In Silico Strategies for Prospective Drug Repositionings

The discovery of new drugs is one of pharmaceutical research's most exciting and challenging tasks. Unfortunately, the conventional drug discovery procedure is chronophagous and seldom successful; furthermore, new drugs are needed to address our clinical challenges (e.g., new antibiotics, new anticancer drugs, new antivirals).Within this framework, drug repositioning—finding new pharmacodynamic properties for already approved drugs—becomes a worthy drug discovery strategy.Recent drug discovery techniques combine traditional tools with in silico strategies to identify previously unaccounted properties for drugs already in use. Indeed, big data exploration techniques capitalize on the ever-growing knowledge of drugs' structural and physicochemical properties, drug–target and drug–drug interactions, advances in human biochemistry, and the latest molecular and cellular biology discoveries.Following this new and exciting trend, this book is a collection of papers introducing innovative computational methods to identify potential candidates for drug repositioning. Thus, the papers in the Special Issue In Silico Strategies for Prospective Drug Repositionings introduce a wide array of in silico strategies such as complex network analysis, big data, machine learning, molecular docking, molecular dynamics simulation, and QSAR; these strategies target diverse diseases and medical conditions: COVID-19 and post-COVID-19 pulmonary fibrosis, non-small lung cancer, multiple sclerosis, toxoplasmosis, psychiatric disorders, or skin conditions

Drug Repurposing

This book focuses on various aspects and applications of drug repurposing, the understanding of which is important for treating diseases. Due to the high costs and time associated with the new drug discovery process, the inclination toward drug repurposing is increasing for common as well as rare diseases. A major focus of this book is understanding the role of drug repurposing to develop drugs for infectious diseases, including antivirals, antibacterial and anticancer drugs, as well as immunotherapeutics

Amelioration of Neuroprotective Effect of Semisynthetic Derivatives of Piperine in Rotenone induced Rat Model of Parkinson’s Disease

BACKGROUND: Parkinson's disease (PD) is the second most common neurodegenerative disorder and defined as a complex disorder with multifactorial pathogenesis. The systemic rotenone model accurately replicates many aspects of the pathology of human PD and has provided insights into the pathogenesis of PD. Piperine is an alkaloid isolated from black pepper and possess antioxidant, antidepressant, anti-inflammatory and neuroprotective effects. AIM OF THE STUDY: The present study has been designed to evaluate the amelioration of neuroprotective effect of semisynthetic derivatives of piperine in rotenone- induced rat model of Parkinson’s disease. METHODS: In the present study, about 113 semisynthetic piperine derivatives (SDP) were subjected to ADMET properties, molecular docking studies using AutoDock 4.2 against target enzymes COMT (3A7D) and MAO-B (3PO7). Black pepper was used for the isolation of piperine. Based on in silico study, 6 compounds were selected and synthesized by three schemes with various substitutions. Analytical studies (UV, IR, NMR and Mass spectra) were done to confirm its structure and in vitro MAO-B inhibitory activity was performed. The compound (SDP 20) offered better IC50 value and hence it was selected for in vivo study. Acute toxicity was performed following OECD TG 423. About 24 Male Wistar rats were divided into 4 groups (n=6). Animals in all the groups received rotenone in the dose of 2.5 mg/kg i.p daily for 28 days. Group I served as negative control. The animals in group II and III received SDP 20 (100 and 200 mg/kg respectively) p.o. The animals in group IV received levodopa (9mg/kg) and carbidopa(2.25mg/kg) p.o. Behavioral parameters (Rota rod, grip strength, locomotion and narrow beam walk test) were performed on weekly intervals throughout the study. Animals were sacrificed on 29th day for neurotransmitter and biochemical estimation and histopathological changes. RESULTS: The compounds were selected based on BBB barrier penetration and docking scores. A total of 6 compounds were synthesized and analytical studies were carried out. The in vitro MAO-B inhibitory activity was performed for the compounds and SDP 20 was selected for in vivo study. In in vivo study it was demonstrated that significant alteration in behavioral parameters, neurochemical changes, oxidative and histopathological changes were observed in rotenone- treated animals. Administration of SDP 20 prevented alterations induced by rotenone. CONCLUSION: These findings supports the PD treatment by lowering the impairments in motor activity. The results also suggest that SDP 20 may offer a promising and new therapeutic lead for the treatment of PD which needs further research

