Virtual Screening and Molecular Docking: Discovering Novel c-KIT Inhibitors.

Gastrointestinal stromal tumors (GISTs) are unusual cancers, which are developed in specialized cells in the gastrointestinal tract wall. Various strategies involving single-agents, combinations, and rapid complementary inhibitor cycling are now being used to control such tumors. Based on promising early clinical trial experience, certain novel KIT and PDGFRA tyrosine kinase inhibitors have shown advanced clinical development. Resistance to tyrosine kinase inhibitors has brought immense difficulties, with patients now requiring additional therapeutic options. This review describes and discusses the last five years (2016-2020) in developing novel c-KIT kinase inhibitors using virtual screening and docking approaches. Computational techniques can be used to complement experimental studies to identify new candidate molecules for therapeutic use. Molecular modeling strategies allow the analysis of the required characteristics that compounds must have to effectively bind c-KIT. Through such analyses, it is possible to both discover and design novel inhibitors against cancer-related proteins that play a critical role in tumor development (including mutant strains). Docking showed potential in the detection of the key residues responsible for ligand recognition and is very helpful to understand the interactions in the active site that can be used to develop new compounds/classes of anticancer drugs and help millions of cancer patients.

Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents.

Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better "drugability".

Recent Theoretical Studies Concerning Important Tropical Infections.

Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated with poverty, flourish in impoverished environments, and thrive best in tropical areas, where they tend to present overlap. They comprise several diseases, and the symptoms vary dramatically from disease to disease, often causing from extreme pain, and untold misery that anchors populations to poverty, permanent disability, and death. They affect more than 1 billion people worldwide; mostly in poor populations living in tropical and subtropical climates. In this review, several complementary in silico approaches are presented; including identification of new therapeutic targets, novel mechanisms of activity, high-throughput screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship and recent molecular docking studies. Current and active research against Sleeping Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully lead to safer, more effective, less costly and more widely available treatments against these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.

Multi-Target Drugs Against Metabolic Disorders.

BACKGROUND: Metabolic disorders are a major cause of illness and death worldwide. Metabolism is the process by which the body makes energy from proteins, carbohydrates, and fats; chemically breaking these down in the digestive system towards sugars and acids which constitute the human body's fuel for immediate use, or to store in body tissues, such as the liver, muscles, and body fat. OBJECTIVE: The efficiency of treatments for multifactor diseases has not been proved. It is accepted that to manage multifactor diseases, simultaneous modulation of multiple targets is required leading to the development of new strategies for discovery and development of drugs against metabolic disorders. METHODS: In silico studies are increasingly being applied by researchers due to reductions in time and costs for new prototype synthesis; obtaining substances that present better therapeutic profiles. DISCUSSION: In the present work, in addition to discussing multi-target drug discovery and the contributions of in silico studies to rational bioactive planning against metabolic disorders such as diabetes and obesity, we review various in silico study contributions to the fight against human metabolic pathologies. CONCLUSION: In this review, we have presented various studies involved in the treatment of metabolic disorders; attempting to obtain hybrid molecules with pharmacological activity against various targets and expanding biological activity by using different mechanisms of action to treat a single pathology.

Environmental photochemical fate and UVC degradation of sodium levothyroxine in aqueous medium.

The synthetic hormone sodium levothyroxine (LTX) is one of the most prescribed drugs in the world and the most effective in hypothyroidism treatment. The presence of LTX in the environment has become a matter of major concern due to the widespread use of this hormone and by the fact that it is only partially removed in conventional water and sewage treatment plants. However, information regarding the photochemical fate of this hormone in environmental or engineered systems is scarce in the literature. In this work, the sunlight-driven direct and indirect LTX degradation was investigated by determining the photolysis quantum yield, ΦLTX = 3.80 (± 0.02) × 10-5, as well as the second-order kinetic constants of the reactions with hydroxyl radicals, kLTX,•OH = 1.50 (± 0.01) × 1010 L mol-1 s-1 and singlet oxygen, kLTX,1O2 = 1.47 (± 0.66) × 108 L mol-1 s-1. Mathematical simulations indicate that LTX photodegradation is favored in shallow, nitrite-rich, and dissolved organic matter (DOM)-poor environments, with LTX half-life times varying from less than 10 days to about 80 days. LTX removals of 85 and 95% were achieved by UVC photolysis and UVC/H2O2 after 120 min, respectively. Three transformation products, triiodothyronine, diiodothyronine, and diiodotyrosine, were identified during LTX degradation by the UVC-based processes studied. The results herein regarding photo-induced kinetics coupled with environmental fate simulations may help evaluate LTX persistence and also the design of water and wastewater treatment processes.

Dengue Virus Inhibition Targets: A Review and Docking Study.

