Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis

Dihydrofolate reductase (DHFR), a housekeeping enzyme in primary metabolism, has been extensively studied as a model of acid-base catalysis and a clinic drug target. Herein, we investigated the enzymology of a DHFR-like protein SacH in safracin (SAC) biosynthesis, which reductively inactivates hemiaminal pharmacophore-containing biosynthetic intermediates and antibiotics for self-resistance. Furthermore, based on the crystal structure of SacH-NADPH-SAC-A ternary complexes and mutagenesis, we proposed a catalytic mechanism that is distinct from the previously characterized short-chain dehydrogenases/reductases-mediated inactivation of hemiaminal pharmacophore. These findings expand the functions of DHFR family proteins, reveal that the common reaction can be catalyzed by distinct family of enzymes, and imply the possibility for the discovery of novel antibiotics with hemiaminal pharmacophore.

AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-

We herein describe AncPhore, a versatile tool for drug discovery, which is characterized by pharmacophore feature analysis and anchor pharmacophore (

Construction and application of pharmacophore model of human carboxylesterase 2 inhibitors / 中国中药杂志

According to human carboxylesterase 2(hCE2) inhibitors reported in the literature, the pharmacophore model of hCE2 inhibitors was developed using HipHop module in Discovery Studio 2016. The optimized pharmacophore model, which was validated by test set, contained two hydrophobic, one hydrogen bond acceptor, and one aromatic ring features. Using the pharmacophore model established, 5 potential hCE2 inhibitors(CS-1,CS-2,CS-3,CS-6 and CS-8) were screened from 20 compounds isolated from the roots of Paeonia lactiflora, which were further confirmed in vitro, with the IC_(50) values of 5.04, 5.21, 5.95, 6.64 and 7.94 μmol·L~(-1), respectively. The results demonstrated that the pharmacophore model exerted excellent forecasting ability with high precision, which could be applied to screen novel hCE2 inhibitors from Chinese medicinal materials.

Rapid discovery of tyrosinase inhibitors from Sophora flavescens:significance for comprehensive utilization of its non-medicinal resources / 中国中药杂志

Sophorae Flavescentis Radix,derived from the root of Sophora flavescens in the Leguminosae family,has been widely used in the medicine,agriculture,animal husbandry,and daily chemical industry. A pharmacophore model-based method for rapid discovery of tyrosinase inhibitors( TIs) from S. flavescens was established by molecular docking under Lipinski rules,and verified by enzyme assays. Briefly,the chemical constituent database of S. flavescens( CDSF) was established based on the previous papers. Theoptimal pharmacophore model( OPM) was constructed by DS 2019 on the basis of known active TIs. Eighty-three hits predominated by flavonoids having higher fitting scores with OPM than the positive control were screened out,and subjected to molecular docking based on the three-dimensional structure of tyrosinase crystal protein. The potential TIs such as kurarinone and nor-kurarinone were rapidly discovered from the compounds with higher docking scores than the positive control under the Lipinski rules. The results were verified by the in vitro enzyme assays. The inhibition activities of tyrosinase from non-medicinal parts of S. flavescens were also tested to explore the relationship between the inhibition activity and chemical compositions. This study is expected to provide data support for the comprehensive application and development of S. flavescens and also a new method for the rapid discovery of active substances or functional constituents in the complex systems.

Construction of pharmacophore model and its application in identification of effective components of Chinese medicine / 中国中药杂志

The effective material basis of Chinese medicine is the key and difficult point in the quality control and modernization research of Chinese medicine. With the increasing application of pharmacophore-based virtual screening in computer-aided drug design, it is possible to employ this technology in the modernization of Chinese medicine. Based on the systematic research method of the pharmacophore model, the present study systematically reviewed the pharmacophore-based technologies and strategies in the identification of active components in Chinese medicine.

