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MolPredictX is a free-access web tool in which it is possible to analyze the prediction of biological activity of chemical molecules. MolPredictX has been available online to the general public for just over a year and has now gone through its first update. We also developed its version for android, being the first free app capable of predicting biological activities. MolPredictX is available for free at https://www.molpredictX.ufpb.br/ , and its mobile application version can be obtained from Google Play.
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Aprendizaje Automático , Aplicaciones Móviles , Programas Informáticos , Internet , Biología Computacional/métodos , HumanosRESUMEN
Anacardic acids are natural compounds found in various plant families, such as Anacardiaceae, Geraniaceae, Ginkgoaceae, and Myristicaceae, among others. Several activities have been reported regarding these compounds, including antibacterial, antioxidant, anticancer, anti-inflammatory, and antiviral activities, showing the potential therapeutic applicability of these compounds. From a chemical point of view, they are structurally made up of salicylic acids substituted by an alkyl chain containing unsaturated bonds, which can vary in number and position, determining their bioactivity and differentiating them from the various existing forms. Our work aimed to explore the potential of anacardic acids, based on studies that address the bioactivity of these compounds, as well as to establish a greater understanding of the structure-activity relationship of these compounds through in silico methods, with a focus on the elucidation of a possible drug target through the application of computer-aided drug design, CADD.
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Cruzipain (CZP), the major cysteine protease present in T. cruzi, the ethiological agent of Chagas disease, has attracted particular attention as a therapeutic target for the development of targeted covalent inhibitors (TCI). The vast chemical space associated with the enormous molecular diversity feasible to explore by means of modern synthetic approaches allows the design of CZP inhibitors capable of exhibiting not only an efficient enzyme inhibition but also an adequate translation to anti-T. cruzi activity. In this work, a computer-aided design strategy was developed to combinatorially construct and screen large libraries of 1,4-disubstituted 1,2,3-triazole analogues, further identifying a selected set of candidates for advancement towards synthetic and biological activity evaluation stages. In this way, a virtual molecular library comprising more than 75 thousand diverse and synthetically feasible analogues was studied by means of molecular docking and molecular dynamic simulations in the search of potential TCI of CZP, guiding the synthetic efforts towards a subset of 48 candidates. These were synthesized by applying a Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) centered synthetic scheme, resulting in moderate to good yields and leading to the identification of 12 hits selectively inhibiting CZP activity with IC50 in the low micromolar range. Furthermore, four triazole derivatives showed good anti-T. cruzi inhibition when studied at 50 µM; and Ald-6 excelled for its high antitrypanocidal activity and low cytotoxicity, exhibiting complete in vitro biological activity translation from CZP to T. cruzi. Overall, not only Ald-6 merits further advancement to preclinical in vivo studies, but these findings also shed light on a valuable chemical space where molecular diversity might be explored in the search for efficient triazole-based antichagasic agents.