IN SILICO METHODS FOR DRUG DESIGN AND DISCOVERY

Computer-aided drug design (CADD) methodologies are playing an ever-increasing role in drug discovery that are critical in the cost-effective identification of promising drug candidates. These computational methods are relevant in limiting the use of animal models in pharmacological research, for aiding the rational design of novel and safe drug candidates, and for repositioning marketed drugs, supporting medicinal chemists and pharmacologists during the drug discovery trajectory.Within this field of research, we launched a Research Topic in Frontiers in Chemistry in March 2019 entitled “In silico Methods for Drug Design and Discovery,” which involved two sections of the journal: Medicinal and Pharmaceutical Chemistry and Theoretical and Computational Chemistry. For the reasons mentioned, this Research Topic attracted the attention of scientists and received a large number of submitted manuscripts. Among them 27 Original Research articles, five Review articles, and two Perspective articles have been published within the Research Topic. The Original Research articles cover most of the topics in CADD, reporting advanced in silico methods in drug discovery, while the Review articles offer a point of view of some computer-driven techniques applied to drug research. Finally, the Perspective articles provide a vision of specific computational approaches with an outlook in the modern era of CADD

Association of Dietary Intake of Polyphenols with an Adequate Nutritional Profile in Postpartum Women from Argentina

HJ-Biplot analysis is a multivariate graphic representation that collects data covariation structure between variables and individuals to represent them in a low-dimensional space with the highest quality in the same reference system. Consequently, it is a promising technique for evaluating dietary exposure to polyphenols and accurately characterizing female nutrition. Herein, we hypothesized that polyphenol intake defines specific clusters with dietary impacts, which can be assessed using HJ-Biplot, based on a cross-sectional study in Argentina. The study included 275 healthy postpartum women who provided information about their food frequency intake and other conditions, which were then used to evaluate polyphenolic intake using the Phenol-Explorer database. Outcomes were established using HJ-Biplot for clustering and ANOVA to compare their impact on diet quality indicators. Two HJ-Biplot models were run (for intakes >20 mg/d and 5∼20 mg/d, respectively) to identify three clusters per model with excellent statistical fitness to explain the data. Thus, specific polyphenolic clusters with potentially bioactive and safe compounds were defined despite significant interindividual variability. In fact, women with the lowest polyphenolic intake exhibited worse dietary quality, body fat, and physical activity. As a result, HJ-Biplot proved to be an effective technique for clustering women based on their dietary intake of these compounds. Furthermore, cluster membership improved the intake of antioxidants, water, fiber, and healthy fats. Additionally, women with formal jobs and a higher educational level showed a better diet. Dietary polyphenols are critical during postpartum because they exert beneficial effects on women and breastfed infants.Fil: Miranda, Agustín Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Ciencias de la Salud. Universidad Nacional de Córdoba. Instituto de Investigaciones en Ciencias de la Salud; ArgentinaFil: Scotta, Ana Veronica. Universidad Nacional de Córdoba; ArgentinaFil: Cortez, Mariela Valentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Ciencias de la Salud. Universidad Nacional de Córdoba. Instituto de Investigaciones en Ciencias de la Salud; ArgentinaFil: González García, Nerea. Universidad de Salamanca; EspañaFil: Galindo Villardón, María Purificación. Universidad de Salamanca; EspañaFil: Soria, Elio Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Ciencias de la Salud. Universidad Nacional de Córdoba. Instituto de Investigaciones en Ciencias de la Salud; Argentin

Repositioning of astemizole for malaria

Malaria remains one of the most important parasitic infectious diseases as far as human suffering is concerned. With almost half of the world's population at risk, its burden is felt worldwide as seen by the high number of deaths recorded each year (405,000 in 2018: WHO World Malaria Report 2019). Unfortunately, over 90% of this mortality rate is recorded in Africa alone, with the highest risk being in children under the age of five (5) and pregnant women. Partly, this is due to the unfortunate spread of resistance to most drugs that were once effective and safe, including Artemisinins which form the basis of the current first-line regimen in the treatment of malaria. For this reason, it is crucial to invest research efforts using various approaches in the drug discovery arsenal to develop novel, and structurally diverse antimalarials with different modes of action. These new antimalarials should not only be able to circumvent resistance but need to be efficacious at different life cycle stages of the parasite (multi-stage activity). This Ph.D. project pursued a drug repositioning approach on Astemizole (AST, Figure 1), a second-generation antihistamine drug which was previously identified as an antimalarial agent by Chong et al., at the Johns Hopkins University School of Medicine through via a high-throughput screening (HTS) of diverse marketed drugs. AST was active against chloroquine-sensitive (CQ-S) and multi-drug resistant (MDR) laboratory strains of the human malaria parasite Plasmodium falciparum (P. falciparum) and demonstrated in vivo efficacy in two mouse infection models of malaria namely, P. Vinckei and P. Yoelii. However, in addition to its low solubility, AST possesses a serious and fatal cardiotoxicity risk, evidenced by its ability to potently inhibit the human ether-á-go-go-related gene (hERG) encoded potassium (K+) channels. This liability led to the withdrawal of AST in most countries during the late 1970's and it is still being discontinued for use in some countries to date

