Estrogen receptor alpha (ERα) acts as the transcription factor and the main therapeutic target against breast cancer. One of the compounds that has been shown to act as an ERα is α-mangostin. ...However, it still has weaknesses due to its low solubility and low potent activity. In this study, α-mangostin was modified by substituting -OH group at C6 using benzoyl derivatives through a step by step in silico study, namely pharmacokinetic prediction (
https://preadmet.bmdrc.kr/adme/
), pharmacophore modeling (LigandScout 4.1), molecular docking simulation (AutoDock 4.2), molecular dynamics simulation (AMBER 16) and a binding free energy analysis using MM-PBSA method. From the computational studies, three compounds which are derived from α-mangostin (AMB-1 (−9.84 kcal/mol), AMB-2 (−6.80 kcal/mol) and AMB-10 (−12.42 kcal/mol)) have lower binding free energy than α-mangostin (−1.77 kcal/mol), as evidenced by the binding free energy calculation using the MM-PBSA method. They can then be predicted to have potent activities as ERα antagonists.
Communicated by Ramaswamy H. Sarma
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•Novel series of linezolid-based oxazolidinones were designed and synthesized by selected modifications.•Potent anticandidiasis activity exhibited by oxazolidinone (2, 3a) against 14 ...strains of C.albicans.•Demonstration of mechanism of action by the inhibition of ergosterol biosynthesis.•Excellent antitubercular activity displayed by oxazolidinone (2, 3a), comparable to linezolid.•Computational studies revealed the superior or comparable binding affinity of the oxazolidinone towards the biological receptors than controls.
The quest for new antifungal and antitubercular drugs is a need of the hour because of morbid co-pathogenesis and an increase in immunocompromised patients. One of the ways forward is to explore and repurpose the established pharmacophores for the desired application. Oxazolidinones are well-known antibacterial agents, with few investigations reported to exploit their antifungal properties. Herein, we report the design and synthesis of a series of linezolid-based oxazolidinones as potent anticandidiasis and antitubercular agents. Studies revealed that two of the novel oxazolidinones 2 and 3a exhibited excellent anticandidiasis activity against different Candida fungus strains, superior to standard drugs. Mechanistic and docking studies revealed that oxazolidinones were better inhibitors of the ergosterol biosynthesis pathway than the controls used. In addition, the oxazolidinones 2 and 3a also exhibited prominent inhibitory activity against M. tuberculosis H37Rv with MIC values of 1 and 2 μg/ml, respectively. Computational studies demonstrated the binding of the compounds to the transcriptional regulatory repressor protein, which was reinforced by the molecular dynamics simulations. The pharmacophore modeling experiments validated the molecular docking results in both the target proteins.
Prion diseases are serious, not curable neurodegenerative disorders caused by the accumulation of the misfolded protein PrPSc that represents the pathological variant of the normally folded cellular ...protein PrPC. Molecules that bind the cellular isoform PrPC preventing its misfolding, could arrest the progression of pathological conditions related to the abnormal PrP protein. In this context, by combining 3D-QSAR model, derived from pharmacophore-based alignment, with molecular docking procedures and physico-chemical properties prediction we have developed a virtual screening protocol to find novel chemicals able to prevent PrPC misfolding. We identified different hits characterized by low toxicity and able to inhibit PrPSc accumulation in vitro in prion-infected neuroblastoma cell lines (ScN2a). In this assay, the pyrroloquinoxaline hydrazone 96 showed the higest potency with an IC50 value of 1.6 μM. Pyrroloquinoxaline 96 was demonstrated also to bind PrPSc aggregates in infected ScN2a cells with a fluorescence pattern comparable to that found for Thioflavin-T. In consideration of its satisfactory physico-chemical properties, including predicted blood brain barrier permeability, 96 could represent an interesting prototypic hit for the development of diagnostic and therapeutic probes for prion diseases.
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•A 3D-QSAR model was generated for the prediction of anti-prion activity.•The model was used in virtual screening protocol coupled with molecular docking on PrPC.•Nine out of eleven selected compounds had a non-toxic profile and showed in vitro anti-prion activity.•Compound 96 is a promising hit interfering with pathological transition of PrPC to PrPSc.•96 displays a fluorescence staining profile suggesting its application as a diagnostic for TSE.
Many biological targets are characterized by high binding pocket flexibility posing a challenge in identifying important ligand binding features. Liver X receptors (LXRs) are members of the nuclear ...hormone receptor super family. Although several X-ray structures for LXRβ bound ligands are available, differences in ligands’ binding poses and interactions in the ligand binding pocket causes a challenge in identifying general elements of ligand binding. In this study, we used several LXR X-ray structures and known LXR ligands to study how LXRβ ligands interact with the LXRβ receptor. Using this information, we generated several pharmacophore models that represents important chemical features necessary for LXR binding and activation. Our results show that generating pharmacophore models based on a combined approach of multiple ligands alignments and considering the ligands’ binding coordinates yielded the best results. The generated pharmacophore model will be useful for future ligand discovery of LXRβ modulators using virtual screening.
•Review of hierarchical virtual screening approaches is presented.•Hierarchical combination of ligand and structure-based methods is preferred over parallel combination.•Molecular docking is a key ...component of many hierarchical virtual screening schemes.•Hierarchical virtual screening may be useful in plucking high-hanging fruits.
Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery.