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Cisteína Endopeptidasas , Simulación del Acoplamiento Molecular , Proteínas Protozoarias , Triazoles , Trypanosoma cruzi , Triazoles/química , Triazoles/farmacología , Triazoles/síntesis química , Cisteína Endopeptidasas/química , Proteínas Protozoarias/antagonistas & inhibidores , Proteínas Protozoarias/química , Trypanosoma cruzi/efectos de los fármacos , Trypanosoma cruzi/enzimología , Inhibidores de Cisteína Proteinasa/química , Inhibidores de Cisteína Proteinasa/farmacología , Inhibidores de Cisteína Proteinasa/síntesis química , Simulación de Dinámica Molecular , Relación Estructura-Actividad , Diseño Asistido por Computadora , Diseño de Fármacos , Humanos , Estructura Molecular , Tripanocidas/farmacología , Tripanocidas/química , Tripanocidas/síntesis química , Enfermedad de Chagas/tratamiento farmacológicoRESUMEN
INTRODUCTION: Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED: In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION: These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Mycobacterium tuberculosis , Tuberculosis , Humanos , Diseño de Fármacos , Tuberculosis/tratamiento farmacológico , Tuberculosis/microbiología , Descubrimiento de Drogas , Desarrollo de Medicamentos , Diseño Asistido por ComputadoraRESUMEN
Helicobacter pylori (Hp) infections pose a global health challenge demanding innovative therapeutic strategies by which to eradicate them. Urease, a key Hp virulence factor hydrolyzes urea, facilitating bacterial survival in the acidic gastric environment. In this study, a multi-methodological approach combining pharmacophore- and structure-based virtual screening, molecular dynamics simulations, and MM-GBSA calculations was employed to identify novel inhibitors for Hp urease (HpU). A refined dataset of 8,271,505 small molecules from the ZINC15 database underwent pharmacokinetic and physicochemical filtering, resulting in 16% of compounds for pharmacophore-based virtual screening. Molecular docking simulations were performed in successive stages, utilizing HTVS, SP, and XP algorithms. Subsequent energetic re-scoring with MM-GBSA identified promising candidates interacting with distinct urease variants. Lys219, a residue critical for urea catalysis at the urease binding site, can manifest in two forms, neutral (LYN) or carbamylated (KCX). Notably, the evaluated molecules demonstrated different interaction and energetic patterns in both protein variants. Further evaluation through ADMET predictions highlighted compounds with favorable pharmacological profiles, leading to the identification of 15 candidates. Molecular dynamics simulations revealed comparable structural stability to the control DJM, with candidates 5, 8 and 12 (CA5, CA8, and CA12, respectively) exhibiting the lowest binding free energies. These inhibitors suggest a chelating capacity that is crucial for urease inhibition. The analysis underscores the potential of CA5, CA8, and CA12 as novel HpU inhibitors. Finally, we compare our candidates with the chemical space of urease inhibitors finding physicochemical similarities with potent agents such as thiourea.
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Helicobacter pylori , Helicobacter pylori/metabolismo , Ureasa/metabolismo , Simulación de Dinámica Molecular , Simulación del Acoplamiento Molecular , Urea/farmacologíaRESUMEN
Virtual small molecule libraries are valuable resources for identifying bioactive compounds in virtual screening campaigns and improving the quality of libraries in terms of physicochemical properties, complexity, and structural diversity. In this context, the computational-aided design of libraries focused against antidiabetic targets can provide novel alternatives for treating type II diabetes mellitus (T2DM). In this work, we integrated the information generated to date on compounds with antidiabetic activity, advances in computational methods, and knowledge of chemical transformations available in the literature to design multi-target compound libraries focused on T2DM. We evaluated the novelty and diversity of the newly generated library by comparing it with antidiabetic compounds approved for clinical use, natural products, and multi-target compounds tested in vivo in experimental antidiabetic models. The designed libraries are freely available and are a valuable starting point for drug design, chemical synthesis, and biological evaluation or further computational filtering. Also, the compendium of 280 transformation rules identified in a medicinal chemistry context is made available in the linear notation SMIRKS for use in other chemical library enumeration or hit optimization approaches.
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QSAR models capable of predicting biological, toxicity, and pharmacokinetic properties were widely used to search lead bioactive molecules in chemical databases. The dataset's preparation to build these models has a strong influence on the quality of the generated models, and sampling requires that the original dataset be divided into training (for model training) and test (for statistical evaluation) sets. This sampling can be done randomly or rationally, but the rational division is superior. In this paper, we present MASSA, a Python tool that can be used to automatically sample datasets by exploring the biological, physicochemical, and structural spaces of molecules using PCA, HCA, and K-modes. The proposed algorithm is very useful when the variables used for QSAR are not available or to construct multiple QSAR models with the same training and test sets, producing models with lower variability and better values for validation metrics. These results were obtained even when the descriptors used in the QSAR/QSPR were different from those used in the separation of training and test sets, indicating that this tool can be used to build models for more than one QSAR/QSPR technique. Finally, this tool also generates useful graphical representations that can provide insights into the data.