Dengue like any neglected tropical disease affects a large part of the world population. In this disease, the infection is caused by arboviruses transmitted by the A. aegypti and A. albopictus mosquito, in which its most severe manifestation is known as dengue hemorrhagic fever. The infected person presents symptoms characteristic of such as fever and rash. Among the ways of fighting dengue by bioactives is the inhibition of NS2B-NS3 protease, inhibition of protein E, and inhibition of sclerotization of the vector cuticle. The cuticle is indispensable for the survival of the mosquito that can be compromised through the inhibition of arylalkylamine N-acetyltransferase (aaNAT). In the studies shown, in silico tests were performed as molecular docking, functional density analysis, molecular orbitals energies with the analyses of the interactions between bioactives and the targets studied. However, in addition to discussing the fight against dengue virus infection through different routes, in this paper, some in silico results of 27 analogs of myricetin have been presented, which showed action on the cuticle sclerotization mechanism.

Computational Approaches in Multitarget Drug Discovery.

Current therapeutic strategies entail identifying and characterizing a single protein receptor whose inhibition is likely to result in the successful treatment of a disease of interest, and testing experimentally large libraries of small molecule compounds "in vitro" and "in vivo" to identify promising inhibitors in model systems and determine if the findings are extensible to humans. This highly complex process is largely based on tests, errors, risk, time, and intensive costs. The virtual computational study of compounds simulates situations predicting possible drug linkages with multiple protein target atomic structures, taking into account the dynamic protein inhibitor, and can help identify inhibitors efficiently, particularly for complex drug-resistant diseases. Some discussions will relate to the potential benefits of this approach, using HIV-1 and Plasmodium falciparum infections as examples. Some authors have proposed a virtual drug discovery that not only identifies efficient inhibitors but also helps to minimize side effects and toxicity, thus increasing the likelihood of successful therapies. This chapter discusses concepts and research of bioactive multitargets related to toxicology.

Multi-Target Antitubercular Drugs.

Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis, which has high levels of mortality worldwide and has already gained resistance to first- and second-line drugs. The study by new chemical entities with promising activities becomes paramount to broaden the therapeutic strategies in the cure of the patients affected with this disease. In this context, in this review we report the discovery of 3 classes of compounds that can simultaneously interact with more than one target of Mycobacterium tuberculosis.

Docking of Natural Products against Neurodegenerative Diseases: General Concepts.

BACKGROUND: Since antiquity, humanity has used medicinal plant preparations to cure its ills, and, as research has progressed, new technologies have enabled more investigations on natural compounds which originate from plants, fungi, and marine species. The health benefits that these natural products provide have become a motive for treatment studies of various diseases. OBJECTIVE: Among them, the neurodegenerative diseases like Alzheimer's and Parkinson's, a major age-related neurodegenerative disorder. Studies with natural products for neurodegenerative diseases (particularly through molecular docking) search for, and then focus on those ligands which offer effective inhibition of the enzymes monoamine oxidase and acetylcholinesterase. METHOD: This review introduces the main concepts involved in docking studies with natural products: and also in our group, which has conducted a docking study of natural products isolated from Tetrapterys mucronata for inhibition of acetylcholinesterase. RESULTS: We observed that compounds 4 and 5 formed more interactions than the theoretical ligand, but that ligands with greater activity also interacted with residues HIS 381 and GLN 527. CONCLUSION: We have reported on our docking study performed with AChE and alkaloids isolated from the plant Tetrapterys mucronata. Our docking results corroborate the experiments conducted, and emphasize the positive contribution that these theoretical studies involving natural products bring to the fight against neurodegenerative diseases.

Computer-aided Drug Design Applied to Parkinson Targets.

BACKGROUND: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by debilitating motor deficits, as well as autonomic problems, cognitive declines, changes in affect and sleep disturbances. Although the scientific community has performed great efforts in the study of PD, and from the most diverse points of view, the disease remains incurable. The exact mechanism underlying its progression is unclear, but oxidative stress, mitochondrial dysfunction and inflammation are thought to play major roles in the etiology. OBJECTIVE: Current pharmacological therapies for the treatment of Parkinson's disease are mostly inadequate, and new therapeutic agents are much needed. METHODS: In this review, recent advances in computer-aided drug design for the rational design of new compounds against Parkinson disease; using methods such as Quantitative Structure-Activity Relationships (QSAR), molecular docking, molecular dynamics and pharmacophore modeling are discussed. RESULTS: In this review, four targets were selected: the enzyme monoamine oxidase, dopamine agonists, acetylcholine receptors, and adenosine receptors. CONCLUSION: Computer aided-drug design enables the creation of theoretical models that can be used in a large database to virtually screen for and identify novel candidate molecules.

In silico and In vivo Toxicological Evaluation of Cissampelos Sympodialis Secondary Metabolites in Rattus Norvegicus.