International Conference on Advances in Biosciences and Biotechnology – ICABB-2019

International Conference on Advances in Biosciences and Biotechnology – ICABB-201

Small molecule-protein interactions exemplified on short-chain dehydrogenases/reductases

The short-chain dehydrogenase/reductase (SDRs) family represents one of the largest enzyme superfamilies, with over 80 members in the human genome. Even though the human genome project has sequenced and mapped the entire human genome, the physiological functions of more than 70% of all SDRs are currently unexplored or insufficiently characterized. To start to fill this gap, the present thesis aimed to employ a combination of molecular modeling approaches and biological assessments for the identification and characterization of novel inhibitors and/or potential substrates of different SDRs. Due to their involvement in steroid biosynthesis and metabolism, SDRs are potential targets of endocrine disrupting chemicals (EDCs). To test the use of pharmacophore-based virtual screening (VS) applications and subsequent in vitro evaluation of virtual hits for the identification and characterization of potential inhibitors, 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2) was selected as an example. 11β-HSD2 has an important role in the placenta by inactivating cortisol and protecting the fetus from high maternal glucocorticoid levels. An impaired placental 11β-HSD2 function has been associated with altered fetal growth and angiogenesis as well as a higher risk for cardio-metabolic diseases in later life. Despite this vital function, 11β-HSD2 is not covered in common off-target screening approaches. Several azole fungicides were identified as 11β-HSD inhibitors amongst approved drugs by testing selected virtually retrieved hits for inhibition of cortisol to cortisone conversion in cell lysates expressing recombinant human 11β-HSD2. Moreover, a significant structure-activity relationship between azole scaffold size, 11β-HSD enzyme selectivity and potency was observed. The most potent 11β-HSD2 inhibition was obtained for itraconazole (IC50 139 ± 14 nM), for its active metabolite hydroxyitraconazole (IC50 223 ± 31 nM), and for posaconazole (IC50 460 ± 98 nM). Interestingly, substantially lower inhibitory 11β-HSD2 activity of these compounds was detected using mouse and rat kidney homogenate preparations, indicating species-specific differences. Impaired placental 11β-HSD2 function exerted by these compounds might, in addition to the known inhibition of P-glycoprotein efflux transport and cytochrome P450 enzymes, lead to locally elevated cortisol levels and thereby could affect fetal programming. Successful employment of pharmacophore-based VS applications requires suitable and reliable in vitro validation strategies. Therefore, the following study addressed the re-evaluation of a potential EDC, the widely used flame retardant tetrabromobisphenol A (TBBPA), on glucocorticoid receptor (GR) and androgen receptor (AR) function. TBBPA was reported earlier in yeast-based reporter assays to potently interfere with GR and moderately with AR function. Human HEK-293 cell-based reporter assays and cell-free receptor binding assays did not show any activity of TBBPA on GR function, which was supported by molecular docking calculations. The antiandrogenic effect, however, could be confirmed, although less pronounced than in the HEK-293 cell system. Nevertheless, the evaluation of the relevant concentrations of an EDC found in the human body is crucial for an appropriate safety assessment. Considering the rapid metabolism of TBBPA and the low concentrations observed in the human body, it is questionable whether relevant concentrations can be reached to cause harmful effects. Thus, it is vital to take the limitations of each testing system including the distinct sensitivities and specificities into account to avoid false positive or false negative results. To extend the applications of in silico tools with demonstrated proof-of-concept, they were further employed to investigate novel substrate specificities for three different SDR members: the two multi-functional enzymes, 11β-HSD1 and carbonyl reductase (CBR) 1 as well as the orphan enzyme DHRS7. A role for 11β-HSD1 in oxysterol metabolism by metabolizing 7-ketocholesterol (7kC) has already been described. However, in contrast to the known receptors for 7α,25-dihydroxycholesterol (7α25OHC), i.e. Epstein-Barr virus-induced gene 2 (EBI2), or 7β,27-dihydroxycholesterol (7β27OHC), i.e. retinoic acid related orphan receptor (ROR)γ, no endogenous receptor has been identified so far for 7kC or its metabolite 7β-hydroxycholesterol. To explore the underlying biosynthetic pathways of such dihydroxylated oxysterols, the role of 11β-HSD1 in the generation of dihydroxylated oxysterols was investigated. For the first time, the stereospecific and seemingly irreversible oxoreduction of 7-keto,25-hydroxycholesterol (7k25OHC) and 7-keto,27-hydroxycholesterol (7k27OHC) to their corresponding 7β-hydroxylated metabolites 7β25OHC and 7β27OHC by recombinant human 11β-HSD1 could be demonstrated in vitro in intact HEK-293 cells. Furthermore, 