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Algoritmos , Relación Estructura-Actividad Cuantitativa , Bases de Datos de Compuestos Químicos , BenchmarkingRESUMEN
A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases or cysteine proteases (CPs), are divided into three categories according to the peptide chain involved. CPs catalyze the hydrolysis of amide, ester, thiol ester, and thioester peptide bonds. They can be divided into several groups, such as papain-like (CA), viral chymotrypsin-like CPs (CB), papain-like endopeptidases of RNA viruses (CC), legumain-type caspases (CD), and showing active residues of His, Glu/Asp, Gln, Cys (CE). The catalytic mechanism of CPs is the essential cysteine residue present in the active site. These mechanisms are often studied through computational methods that provide new information about the catalytic mechanism and identify inhibitors. The role of computational methods during drug design and development stages is increasing. Methods in Computer-Aided Drug Design (CADD) accelerate the discovery process, increase the chances of selecting more promising molecules for experimental studies, and can identify critical mechanisms involved in the pathophysiology and molecular pathways of action. Molecular dynamics (MD) simulations are essential in any drug discovery program due to their high capacity for simulating a physiological environment capable of unveiling significant inhibition mechanisms of new compounds against target proteins, especially CPs. Here, a brief approach will be shown on MD simulations and how the studies were applied to identify inhibitors or critical information against cysteine protease from several microorganisms, such as Trypanosoma cruzi (cruzain), Trypanosoma brucei (rhodesain), Plasmodium spp. (falcipain), and SARS-CoV-2 (Mpro). We hope the readers will gain new insights and use our study as a guide for potential compound identifications using MD simulations.
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Bacteria resistance to antibiotics is a concerning global health problem; in this context, methicillin-resistant Staphylococcus aureus (MRSA) is considered as a high priority by the World Health Organization. Furthermore, patients with a positive result for COVID-19 received early antibiotic treatment, a fact that potentially encourages the increase in antibiotic resistance. Therefore, there is an urgency to develop new drugs with molecular mechanisms different from those of the actual treatments. In this context, enzymes from the shikimate pathway, a route absent in humans, such as dehydroquinate dehydratase (DHQD), are considered good targets. In this work, a computer-aided drug design strategy, which involved exhaustive virtual screening and molecular dynamics simulations with MM-PBSA analysis, as well as an in silico ADMETox characterization, was performed to find potential noncovalent inhibitors of DHQD from MRSA (SaDHQD). After filtering the 997 million compounds from the ZINC database, 6700 compounds were submitted to an exhaustive virtual screening protocol. From these data, four molecules were selected and characterized (ZINC000005753647 (1), ZINC000001720488 (2), ZINC000082049768 (3), and ZINC000644149506 (4)). The results indicate that the four potential inhibitors interacted with residues important for substrate binding and catalysis, with an estimated binding free energy like that of the enzyme's substrate. Their ADMETox-predicted properties suggest that all of them support the structural characteristics to be considered good candidates. Therefore, the four compounds reported here are excellent option to be considered for future in vitro studies to design new SaDHQD noncovalent inhibitors and contribute to the search for new drugs against MRSA.
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Aim: Discovery of novel SARS-CoV-2 main protease (Mpro) inhibitors using a structure-based drug discovery strategy. Materials & methods: Virtual screening employing covalent and noncovalent docking was performed to discover Mpro inhibitors, which were subsequently evaluated in biochemical and cellular assays. Results: 91 virtual hits were selected for biochemical assays, and four were confirmed as reversible inhibitors of SARS CoV-2 Mpro with IC50 values of 0.4-3 µM. They were also shown to inhibit SARS-CoV-1 Mpro and human cathepsin L. Molecular dynamics simulations indicated the stability of the Mpro inhibitor complexes and the interaction of ligands at the subsites. Conclusion: This approach led to the discovery of novel thiosemicarbazones as potent SARS-CoV-2 Mpro inhibitors.