Cissampelos sympodialis is a plant in northeastern Brazil used by the populace for treating respiratory diseases. Several studies have shown that ethanol leaf extracts have immunomodulatory and anti-inflammatory activities. Infusions are widely used, popular, and an ancient technique in traditional medicine, using hot water alone as the means of extraction. This study aimed to investigate acute toxicological potential of leaf infusions of Cissampelos sympodialis, when applied orally at a dose of 2000mg/kg to Rattus norvegicus, combined with an in silico study of 117 alkaloids present in the Cissampelos genus; five (5) of which were determined to have high toxicity (21, 8, 93, 32 and 88), and five (5) having both low toxicity (57, 77, 28, 25 and 67) and low liver metabolism. The in vivo toxicological evaluation showed that male water consumption decreased, and the feed intake decreased in both sexes. Yet, the figures as to change in weight gain of the animals were not statistically sufficient. As for the biochemical parameters, there was an increase in urea, and decreases in uric acid and AST in males. In females, there was a decrease in albumin and globulin which consequently leads to a total protein decrease. Despite biochemical changes suggestive of kidney damage, the histological sections revealed no kidney or liver changes. The results therefore indicate that despite presenting alkaloids which may be toxic, the genus Cissampelos, or leaf infusions of Cissampelos sympodialis, when applied orally at a dose of 2000mg/kg present low toxicity.

Docking Studies for Multi-Target Drugs.

The most basic principle of drug action is found in the lock and key model, where the highest possible affinity for a target that also avoids side effects is desired. For many years this was understood as being "one drug, for one target, for one disease", however researchers began to observe that certain diseases are best treated with multi-target drugs. In recent years, studies have sought out polypharmacological compounds acting on multiple targets against complex (multifactorial) diseases, such as cancer, neurodegenerative disease, and certain infections. One of the computational tools used in research for multifunctional drugs is Molecular Docking. Through this methodology of Computer-Aided Drug Design, we observe complexes formed between ligands and interesting targets (often many), for a particular disease. This review reports on docking studies as used in investigations of new multi-target compounds; it also shows the various ways that such studies are used in the search for multifunctional compounds.

Hybrid Compounds as Direct Multitarget Ligands: A Review.

Molecular Hybridization is an approach in rational drug design where new chemical entities are obtained by combining two or more pharmacophoric units from different bioactive compounds into a single molecule. Through this approach, medicinal chemists hope that the new hybrid derivative presents: better affinity and efficacy when compared to the parent drugs; a modified selectivity profile with improvement over pharmacokinetic and pharmacodynamic restrictions; dual or multiple modes of action; reduction of undesirable side effects; decreases in drug-drug interactions; reduced emergence or spread of drug resistance in microorganisms and protozoans; and lower cost. The approach has been successfully used by many research groups around the world and has had very promising results with diseases having multifactorial profiles, like Alzheimer´s, Parkinson´s disease, cancer, inflammation, and hypertension among others. The purpose of this paper is to conduct an updated review of molecular hybridization and multitarget profiling (a rational drug design approach), and its applications to the design and discovery of novel hybrid compounds with anti-inflammatory, antimicrobial, anticancer and antiprotozoal (leishmaniasis, malaria, and schistosomiasis) activities over the last six years.

Metabolomics as a Functional Tool in Screening Gastro Intestinal Diseases: Where are we in High Throughput Screening?

Identifying novel bio markers in gastro intestinal disease is a promising method where a comprehensive analysis of the metabolome is performed. Metabolomics has evolved enormously in the past decade, paving a path in gastro intestinal disease research, especially diseases which lead to high morbidity and mortality. Metabolomics involves identifying metabolites such as anti-oxidants, and amino acids etc., which are screened in the urine, feces and tissue samples. Certain cases employ advanced tools like GC-MS, 1HNMR and GC-MS/SPME which reveal valuable information concerning disease severity and differentiation. In light of escalating health care costs and risky invasive procedures, metabolomics can be chosen as a safe yet precise method for screening diseases like ulcerative colitis, Crohns' disease, celiac disease, and gastro intestinal cancers. The present review focuses on major advancements in gastro intestinal metabolomics, giving attention to which parameters are assessed, and to recent changes in metabolite analysis.

Natural Products as a Source for Antileishmanial and Antitrypanosomal Agents.

Natural products are compounds extracted from plants, marine organisms, fungi or bacteria. Many researches for new drugs are based on these natural molecules, mainly by beneficial effects on health, health, efficacy, and therapeutic safety. Leishmaniosis, Chagas disease and African sleeping sickness are neglected diseases caused by the Leishmania and Trypanosoma ssp. parasites. These infections mainly affect population of developing countries; they have different symptoms, and may often lead to death. The therapeutic drugs available to treat these diseases are either obsolete, toxic, or have questionable efficacy, possibly through encountering resistance. Discovery of new, safe, effective, and affordable molecules is urgently needed. Natural organisms, as marine metabolites, alkaloids, flavonoids, steroids, terpene and coumarins provide innumerable molecules with the potential to treat these diseases. This study examines studies of natural bioactive compounds as antileishmanial and antitrypanosomal agents.

