Prediction of Promiscuous P-Glycoprotein Inhibition Using a Novel Machine Learning Scheme

BACKGROUND: P-glycoprotein (P-gp) is an ATP-dependent membrane transporter that plays a pivotal role in eliminating xenobiotics by active extrusion of xenobiotics from the cell. Multidrug resistance (MDR) is highly associated with the over-expression of P-gp by cells, resulting in increased efflux of chemotherapeutical agents and reduction of intracellular drug accumulation. It is of clinical importance to develop a P-gp inhibition predictive model in the process of drug discovery and development. METHODOLOGY/PRINCIPAL FINDINGS: An in silico model was derived to predict the inhibition of P-gp using the newly invented pharmacophore ensemble/support vector machine (PhE/SVM) scheme based on the data compiled from the literature. The predictions by the PhE/SVM model were found to be in good agreement with the observed values for those structurally diverse molecules in the training set (n = 31, r(2) = 0.89, q(2) = 0.86, RMSE = 0.40, s = 0.28), the test set (n = 88, r(2) = 0.87, RMSE = 0.39, s = 0.25) and the outlier set (n = 11, r(2) = 0.96, RMSE = 0.10, s = 0.05). The generated PhE/SVM model also showed high accuracy when subjected to those validation criteria generally adopted to gauge the predictivity of a theoretical model. CONCLUSIONS/SIGNIFICANCE: This accurate, fast and robust PhE/SVM model that can take into account the promiscuous nature of P-gp can be applied to predict the P-gp inhibition of structurally diverse compounds that otherwise cannot be done by any other methods in a high-throughput fashion to facilitate drug discovery and development by designing drug candidates with better metabolism profile

In Silico Prediction of Estrogen Receptor Subtype Binding Affinity and Selectivity Using Statistical Methods and Molecular Docking with 2-Arylnaphthalenes and 2-Arylquinolines

Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ERα and ERβ inhibitory activities was built, and quantitative structure-activity relationship (QSAR) methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR) and a nonlinear statistical method (Bayesian regularized neural network, BRNN) were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ERα and ERβ, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ERα: for MLR, Rtr2 = 0.72, Qte2 = 0.63; for PLSR, Rtr2 = 0.92, Qte2 = 0.84. ERβ: for MLR, Rtr2 = 0.75, Qte2 = 0.75; for PLSR, Rtr2 = 0.98, Qte2 = 0.80). The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in Rtr2 = 0.74 and Qte2 = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ERα and ERβ is more correlated with the atom fragment type, polarity, electronegativites and hydrophobicity. The substitutent in position 8 of the naphthalene or the quinoline plane and the space orientation of these two planes contribute the most to the subtype selectivity on the basis of similar hydrogen bond interactions between binding ligands and both ER subtypes. The QSAR models built together with the docking procedure should be of great advantage for screening and designing ER ligands with improved affinity and subtype selectivity property

Review of QSAR Models and Software Tools for predicting Biokinetic Properties

In the assessment of industrial chemicals, cosmetic ingredients, and active substances in pesticides and biocides, metabolites and degradates are rarely tested for their toxicologcal effects in mammals. In the interests of animal welfare and cost-effectiveness, alternatives to animal testing are needed in the evaluation of these types of chemicals. In this report we review the current status of various types of in silico estimation methods for Absorption, Distribution, Metabolism and Excretion (ADME) properties, which are often important in discriminating between the toxicological profiles of parent compounds and their metabolites/degradation products. The review was performed in a broad sense, with emphasis on QSARs and rule-based approaches and their applicability to estimation of oral bioavailability, human intestinal absorption, blood-brain barrier penetration, plasma protein binding, metabolism and. This revealed a vast and rapidly growing literature and a range of software tools. While it is difficult to give firm conclusions on the applicability of such tools, it is clear that many have been developed with pharmaceutical applications in mind, and as such may not be applicable to other types of chemicals (this would require further research investigation). On the other hand, a range of predictive methodologies have been explored and found promising, so there is merit in pursuing their applicability in the assessment of other types of chemicals and products. Many of the software tools are not transparent in terms of their predictive algorithms or underlying datasets. However, the literature identifies a set of commonly used descriptors that have been found useful in ADME prediction, so further research and model development activities could be based on such studies.JRC.DG.I.6-Systems toxicolog

Structural Requirements of N-Substituted Spiropiperidine Analogues as Agonists of Nociceptin/Orphanin FQ Receptor