Virtual screen of effective AChE inhibitory constituents from Glycyrrhizae Radix et Rhizoma based on pharmacophore and molecular docking / 中国中药杂志

This research is to predict anti-Alzheimer's disease active constituents on the target of acetylcholinesterase(AChE) from Glycyrrhizae Radix et Rhizoma with the help of pharmacophore and molecular docking. AChE ligand-based pharmacophore model was set up and the molecular library of the constituents from Glycyrrhizae Radix et Rhizoma were established by collecting literature. Then the constituents from Glycyrrhizae Radix et Rhizoma were screen for the potential AChE inhibitory potency in silico through matching with the best pharmacophore model. The flexible docking was used to evaluate the interactions between compounds screened from pharmacophore model and AChE protein(PDB ID:4 EY7). The interactions were expressed including but not limited to CDOCKER interaction energy, hydrogen bonds and non-bonding interactions. The molecular library of Glycyrrhizae Radix et Rhizoma contains 44 chemical constituents. As for the pharmacophore model, six kinds of potential AChE inhibitory constituents from Glycyrrhizae Radix et Rhizoma were considered to be the promising compounds according to the results of searching 3 D database of pharmacophore model. The molecular docking was possessed and the interaction patterns were given to show the detail interactions. The compounds screening from the pharmacophore model were consistent with the existing studies to some degree, indicating that the virtual screen protocols of AChE inhibitory constituents from Glycyrrhizae Radix et Rhizoma based on pharmacophore and molecular docking was reliable.

Effects and mechanism research of astragaloside IV improving insulin resistance of HepG2 cells based on pharmacophore and molecular docking / 中草药

Objective: To research the effects of astragaloside IV (AST IV) on improving insulin resistance in HepG2 cells, and predict and verify the AST IV possible targets based on pharmacophore model matching and molecular docking. Methods: HepG2 cells insulin resistance model was induced with high concentration insulin. After being interfered by AST IV, the glucose consumption was characterized by glucose test, AST IV possible targets were predicted by pharmacophore model matching and molecular docking, the expressions of related pathway protein were detected by Western blotting. Results: AST IV significantly increased the glucose consumption in insulin-resistant HepG2 cells, the possible target of AST IV may be related to tyrosine phosphotase 1B (PTP1B) based on pharmacophore model matching and molecular docking. The Western blotting results showed that, the level of PTP1B was significantly increased and the levels of p-IR and p-IRS-1 were significantly decreased in insulin-resistant HepG2 cells. The intervention of AST IV decreased the levels of PTP1B, and increased the levels of p-IR and p-IRS-1. Conclusion: AST IV can significantly improve insulin resistance of insulin induced HepG2 cells, and its mechanism is related to inhibiting PTP1B and activating insulin signaling pathways.

Application of in silico screening technology in the medical research of natural products / 国际药学研究杂志

Natural products have always been one of the important sources of new chemical drugs. In recent years, with the continuous increase in the number of natural products reported, the separation and enrichment of new natural compounds have become more and more difficult, and the traditional high throughput screening methods have been unable to meet the needs of new drug development. Given its high efficiency and low cost, in silico(virtual)screening technology has gradually become indispensable in the research and development of new natural products. In this article, we introduce and compare the advantages and disadvantages of four in silico screening methods, collect and sort out the application cases of the virtual screening technology in the research of new natural products in recent years to provide a reference for researchers.

Ligand- and structure-based pharmacophore modeling, docking study reveals 2-[[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3-b] pyridin-6-yl] amino] ethanol as a potential anticancer agent of CDK9/cyclin T1 kinase

Objective: CDK9/Cyclin T1 kinase is a protein kinase, indirectly involved in the cell cycle progression in the form of transcription elongation, CDK9 specific inhibitors may be a potential alternative treatment not only for cancer but also other life-threatening diseases. Materials and Methods: Ligand-based and structure-based pharmacophore model was developed for discovering of the new anticancer agents. These models used as three-dimensional query for virtual screening against the chemical structure databases such as Maybridge HitFinder, MDPI, and ZINC. Subsequently, the potential hit compound was filtered by the ADMET and docking score. Results: After applying all filtration, 11 hits were found as potential hits based on good docking scores as well as good ADMET properties. Compound 2-[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3-b] pyridin-6-yl] amino] ethanol was found to be most potent among all the potential hits. These hits could be used as an anticancer agent in near future. Conclusions: So many advances in the treatment of death leading diseases have been made over the past few decades, However, looking for the development in this research ligand-based and structure-based pharmacophore modeling was done, hit1 2-[4-[6-(isopropylamino) pyrimidin-4-yl]-1H-pyrrolo[2,3 b] pyridin-6 yl] amino] ethanol was found to be more potent and selective. It is understandable that these hits could be as selective and potent anticancer agents of cyclin-dependent kinase complex