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COVID-19 , Tiosemicarbazonas , Humanos , SARS-CoV-2 , Antivirales/farmacología , Antivirales/química , Tiosemicarbazonas/farmacología , Simulación del Acoplamiento Molecular , Inhibidores de Proteasas/farmacología , Inhibidores de Proteasas/química , Proteínas no Estructurales ViralesRESUMEN
Introduction: Leishmaniasis is a disease with high mortality rates and approximately 1.5 million new cases each year. Despite the new approaches and advances to fight the disease, there are no effective therapies. Methods: Hence, this study aims to screen for natural products' structural analogs as new drug candidates against leishmaniasis. We applied Computer-aided drug design (CADD) approaches, such as virtual screening, molecular docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA) binding free estimation, and free energy perturbation (FEP) aiming to select structural analogs from natural products that have shown anti-leishmanial and anti-arginase activities and that could bind selectively against the Leishmania arginase enzyme. Results: The compounds 2H-1-benzopyran, 3,4-dihydro-2-(2-methylphenyl)-(9CI), echioidinin, and malvidin showed good results against arginase targets from three parasite species and negative results for potential toxicities. The echioidinin and malvidin ligands generated interactions in the active center at pH 2.0 conditions by MM-GBSA and FEP methods. Conclusions: This work suggests the potential anti-leishmanial activity of the compounds and thus can be further in vitro and in vivo experimentally validated.
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Productos Biológicos , Diseño de Fármacos , Leishmania , Leishmaniasis , Humanos , Arginasa/metabolismo , Arginasa/farmacología , Arginasa/uso terapéutico , Productos Biológicos/farmacología , Leishmania/metabolismo , Leishmaniasis/tratamiento farmacológico , Simulación del Acoplamiento MolecularRESUMEN
The leishmaniasis is a neglected disease caused by a group of protozoan parasites from the genus Leishmania whose treatment is limited, obsolete, toxic, and ineffective in certain cases. These characteristics motivate researchers worldwide to plan new therapeutic alternatives for the treatment of leishmaniasis, where the use of cheminformatics tools applied to computer-assisted drug design has allowed research to make great advances in the search for new drugs candidates. In this study, a series of 2-amino-thiophene (2-AT) derivatives was screened virtually using QSAR tools, ADMET filters and prediction models, allowing direct the synthesis of compounds, which were evaluated in vitro against promastigotes and axenic amastigotes of Leishmania amazonensis. The combination of different descriptors and machine learning methods led to obtaining robust and predictive QSAR models, which was obtained from a dataset composed of 1862 compounds extracted from the ChEMBL database, with correct classification rates ranging from 0.53 (for amastigotes) to 0.91 (for promastigotes), allowing to select eleven 2-AT derivatives, which do not violate Lipinski's rules, exhibit good druglikeness, and with probability ≤70% of potential activity against the two evolutionary forms of the parasite. All compounds were properly synthesized and 8 of them were shown to be active at least against one of the evolutionary forms of the parasite with IC50 values lower than 10 µM, being more active than the reference drug meglumine antimoniate, and showing low or no citotoxicity against macrophage J774.A1 for the most part. Compounds 8CN and DCN-83, respectively, are the most active against promastigote and amastigote forms, with IC50 values of 1.20 and 0.71 µM, and selectivity indexes (SI) of 36.58 and 119.33. Structure Activity Relationship (SAR) study was carried out and allowed to identify some favorable and/or essential substitution patterns for the leishmanial activity of 2-AT derivatives. Taken together, these findings demonstrate that the use of ligand-based virtual screening proved to be quite effective and saved time, effort, and money in the selection of potential anti-leishmanial agents, and confirm, once again that 2-AT derivatives are promising hit compounds for the development of new anti-leishmanial agents.