The nociceptin/orphanin FQ (NOP) receptor is involved in a wide range of biological functions, including pain, anxiety, depression and drug abuse. Especially, its agonists have great potential to be developed into anxiolytics. In this work, both the ligand- and receptor-based three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were carried out using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques on 103 N-substituted spiropiperidine analogues as NOP agonists. The resultant optimal ligand-based CoMSIA model exhibited Q2 of 0.501, R2ncv of 0.912 and its predictive ability was validated by using an independent test set of 26 compounds which gave R2pred value of 0.818. In addition, docking analysis and molecular dynamics simulation (MD) were also applied to elucidate the probable binding modes of these agonists. Interpretation of the 3D contour maps, in the context of the topology of the active site of NOP, provided insight into the NOP-agonist interactions. The information obtained from this work can be used to accurately predict the binding affinity of related agonists and also facilitate the future rational design of novel agonists with improved activity

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods, and Applications

The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the "multicomponent-multitarget" and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM

In Silico Identification of Structure Requirement for Novel Thiazole and Oxazole Derivatives as Potent Fructose 1,6-Bisphosphatase Inhibitors

Fructose 1,6-bisphosphatase (FBPase) has been identified as a drug discovery target for lowering glucose in type 2 diabetes mellitus. In this study, a large series of 105 FBPase inhibitors were studied using a combinational method by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in potency. The optimal 3D models exhibit high statistical significance of the results, especially for the CoMFA results with rncv2, q2 values of 0.986, 0.514 for internal validation, and rpred2, rm2 statistics of 0.902, 0.828 statistics for external validation. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules. (1) Substituents with a proper length and size at the C5 position of the thiazole core are required to enhance the potency; (2) A small and electron-withdrawing group at the C2 position linked to the thiazole core is likely to help increase the FBPase inhibition; (3) Substituent groups as hydrogen bond acceptors at the C2 position of the furan ring are favored. In addition, the agreement between 3D-QSAR, molecular docking and molecular dynamics simulation proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential FBPase inhibitors