Identification of polyketide synthase 13 inhibitor: Pharmacophore-based virtual screening and molecular dynamics simulation

Polyketide synthase 13 (Pks13) is one of prominent targets to treat Mycobacterium tuberculosis (Mtb). In the presentstudy, pharmacophore features for Pks13, including two hydrogen bond donors, one hydrogen bond acceptor, and onehydrophobic feature, were built using a novel Pks13 inhibitor, TAM16. The pharmacophore features were then usedto perform virtual screening on ZINC database to identify small molecules of Pks13 inhibitors. The obtained virtualhits of 107 small molecules were subjected to molecular docking studies employing iDock software to reveal theirbinding orientation to Pks13. Furthermore, four best hits, each bound to Pks13, were submitted to 40-ns moleculardynamics simulation to explore their conformational changes throughout simulation. The result showed that all hitcompounds, i.e., Lig79/ZINC09281113, Lig94/ZINC09584070, Lig95/ZINC09209668, and Lig97/ZINC09216165,have better stabilities than that of TAM16 as indicated by their lower values of root-mean-square-deviation and rootmean-square-fluctuation. In a similar way, prediction of binding free energy using molecular mechanics Poisson–Boltzmann Surface Area method showed that all hit compounds have lower binding free energies than that of TAM16,indicating their potential as novel compounds of Pks13 inhibitors.

Structure-based pharmacophore design and screening for potential inhibitors of E protein of dengue virus as a loom for dengue

Dengue virus (DENV) poses a continuous threat worldwide with an estimated 2.5 billion people at the risk of dengueinfection. It was believed to be the infection of the tropical regions, but reports of dengue infection have now extendedand spread around the globe. The dengue E protein is involved in the viral fusion and could thus acts a potentialtarget against dengue virus. In the present study, structure-based pharmacophore design and screening and absorption,distribution, metabolism, excretion, and toxicity (ADMET) analysis using Discovery studio (4.0) was applied toidentify potential hits against the hydrophobic pocket of dengue E protein. The pharmacophore feature of screenedcompounds was further validated and finally three lead compounds were obtained. The pharmacophore model andthe docking study were generated three lead molecules Ophiopoginin D with a binding energy of −146.36 Kcal/mol followed by Calmisttrin D with a binding energy of −118.73 Kcal/mol and BTB 08305 with a binding energy of−99.96 Kcal/mol and exhibited best-fit value. ADMET profile showed that all the three lead molecules are non-toxic,non-carcinogenic, and non-hepatotoxic by in silico study. The compound Calmisttrin D exhibited good blood brainbarrier permeability and human intestinal adsorption, and thus hypothesized to have antiviral activity against denguevirus and so further in vitro and in vivo evaluation is recommended.

In silico predictive for modification of chalcone with pyrazole derivatives as a novel therapeutic compound for targeted breast cancer treatment

One of the most common triggers of breast cancer is over-expression of estrogen receptor alpha (ERα). Long-termtherapy of tamoxifen, an ERα antagonist, can reduce patient’s quality of life because of its side effects. In the previousstudy, 2’,4’-dihydroxy-6-methoxy-3,5-dimethylchalcone (ChalcEA) was isolated as an active compound from theEugenia aquea leaves that is responsible for breast cancer treatment with positive ERα, however, the potency is lowerthan tamoxifen. The aim of this study is to find the best-modified chalcone that binds well with the ERα. Drug designapproaches used in this study were Structure-Based (Autodock 4.1) and Ligand-Based (LiganScout 4.1). Prediction ofabsorption, distribution, and toxicity parameters was employed using preADMET and Toxtree. Interactions betweentamoxifen and ERα were determined and the differences in the binding modes between tamoxifen and chalcones wereobserved. Modifina3 had pharmacophore fit score value of 76.42% and the molecular docking studies showed thelowest free energy binding (∆G) of −11.07 kcal/mol while tamoxifen of −10.15 kcal/mol. Modifina3 had absorptionand distribution properties with the percentage human intestinal absorption of 95.90%, CaCO2 of 46.95%, and proteinplasma binding of 93.55%. Toxicity prediction of Modifina3 was categorized in class III and risk assessment requirescompound specific toxicity data. These results suggest that Modifina3 has the potency to be a novel therapeuticcompound for potent ERα inhibitor targeted breast cancer.