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Antiprotozoarios , Leishmania , Leishmaniasis , Humanos , Antiprotozoarios/química , Tiofenos/farmacología , Tiofenos/uso terapéutico , Leishmaniasis/tratamiento farmacológico , Leishmaniasis/parasitología , Diseño de FármacosRESUMEN
BACKGROUND: In the last decade, cancer has been a leading cause of death worldwide. Despite the impressive progress in cancer therapy, firsthand treatments are not selective to cancer cells and cause serious toxicity. Thus, the design and development of selective and innovative small molecule drugs is of great interest, particularly through in silico tools. OBJECTIVE: The aim of this review is to analyze different subsections of computer-aided drug design (CADD) in the process of discovering anticancer drugs. METHODS: Articles from the 2008-2021 timeframe were analyzed and based on the relevance of the information and the JCR of its journal of precedence, were selected to be included in this review. RESULTS: The information collected in this study highlights the main traditional and novel CADD approaches used in anticancer drug discovery, its sub-segments, and some applied examples. Throughout this review, the potential use of CADD in drug research and discovery, particularly in the field of oncology, is evident due to the many advantages it presents. CONCLUSION: CADD approaches play a significant role in the drug development process since they allow a better administration of resources with successful results and a promising future market and clinical wise.
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Antineoplásicos , Neoplasias , Humanos , Diseño Asistido por Computadora , Diseño de Fármacos , Antineoplásicos/farmacología , Antineoplásicos/uso terapéutico , Descubrimiento de Drogas/métodos , Neoplasias/tratamiento farmacológicoRESUMEN
Major depressive disorder (MDD) is characterized by a series of disabling symptoms like anhedonia, depressed mood, lack of motivation for daily tasks and self-extermination thoughts. The monoamine deficiency hypothesis states that depression is mainly caused by a deficiency of monoamine at the synaptic cleft. Thus, major efforts have been made to develop drugs that inhibit serotonin (SERT), norepinephrine (NET) and dopamine (DAT) transporters and increase the availability of these monoamines. Current gold standard treatment of MDD uses drugs that target one or more monoamine transporters. Triple reuptake inhibitors (TRIs) can target SERT, NET, and DAT simultaneously, and are believed to have the potential to be early onset antidepressants. Quantitative structure-activity relationship models were developed using machine learning algorithms in order to predict biological activities of a series of triple reuptake inhibitor compounds that showed in vitro inhibitory activity against multiple targets. The results, using mostly interpretable descriptors, showed that the internal and external predictive ability of the models are adequate, particularly of the DAT and NET by Random Forest and Support Vector Machine models. The current work shows that models developed from relatively simple, chemically interpretable descriptors can predict the activity of TRIs with similar structure in the applicability domain using ML methods.Communicated by Ramaswamy H. Sarma.
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Trastorno Depresivo Mayor , Humanos , Trastorno Depresivo Mayor/tratamiento farmacológico , Antidepresivos/farmacología , Proteínas de Transporte de Membrana/metabolismo , Inhibidores de Captación de Dopamina/farmacología , Transporte BiológicoRESUMEN
Protein-protein interaction (PPI) inhibitors have an increasing role in drug discovery. It is hypothesized that machine learning (ML) algorithms can classify or identify PPI inhibitors. This work describes the performance of different algorithms and molecular fingerprints used in chemoinformatics to develop a classification model to identify PPI inhibitors making the codes freely available to the community, particularly the medicinal chemistry research groups working with PPI inhibitors. We found that classification algorithms have different performances according to various features employed in the training process. Random forest (RF) models with the extended connectivity fingerprint radius 2 (ECFP4) had the best classification abilities compared to those models trained with ECFP6 o MACCS keys (166-bits). In general, logistic regression (LR) models had lower performance metrics than RF models, but ECFP4 was the representation most appropriate for LR. ECFP4 also generated models with high-performance metrics with support vector machines (SVM). We also constructed ensemble models based on the top-performing models. As part of this work and to help non-computational experts, we developed a pipeline code freely available.