7k25OHC and 7k27OHC were found to be potently inhibited the 11β-HSD1-dependent oxoreduction of cortisone to cortisol. Molecular modeling experiments confirmed these results and suggested competition of 7k25OHC and 7k27OHC with cortisone in the enzyme binding pocket. For a more detailed enzyme characterization, 11β-HSD1 pharmacophore models were generated and employed for VS of the human metabolome database and the lipidmaps structure database. The VS yielded several hundred virtual hits, including the successful filtering of known substrates such as endogenous 11-ketoglucocorticoids, synthetic glucocorticoids, 7kC, and several bile acids known to inhibit the enzyme. Further hits comprised several eicosanoids including prostaglandins, leukotrienes, cyclopentenone isoprostanes, levuglandins or hydroxyeicosatetraenoic acids (HETEs) and compounds of the kynurenine pathway. The important role of these compounds as well as 11β-HSD1 in inflammation emphasizes a potential association. However, further biological validation is of utmost necessity to explore a potential link. The closest relative of 11β-HSD1 is the orphan enzyme DHRS7, which has been suggested to act as tumor suppressor. Among others, cortisone and 5α-dihydrotestosterone have been identified as substrates of DHRS7, although effects in functional assays could only be observed at high concentrations that may not be of physiological relevance. Hence, the existence of other yet unexplored substrates of DHRS7 can be assumed, and the generation of homology models to study the structural features of the substrate binding site of DHRS7 was employed. The predictivity of the constructed models is currently limited, due to a highly variable region comprising a part of the ligand binding site but particularly the entry of the binding pocket, and requires further optimizations. Nevertheless, the models generally displayed a cone-shaped binding site with a rather hydrophobic core. This may suggest larger metabolites to be converted by DHRS7. Moreover, the flexible loops surrounding the binding pocket may lead to the induction of an induced fit upon ligand binding. However, further studies are crucial to confirm these findings. CBR1 is well-known for its role in phase I metabolism of a variety of carbonyl containing xenobiotic compounds. Several endogenous substrates of CBR1 have been reported such as prostaglandins, S-nitrosoglutathione or lipid aldehydes. The physiological relevance of these endogenous substrates, however, is not fully understood. Thus, the physiological roles of CBR1 was further explored by identifying a novel function for CBR1 in the metabolism glucocorticoids. CBR1 was found to catalyze the conversion of cortisol into 20β-dihydrocortisol (20β-DHF), which was in turn detected as the major route of cortisol metabolism in horses and elevated in adipose tissue derived from obese horses, humans and mice. Additionally, 20β-DHF was demonstrated as weak endogenous agonist of the GR, suggesting a novel pathway to modulate GR activation by CBR1-depenent protection against excessive GR activation in obesity. In conclusion, this thesis emphasized the employment of molecular modeling approaches as an initial filter to identify toxicological relevant compound classes for the identification of potential EDCs and, moreover, as valuable tools to identify novel substrates of multifunctional SDRs and to unravel novel functions for the large majority of yet unexplored orphan SDR members, while carefully considering the limitations of this strategy

New Insights into Molecular Mechanisms Underlying Neurodegenerative Disorders

Neurodegenerative disorders encompass a broad range of sporadic and/or familial debilitating conditions characterized by the progressive dysfunction and loss of selective neuronal populations, determining different clinical phenotypes. Emerging research data indicate an interplay of genetic factors and epigenetic mechanisms underlying neurodegenerative processes, which lead to increased prevalence of neurodegenerative disorders. In concert with the constant increase in the aging population, neurodegenerative disorders currently represent a major challenge to public health worldwide. Despite recent advances in clinical and preclinical research, the pathogenesis of these disorders still remains poorly understood, without effective treatments being available to halt the neurodegenerative processes, but rather aiming at relieving symptoms. Therefore, a critical evaluation of current research data and in-depth understanding of the molecular mechanisms that lead to neurodegeneration are crucial in order to identify potential therapeutic targets that can pave the way to the development of novel and promising therapies. This Special Issue is focused on novel molecular data in the field of neurodegeneration that associate with the onset and progression of neurodegenerative diseases. We are particularly interested in original articles and reviews that provide new insights into the main molecular pathogenic mechanisms underlying neurodegenerative disorders, aiming to identify potential biomarkers and novel therapeutic strategies