Virtual screening study of cathepsin S natural inhibitor / 中国中药杂志

Cathepsin S is a cysteine protease which is closely related to autoimmune diseases,psoriasis and other diseases. In this study,we used virtual screening method to screen compounds,which from the natural product library of traditional Chinese medicine,with potential inhibitory effect on cathepsin S. The work involved in study on inhibitory mechanism of representative compounds,then analysis of the distribution of these compounds in traditional Chinese medicine and the correlation with disease,so as to provide a new drug research and data-base for cathepsin S. The complex crystal structure of cathepsin S,2FQ9,was used to establish the pharmacophore model of cathepsin S inhibitor,and the best pharmacophore model was selected. As a result,fifty compounds were selected from TCMD database. After molecular docking,65 potential inhibitors were identified. Potential inhibitors can produce multiple intermolecular interactions with targets,resulting in inhibition. There are 58 kinds of traditional Chinese medicines which include 65 natural inhibitors. Data collection and analysis of the nature,flavor xing,channel entry and modern pharmacological effects of these traditional Chinese medicines showed that most of them were related to the biological activity of cathepsin S,which supported the validity of the screening results. Cathepsin S has a certain correlation with autoimmune diseases and can be used as a target for further study of traditional Chinese medicine.

Lipid regulation mechanism and dosage form selection of Xixian Tongshuan Preparation based on molecular simulation methods / 中国中药杂志

Atherosclerosis is the main cause of stroke, and dyslipidemia is the most important risk factor for atherosclerosis. In this paper, pharmacophore and molecular docking models of eight key lipid-lowering targets, namely NPC1 L1, HMG-CoA reductase, SQS, MTP, CETP, PPARα, LXRα and LXRβ, were used to screen out the small molecular database of traditional Chinese medicine(TCM), which was made up of ingredients of thirteen Chinese herbal medicines contained in Xixian Tongshuan Preparation. The screening results indicated that the preparation could showed an effect in regulating lipid on target NPC1 L1, HMG-CoA reductase, LXRβ and SQS through four groups of potential active compounds, namely prupersin A in peach kernel and suffruticoside A in gastrodiaelata, limocitrin-β-D-glucoside in Ligusticum chuanxiong, 2'-(2,3-dihydroxybenzoyl)-sweroside in Pinellia ternate and quercitrin in Panax notoginseng, 4-tert-butyl-2-[(5-tert-butyl-2-hydroxy-phenyl)methoxy-methyl]-6-(hydroxymethyl)phenol in Gastrodia elata. Moreover, the properties and extraction process of the most potentialactive compounds were consistent with the preparation process of Xixian Tongshuan Capsules, which indicated that the capsule had more advantages than the pill in the existing two dosage forms of Xixian Tongshuan Preparation. This study analyzed the pharmacodynamic basis and mechanism of Xixian Tongshuan Capsules in regulating lipid for treating stroke, and provided evidence for its further research and clinical application.

Anti-inflammatory mechanism of Xixian Tongshuan Preparation based on molecular simulation methods / 中国中药杂志