Cancer remains a leading cause of morbidity and mortality worldwide. Hence, the increase in cancer cases observed in the elderly population, as well as in children and adolescents, makes human ...malignancies a prime target for anticancer drug development. Although highly effective chemotherapeutic agents are continuously developed and approved for clinical treatment, the major impediment towards curative cancer therapy remains multidrug resistance (MDR). In recent years, intensive studies have been carried out on the identification of new therapeutic molecules to reverse MDR efflux transporters of the ATP-binding cassette (ABC) superfamily. Although a great deal of progress has been made in the development of specific inhibitors for certain MDR efflux pumps in experimental studies, advanced computational studies can accelerate this drug development process. In the literature, there are many experimental studies on the impact of natural products and synthetic small molecules on the reversal of cancer MDR. Molecular modeling methods provide an opportunity to explain the activity of these molecules on the ABC-transporter family with non-covalent interactions as well as it is possible to carry out studies for the discovery of new anticancer drugs specific to MDR with these methods. The coordinate file of the 3-dimensional (3D) structure of the target protein is indispensable for molecular modeling studies. In some cases where a 3D structure cannot be obtained by experimental methods, the homology modeling method can be applied to obtain the file containing the target protein's information including atomic coordinates, secondary structure assignments, and atomic connectivity. Homology modeling studies are of great importance for efflux transporter proteins that still lack 3D structures due to crystallization problems with multiple hydrophobic transmembrane domains. Quantum mechanics, molecular docking and molecular dynamics simulation applications are the most frequently used molecular modeling methods in the literature to investigate non-covalent interactions between the drug-ABC transporter superfamily. The quantitative structure-activity relationship (QSAR) model provides a relationship between the chemical properties of a compound and its biological activity. Determining the pharmacophore region for a new drug molecule by superpositioning a series of molecules according to their physicochemical properties using QSAR models is another method in which molecular modeling is used in computational drug development studies with ABC transporter proteins. There are also in silico absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) studies conducted to make a prediction about the pharmacokinetic properties, and drug-likeness of new molecules. Drug repurposing studies, which have become a trending topic in recent years, involve identifying possible new targets for an already approved drug molecule. There are few studies in the literature in which drug repurposing performed by molecular modelling methods has been applied on ABC transporter proteins.
The aim of the current paper is to create a complete review of drug development studies including aforementioned molecular modeling methods carried out between the years 2019-2021. Furthermore, an intensive investigation is also conducted on licensed applications and free web servers used in in silico studies. The current review is an up-to-date guide for researchers who plan to conduct computational studies with MDR transporter proteins.
•Phytochemicals isolated from Cannabis sativa can improve behavioral symptoms associated with neurological diseases including AD.•Morphinan-6-one demonstrated inhibitory actions against AChE and DDC, ...suggesting that it might have dual functions in AD.•Morphinan-6-one is hypothesized to be a modulatory molecule for acetylcholinesterase.
This study was aimed at evaluating the inhibitory effects of the phytochemicals from the Cannabis sativa (Cannabis) leaf extracts against Alzheimer’s disease (AD) protein targets. Twelve compounds derived from the Cannabis sativa leaf extracts were evaluated as potential inhibitors of acetylcholinesterase (AChE), dopa decarboxylase (DDC), serotonin receptor 2C (HTR2C) and monoamine oxidase (MAO). Ligand-based and receptor-ligand complex were used to derive the pharmacophore hypothesis. In silico study through molecular docking simulation method was adopted to analyze the inhibitory activity of the compounds in question. Molecular dynamic simulation (MDs) was performed to assess the stability of the top-ranked phytochemicals. The binding energies of these compounds to the four targets were investigated by the Molecular Mechanics for the Generalized Born Model and Solvent Accessibility method (MM-GBSA). The binding-free energy suggests that cannabinol, cannabichromene, linoelaidic acid and morphinan-6-one can be utilized as lead compounds in drug discovery and development of AD to inhibit activity of AChE, DCC gene, MAO and HTR2C. The MDs indicated that AChE-Cannabinol, DCC-Cannabicoumaronone, MAO-Linoelaidic acid, and HTR2C-morphinan-6-one were stable over the entire course of 100 ns suggesting their role in the regulation of the diseases in which their respective receptors are implicated.
•Screening for potent α-ketoamide inhibitors targeting the SARS CoV-2 Mpro protein.•QSAR model was used to predict the SARS-CoV-2 Mpro inhibitory activity of α-ketoamides.•Molecular docking, ...molecular dynamics simulation and ADMET were performed on selected compounds.•Three hits with promising pharmacokinetic properties could be explored for the treatment of COVID-19.
The COVID-19 has been creating a global crisis, causing countless deaths and unbearable panic. Despite the progress made in the development of the vaccine, there is an urge need for the discovery of antivirals that may better work at different stages of SARS-CoV-2 reproduction. The main protease (Mpro) of the SARS-CoV-2 is a crucial therapeutic target due to its critical function in virus replication. The α-ketoamide derivatives represent an important class of inhibitors against the Mpro of the SARS-CoV. While there is 99% sequence similarity between SARS-CoV and SARS-CoV-2 main proteases, anti-SARS-CoV compounds may have a huge demonstration's prospect of their effectiveness against the SARS-CoV-2. In this study, we applied various computational approaches to investigate the inhibition potency of novel designed α-ketoamide-based compounds. In this regard, a set of 21 α-ketoamides was employed to construct a QSAR model, using the genetic algorithm-multiple linear regression (GA-MLR), as well as a pharmacophore fit model. Based on the GA-MLR model, 713 new designed molecules were reduced to 150 promising hits, which were later subject to the established pharmacophore fit model. Among the 150 compounds, the best selected compounds (3 hits) with greater pharmacophore fit score were further studied via molecular docking, molecular dynamic simulations along with the Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Our approach revealed that the three hit compounds could serve as potential inhibitors against the SARS-CoV-2 Mpro target.
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