reflexão sobre as práticas, bem como para odesenvolvimento de habilidades e potencialidades dos envolvidos, visando ao aprimoramentoda prescrição, dispensação e uso dos medicamentos na comunidade...