Recent Advancement in Natural Hyaluronidase Inhibitors.

The use of natural products for the treatment of disease is one of the oldest cultures exists. Currently, the research of new drugs using natural products shows a poorly explored biodiversity and a great interest of marketing. The enzymatic inhibition by some natural products is investigated among these is the inhibition of hyaluronidase and the consequent reduction of the degradation of hyaluronic acid. So there is a reduction of inflammation and angiogenesis. This study reports the main natural species studied in inhibiting human hyaluronidase that can be the subject of future research for new drugs.

Multi-Target Drugs for Neglected Diseases.

BACKGROUND: Diseases perceived as neglected tropical infections are generally caused by parasites which reach poor, underserved populations (primarily infrastructure), cause serious damage to health, and many deaths. AIDS and tuberculosis, (although not classified as neglected by WHO), are discriminated against infections which cause great social damage. The drugs currently used to treat these diseases do not have the desired effectiveness, enable the emergence of resistant strains, and in most cases are difficult to obtain. Few pharmaceutical companies are investing in new drug research for neglected diseases, for lack of financial return. This review reports the major neglected diseases, AIDS, tuberculosis, their targets, and research on multi-target drugs. METHODS: The studies for new drugs against these infections involve in silico methods, synthesis, structural determinations, analytical analysis and other experimental assays. RESULTS: A new single compound, forecasting possible pharmacodynamic and pharmacokinetic interactions becomes a simpler process; it is also believed that these drugs are safer and more efficient, since they act with synergism on different targets. It occurs but the emergence of new resistant strains and side effects. CONCLUSION: Multi-target drugs represent a new alternative to find new lead compounds. A ligand that targets two or more receivers may be seen as a potential drug, combating infection by different routes.

Artificial Neural Network Methods Applied to Drug Discovery for Neglected Diseases.

Among the chemometric tools used in rational drug design, we find artificial neural network methods (ANNs), a statistical learning algorithm similar to the human brain, to be quite powerful. Some ANN applications use biological and molecular data of the training series that are inserted to ensure the machine learning, and to generate robust and predictive models. In drug discovery, researchers use this methodology, looking to find new chemotherapeutic agents for various diseases. The neglected diseases are a group of tropical parasitic diseases that primarily affect poor countries in Africa, Asia, and South America. Current drugs against these diseases cause side effects, are ineffective during the chronic stages of the disease, and are often not available to the needy population, have relative high toxicity, and face developing resistance. Faced with so many problems, new chemotherapeutic agents to treat these infections are much needed. The present review reports on neural network research, which studies new ligands against Chagas' disease, sleeping sickness, malaria, tuberculosis, and leishmaniasis; a few of the neglected diseases.

Theoretical research into anticancer activity of diterpenes isolated from the paraiban flora.

Many studies of the scientific literature discuss the anticancer activity of diterpenes inhibiting the Akt/IKK/NF-kappaB pro-survival signaling cascade, mainly by the activation of serine/threonine phosphatase PP2A. The aim of this work was to evaluate and compare the anticancer potential of three atisane, three kaurane and three trachylobane diterpenes extracted from the roots of Xylopia langsdorffiana. Thus, we investigated the reactivity (H-L(GAP) parameter), HOMO atmosphere favorable to neutralize the radical reactivity, and the docking of compounds with PP2A. With all approaches, this theoretical study showed that atisane diterpenes have favorable characteristics for antitumor activity, like electron donating ability and greater hydrophilic interactions with the enzyme, by inhibition of Akt/IKK/NF-kappaB, and activation of PP2A.

Prediction of anticancer activity of diterpenes isolated from the paraiban flora through a PLS model and molecular surfaces.

The aim of this work was to predict the anticancer potential of 3 atisane, and 3 trachylobane diterpene compounds extracted from the roots of Xylopia langsdorffiana. The prediction of anticancer activity as expressed against PC-3 tumor cells was made using a PLS model built with 26 diterpenes in the training set. Significant statistical measures were obtained. The six investigated diterpenes were applied to the model and their activities against PC-3 cells were calculated. All the diterpenes were active, with atisane diterpenes showing the higher pICso values. In human prostate carcinoma PC-3 cells, the apoptosis mechanism is related to an inhibition of IKK/NF-KB. Antioxidant potential implies a greater electronic molecular atmosphere (increased donor electron capacity), which can reduce radical reactivity, and facilitate post donation charge accommodation. Molecular surfaces indicated a much greater electronic cloud over atisane diterpenes.