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Quimioinformática , Aprendizaje Automático , Modelos Logísticos , Algoritmos , Máquina de Vectores de SoporteRESUMEN
Dengue virus (DENV) disease has become one of the major challenges in public health. Currently, there is no antiviral treatment for this infection. Since human transmission occurs via mosquitoes of the Aedes genus, most efforts have been focused on the control of this vector. However, these control strategies have not been totally successful, as reflected in the increasing number of DENV infections per year, becoming an endemic disease in more than 100 countries worldwide. Consequently, the development of a safe antiviral agent is urgently needed. In this sense, rational design approaches have been applied in the development of antiviral compounds that inhibit one or more steps in the viral replication cycle. The entry of viruses into host cells is an early and specific stage of infection. Targeting either viral components or cellular protein targets are an affordable and effective strategy for therapeutic intervention of viral infections. This review provides an extensive overview of the small organic molecules, peptides, and inorganic moieties that have been tested so far as DENV entry direct-acting antiviral agents. The latest advances based on computer-aided drug design (CADD) strategies and traditional medicinal chemistry approaches in the design and evaluation of DENV virus entry inhibitors will be discussed. Furthermore, physicochemical drug properties, such as solubility, lipophilicity, stability, and current results of pre-clinical and clinical studies will also be discussed in detail.
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Virus del Dengue , Dengue , Hepatitis C Crónica , Animales , Antivirales/química , Antivirales/farmacología , Antivirales/uso terapéutico , Dengue/tratamiento farmacológico , Hepatitis C Crónica/tratamiento farmacológico , Humanos , Mosquitos VectoresRESUMEN
BACKGROUND: Neglected diseases require special attention when looking for new therapeutic alternatives, as these are diseases of extreme complexity and severity that affect populations belonging to lower social classes who lack access to basic rights, such as sanitation. INTRODUCTION: Among the alternatives available for obtaining new drugs is Medicinal Chemistry, which is responsible for the discovery, identification, invention, and preparation of prototypes. In this perspective, the present work aims to make a bibliographic review on the recent studies of Medicinal Chemistry applied to neglected diseases. METHODS: A literature review was carried out by searching the "Web of Sciences" database, including recent articles published on the Neglected Drug Design. RESULTS: In general, it was noticed that the most studied neglected diseases corresponded to Chagas disease and leishmaniasis, with studies on organic synthesis, optimization of structures, and molecular hybrids being the most used strategies. It is also worth mentioning the growing number of computationally developed studies, providing speed and optimization of costs in the procurement process. CONCLUSION: The CADD approach and organic synthesis studies, when applied in the area of Medicinal Chemistry, have proven to be important in the research and discovery of drugs for Neglected Diseases, both in terms of planning the experimental methodology used to obtain it and in the selection of compounds with higher activity potential.
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Química Farmacéutica , Diseño de Fármacos , Enfermedades Desatendidas/tratamiento farmacológico , Enfermedad de Chagas/tratamiento farmacológico , Humanos , Leishmaniasis/tratamiento farmacológicoRESUMEN
Glycogen synthase kinase-3 beta (GSK-3ß) is an enzyme pertinently linked to neurodegenerative diseases since it is associated with the regulation of key neuropathological features in the central nervous system. Among the different kinds of inhibitors of this kinase, the allosteric ones stand out due to their selective and subtle modulation, lowering the chance of producing side effects. The mechanism of GSK-3ß allosteric modulators may be considered still vague in terms of elucidating a well-defined binding pocket and a bioactive pose for them. In this context, we propose to reinvestigate and reinforce such knowledge by the application of an extensive set of in silico methodologies, such as cavity detection, ligand 3D shape analysis and docking (with robust validation of corresponding protocols), and molecular dynamics. The results here obtained were consensually consistent in furnishing new structural data, in particular by providing a solid bioactive pose of one of the most representative GSK-3ß allosteric modulators. We further applied this to the prospect for new compounds by ligand-based virtual screening and analyzed the potential of the two obtained virtual hits by quantum chemical calculations. All potential hits achieved will be subsequently tested by in vitro assays in order to validate our approaches as well as to unveil novel chemical entities as GSK-3ß allosteric modulators.