A strategy to overcome the drug resistance in epilepsy

The resistance to antiepileptic drugs (AEDs) remains a major unsolved therapeutic problem, which affects 30-40% of patients with epilepsy. The overexpression of multidrug efflux transporters, as the P-glycoprotein (P-gp), at the level of the blood-brain barrier of epileptic patients has been suggested as a key mechanism underlying the refractory epilepsy. Bearing this in mind, efforts have been made to search for therapeutically useful P-gp inhibitors. In an attempt to find potent and safer P-gp inhibitor drugs, a particular emphasis has been given to flavonoid compounds. Actually, apart from their potential value as P-gp inhibitors, these phytochemical compounds have been recognised as having a panoply of important pharmacological properties like anti-inflammatory, antioxidant, antitumoral, antimicrobial, antiviral, hormonal and even anticonvulsant effects. Taking this into account, the purpose of the present thesis was to conduct a comprehensive in vitro and in vivo evaluation of the potential of flavonoids as P-gp inhibitors, but also to explore a strategy of flavonoid/AED combined therapy as a possible approach to overcome the P-gp–mediated pharmacoresistance in epilepsy. This project involved the development and validation of appropriate and reliable bioanalytical techniques to support the accomplishment of the intended studies. Thus, high-performance liquid chromatography methods coupled with diode array detection (HPLC-DAD) were properly validated for the quantification of the target AEDs and some of their main metabolites in cell culture samples and in rat plasma and brain matrices. An additional HPLC-DAD technique was also developed to quantify several AEDs and metabolites in human plasma, which has shown to be a useful tool for the therapeutic drug monitoring in the clinical practice. According to the results of a set of in vitro assays, five out of eleven flavonoids tested, namely baicalein, (-)-epigallocatechin gallate [(-)-EPG], kaempferol, quercetin and silymarin demonstrated to have an interesting potential in inhibiting the P-gp activity. These promising flavonoids also promoted a significant increase in the intracellular accumulation of the AEDs carbamazepine (CBZ), oxcarbazepine (OXC) and phenytoin (PHT) and their active metabolites carbamazepine-10,11-epoxide (CBZ-E) and licarbazepine (LIC) in the Madin-Darby canine kidney cell line transfected with the human multidrug resistance-1 gene which encodes the human P-gp (MDCK-MRD1), showing up as important drug candidates to overcome the AED-resistance. Actually, excluding LTG, all the AEDs tested (CBZ, OXC and PHT) as well as their active metabolites (CBZ-E and LIC) were found to be P-gp substrates in the MDCK-MDR1 cells. Additionally, CBZ, CBZ-E, LIC, LTG, OXC and PHT promoted a statistically significant decrease of the intracellular concentration of rhodamine 123 (a classic P-gp probe substrate), suggesting an inducer effect on the functional activity of P-gp. An assessment of the potential synergic effects of baicalein, (-)-EPG, kaempferol, quercetin and silymarin on the P-gp inhibition was also performed, firstly in in vitro conditions and then in in vivo experiments. Indeed, when compared to their individual activity, some dual flavonoid combinations exhibited an increased potential in inhibiting the P-gp in the in vitro assays. Moreover, the dual combinations of (-)-EPG/silymarin and kaempferol/baicalein demonstrated a great potential in enhancing the intracellular accumulation of CBZ, OXC and PHT and their metabolites CBZ-E and LIC in the MDCK-MDR1 cells and such effects were comparable to those promoted by verapamil (the standard P-gp inhibitor). The effect of the combination of (-)-EPG/silymarin was also tested in transport assays of LIC (P-gp substrate) through MDCK-MDR1 cells mounted in Ussing chambers; as expected, this combination of flavonoids increased the apparent permeability coefficient of LIC. Overall, these in vitro findings were further supported by in vivo results. In fact, after the pretreatment of male Wistar rats with silymarin an increasing in the plasma concentrations of the studied AEDs (CBZ, OXC and PHT) was observed. Nevertheless, it should be highlighted that the main effects induced by silymarin were found on the OXC pharmacokinetics, for which was found a statistically significant increase in the peak plasma concentration (50%) and in the extent of systemic exposure (41%), having a direct impact on the drug concentrations reached in the brain. On the other hand, the use of dual combinations of (-)-EPG/silymarin on the inhibition of the activity of P-gp was also evaluated in vivo in Wistar rats, being noticeable the synergic potential of (-)-EPG/silymarin combinations in enhancing the degree of systemic exposure to OXC and LIC (a pharmacologically active metabolite of OXC), and it occurred in a comparable extent to that observed for verapamil (positive control). Indeed, the pretreatment of male Wistar rats with dual silymarin/(-)-EPG combinations originated peak plasma concentrations of OXC similar to those achieved in the presence of verapamil. Moreover, the effects promoted by silymarin/(-)-EPG combinations on the magnitude of systemic drug exposure were also reflected in the corresponding drug levels attained in the brain (biophase). Hence, according to our findings, it seems that the flavonoid/AED combined therapy can be thought as a promising approach that should continue to be exploited in order to overcome the P-gp–mediated pharmacoresistance. The availability of this in vitro and in vivo information also adds support to the efflux transporter hypothesis in explaining the pharmacoresistant epilepsy. Considering all its intrinsic potential and indisputable properties, the flavonoid-type compounds may emerge as an alternative to the available P-gp inhibitors for a prospective management of patients with drug-refractory epilepsy.A epilepsia é uma das doenças neurológicas crónicas mais comuns e tem um grande impacto negativo na qualidade de vida dos doentes, sendo de extrema importância os esforços continuados para desenvolver novos fármacos antiepiléticos e novas abordagens terapêuticas. Contudo, apesar dos avanços significativos alcançados nos últimos anos, os fenómenos de farmacorresistência associados aos fármacos antiepiléticos são provavelmente um dos principais problemas no que diz respeito à terapêutica da epilepsia, afetando 30-40% dos doentes. De facto, esta situação tem proporcionado um ímpeto crescente para o desenvolvimento de abordagens terapêuticas inovadoras e mais eficazes. A sobreexpressão de transportadores de efluxo de fármacos, como a glicoproteína-P (P-gp), ao nível da barreira hematoencefálica, tem sido sugerida como um dos principais mecanismos subjacentes à epilepsia refratária. Desta forma, vários esforços têm sido realizados no sentido de descobrir e desenvolver inibidores da P-gp que sejam úteis de um ponto de vista terapêutico. No entanto, as múltiplas desvantagens apresentadas pelas primeiras gerações de inibidores da P-gp demonstraram a necessidade de encontrar agentes mais potentes e mais seguros, tendo sido dado um ênfase especial nos últimos anos a compostos flavonoides. Além do seu interesse potencial como inibidores da P-gp, uma panóplia de outras propriedades farmacológicas importantes têm sido atribuídas a estes compostos fitoquímicos, entre as quais, por exemplo, efeitos anti-inflamatórios, antioxidantes, antitumorais, antimicrobianos, antivirais, hormonais e, mesmo, anticonvulsivantes. Tendo em consideração todos estes aspetos, a presente tese teve como principal objetivo realizar uma avaliação abrangente, in vitro e in vivo, do papel potencial dos flavonoides como inibidores da P-gp, e também explorar uma estratégia de terapia combinada de flavonoides/fármacos antiepiléticos como possível abordagem para superar a farmacorresistência verificada na epilepsia. Este projeto envolveu o desenvolvimento e validação de técnicas bioanalíticas apropriadas e fiáveis para apoiar a execução dos estudos pretendidos. Neste contexto, métodos de cromatografia líquida de alta eficiência acoplados à deteção por fotodíodos (HPLC-DAD) foram devidamente desenvolvidos e validados para a quantificação dos fármacos antiepiléticos alvo de interesse e de alguns dos seus principais metabolitos em amostras de cultura celular e em matrizes de plasma e cérebro de rato. Uma técnica adicional de HPLC-DAD foi também desenvolvida para a quantificação de vários fármacos antiepiléticos e metabolitos em plasma humano, constituindo uma ferramenta útil para apoiar a monitorização terapêutica destes fármacos na prática clínica. De acordo com os resultados obtidos num conjunto de ensaios in vitro, cinco dos onze flavonoides testados, nomeadamente, a baicaleína, a (-)-epigalocatequina galato [(-)-EPG], o kaempferol, a quercetina e a silimarina demonstraram ter um potencial interessante na inibição da atividade da P-gp. Estes flavonoides promoveram também um aumento significativo da acumulação intracelular dos fármacos antiepiléticos carbamazepina (CBZ), oxcarbazepina (OXC) e fenitoína (PHT), e dos seus metabolitos ativos carbamazepina-10,11-epóxido (CBZ-E) e licarbazepina (LIC), na linha celular Madin-Darby canine kidney, transfetada com o gene de resistência a múltiplos fármacos 1 (MDR1) que codifica para a P-gp humana (MDCK-MRD1), evidenciando-se como candidatos promissores para reverter a resistência associada aos fármacos antiepiléticos. Além disso, com exceção da lamotrigina (LTG), todos os fármacos antiepiléticos testados (CBZ, PHT e OXC), assim como os seus respetivos metabolitos ativos (CBZ-E e LIC), demonstraram ser substratos da P-gp neste modelo celular. Adicionalmente, a CBZ, CBZ-E, LIC, LTG, OXC e PHT promoveram uma diminuição significativa nas concentrações intracelulares de rodamina 123 (um substrato “sonda” clássico da P-gp), o que sugere um efeito indutor, mediado pelos próprios fármacos e metabolitos, da atividade funcional da P-gp. Reconhecendo-se as várias propriedades biológicas atribuídas aos flavonoides e tendo-se em consideração que misturas complexas de flavonoides são consumidas diariamente na nossa dieta, não se poderá ignorar o seu potencial farmacológico sinérgico. Neste sentido, foi concretizada uma avaliação dos potenciais efeitos sinérgicos da baicaleína, (-)-EPG, kaempferol, quercetina e silimarina relativamente à inibição da P-gp, primeiro in vitro e depois in vivo. Na verdade, comparativamente aos resultados individuais obtidos, algumas combinações duais de flavonoides apresentaram um potencial acrescido para inibição da P-gp in vitro. Além disso, algumas dessas combinações, nomeadamente (-)-EPG/silimarina e kaempferol/baicaleína, proporcionaram um aumento substancial da acumulação intracelular de CBZ, OXC e PHT, bem como dos seus metabolitos CBZ-E e LIC, na linha celular MDCK-MDR1, sendo estes efeitos comparáveis aos obtidos com o verapamilo, inibidor de referência da P-gp. Assim, enquanto os flavonoides baicaleína, (-)-EPG, kaempferol, quercetina e silimarina testados individualmente aumentaram em 1,2 a 31 vezes a acumulação intracelular dos fármacos antiepiléticos e metabolitos ativos considerados nas células MDCK-MDR1, as combinações duais desses flavonoides permitiram alcançar aumentos de cerca de 1,5 a 76 vezes. Adicionalmente, o efeito da combinação da (-)-EPG com a silimarina foi também avaliado em ensaios de transporte com a LIC (substrato da P-gp) através de uma monocamada de células MDCK-MDR1 montadas em câmaras de Ussing; como esperado, esta combinação aumentou o coeficiente de permeabilidade aparente da LIC. Em geral, os resultados dos estudos in vitro foram suportados pelos resultados dos estudos in vivo. De facto, após pré-tratamento de ratos Wistar machos com silimarina observou-se um aumento nas concentrações plasmáticas dos fármacos antiepiléticos alvo (CBZ, OXC e PHT). No entanto, é de ressaltar que os principais efeitos induzidos pela silimarina foram notados na farmacocinética da OXC, para a qual foi observado um aumento estatisticamente significativo na sua concentração plasmática máxima (50%) e na sua extensão de exposição sistémica (41%), tendo tais efeitos um impacto direto nas concentrações farmacológicas alcançadas no cérebro. Por outro lado, o uso de combinações duais de (-)-EPG/silimarina na inibição da atividade da P-gp foi também avaliado in vivo em ratos Wistar, sendo evidente o potencial sinérgico destesdois flavonoides no aumento do grau de exposição sistémica à OXC e LIC (metabolito farmacologicamente ativo da OXC), o que ocorreu numa extensão comparável à observada para o verapamilo (controlo positivo). De facto, o pré-tratamento de ratos Wistar com combinações de silimarina/(-)-EPG originou concentrações plasmáticas máximas de OXC semelhantes àquelas obtidas na presença do verapamilo. Além disso, os efeitos promovidos pelas combinações de silimarina/(-)-EPG no que diz respeito à magnitude da exposição sistémica ao fármaco foram também refletidos nos níveis de OXC e LIC alcançados no cérebro (biofase). Assim, de acordo com os nossos resultados, a terapia combinada de flavonoides/fármacos antiepiléticos pode ser considerada como uma abordagem promissora que deve continuar a ser explorada no sentido de superar a farmacorresistência mediada pela P-gp. A disponibilidade desta informação resultante de ensaios in vitro e in vivo contribui também para apoiar a hipótese do envolvimento de transportadores de efluxo, em particular da P-gp, na condição de epilepsia farmacorresistente. Considerando todo o seu potencial intrínseco e propriedades biológicas indiscutíveis, os compostos de tipo flavonoide podem então emergir como uma alternativa aos inibidores da P-gp disponíveis para um tratamento prospetivo dos doentes com epilepsia refratária.The experimental work presented in this thesis was carried out at the Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior (CICS-UBI) and at the Center for Neuroscience and Cell Biology (CNC), University of Coimbr

INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY

INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY Fatima Magdi Hamza Baldo This research aims to utilise ligand-based target prediction to (i) understand the mechanism of action of African natural products (ANPs), (ii) help identify patterns of phylogenetic use in African traditional medicine and (iii) elucidate the mechanism of action of phenotypically active small molecules and natural products with anti-trypanosomal activity. In Chapter 2 the objective was to utilise ligand-based target prediction to understand the mechanism of action of natural products (NPs) from African medicinal plants used against cancer. The Random Forest classifier used in this work compares the similarity of the input compounds from the natural product dataset with compound-target combinations in the training set. The more similar they are in structure, the more likely they are to modulate the same target. Natural products from plants used against cancer in Africa were predicted to modulate targets and pathways directly associated with the disease, thus understanding their mechanism of action e.g. “flap endonuclease 1” and “Mcl-1”. The “Keap1-Nrf2 Pathway” and “apoptosis modulation by HSP70”, two pathways previously linked to cancer (which are not currently targeted by marketed drugs, but have been of increasing interest in recent years) were predicted to be modulated by ANPs. In Chapter 3, we aimed to identify phylogenetic patterns in medicinal plant use and the role this plays in predicting medicinal activity. We combined chemical, predicted target and phylogenetic information of the natural products to identify patterns of use for plant families containing plant species used against cancer in African, Malay and Indian (Ayurveda) traditional medicine. Plant families that are close phylogenetically were found to produce similar natural products that act on similar targets regardless of their origin. Additionally, phylogenetic patterns were identified for African traditional plant families with medicinal species used against cancer, malaria and human African trypanosomiasis (HAT). We identified plant families that have more medicinal species than would statistically be expected by chance and rationalised this by linking their activity to their unique phyto-chemistry e.g. the napthyl-isoquinoline alkaloids, uniquely produced by Acistrocladaceae and Dioncophyllaceae, are responsible for anti-malarial and anti-trypanosome activity. In Chapter 4, information from target prediction and experimentally validated targets was combined with orthologue data to predict targets of phenotypically active small molecules and natural products screened against Trypanosoma brucei. The predicted targets were prioritised based on their essentiality for the survival of the T. brucei parasite. We predicted orthologues of targets that are essential for the survival of the trypanosome e.g. glycogen synthase kinase 3 (GSK3) and rhodesain. We also identified the biological processes predicted to be perturbed by the compounds e.g. “glycolysis”, “cell cycle”, “regulation of symbiosis, encompassing mutualism through parasitism” and “modulation of development of symbiont involved in interaction with host”. In conclusion, in silico target prediction can be used to predict protein targets of natural products to understand their molecular mechanism of action. Phylogenetic information and phytochemical information of medicinal plants can be integrated to identify plant families with more medicinal species than would be expected by chance

Database development and machine learning prediction of pharmaceutical agents

Ph.DDOCTOR OF PHILOSOPH

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