Inflammatory response is caused by exogenous and endogenous stimuli,resulting in a non-specific resistance reaction.After acute ischemic cerebral infarction,inflammatory factors gather and adhere in the ischemic area of leukocyte infiltration,and the released inflammatory factors causes the injury cascade,aggravate the brain tissue damage and the symptoms of neurological deficits,and hinder the repair of brain neurons and the recovery of nerve function. In this paper,the key targets in the arachidonic acid metabolic pathway were studied. The Hiphop pharmacophore model of s PLA2-ⅡA and COX-2 inhibitors was built. According tothe two previously constructed 5-LOX and LTA4 H target inhibitors,the pharmacophore model was used to initially screen out the composition database of all of 13 traditional Chinese medicines in Xixian Tongshuan Preparation. The molecular matching study was carried out by selecting the matching value greater than 0. 6,and the component with the CDOCKER score greater than 80% of the original ligand score was used as the potential active inhibitor of the target. Considering the pharmacophore matching value,the molecular docking score and the interaction between the components and the target,one Chuanxiong component and one safflower component were selected as potential inhibitors of s PLA2-ⅡA; two Chuanxiong components,two Panax notoginseng,one safflower component,one angelica component,one valerian component were taken as a potential inhibitor of COX-2; two Gentiana components,one safflower component,one valerian component,one P. notoginseng component and one Angelica component were taken as potential inhibitors of 5-LOX; and two Gentiana components,two Chuanxiong components,and two safflower components were taken as potential inhibitors of LTA4 H. This study screened out the potential inhibitors of the four targets in a high-efficiency and low-cost manner,and explained that Xixian Tongshuan Preparation showed an effect in the treatment of inflammatory responses caused by ischemic stroke by acting both LOX pathway and COX pathway in the metabolic pathway.

Anti-platelet aggregation mechanism of Xixian Tongshuan Preparation based on molecular simulation methods / 中国中药杂志

The thrombus is a deposit that is formed on the surface of the endovascular or at the site of repair,and known as the main complication of cardiovascular disease and the cause of death. At the same time,thrombus is mainly treated by the following three ways: anticoagulation,anti-platelet aggregation and thrombolysis. In this study,the chemical constituents of seven traditional Chinese medicines in the Xixian Tongshuan Preparation were collected to construct a component database. Subsequently,the pharmacophore were used to screen out the component database,and molecular docking was used to screen out the results of pharmacophore for explaining the material basis and mechanism that Xixian Tongshuan Preparation exerts anti-thrombotic activity by inhibiting platelet aggregation. First of all,P2 Y12,GPⅡb/Ⅲa and PAR1 were selected as study vectors,the optimal models of inhibitors were obtained respectively through verification and evaluation of the pharmacophore models. Afterwards,the component database was screened out by the optimal pharmacophore models of PAR1,P2 Y12 and GP Ⅱ b/Ⅲ a,and the molecular docking method was used to further refine the screening results. The screening results indicated that the anti-platelet aggregation effect of Xixian Tongshuan Preparation was correlated with the inhibition of P2 Y12,PAR1 and GPⅡb/Ⅲa expressions with saffower yellower,hirudin and candidin and notoginseng triterpenes,folinic acid,respectively. The material basis and mechanism of anti-platelet aggregation of Xixian Tongshuan Preparation provided a theoretical basis for the clinical use of the preparation and the lead compounds for the development of anti-platelet aggregation drugs.

Study on Homology Modeling of eEF 2K Protein and Virtual Screening of Its Inhibitors Molecules / 中国药房

OBJECTIVE： To screen potential eEF2K inhibitor molecules， and to provide reference for the design and R&D of eEF2K inhibitor. METHODS： The eEF2K crystal structure model was constructed by homology modeling technique. The model was optimized by Loop optimization and molecular dynamics. With the help of SAVES online server， the above models were evaluated from three aspects such as Verify_3D， EERAT and Laplace diagram. Totally 55 eEF2K inhibitor molecules were collected. Hypogen pharmacophore model with activity prediction ability was constructed based on 28 of them （odd number， as training set） by Insight Ⅱ software and validated by other 27 （even number， as test set）. The optimal pharmacophore model was screened by fitting the predicted and experimental values of activity [i.e. negative logarithm of half inhibitory concentration （pIC50）] and using Ligand profiler thermogram. The virtual screening of small molecules of eEF2K inhibitors was carried out by combining the above pharmacophore model， Lipinski’s five rules and molecular docking method. RESULTS & CONCLUSIONS： The overall quality factor score of the crystal structure model of eEF2K protein was 93.697. Among them， 83.33％ of the amino acid Verify_3D score was more than or equal to 0.2， and 1.7％ of the total amino acids were located in the non-permissible region. The amino acid conformation and skeleton structure of the model were reasonable and the reliability of the model was high. Totally 9 Hypogen pharmacophore models （No. 02-10） with active predictive function were constructed， among which No. 03 pharmacophore model included 2 hydrogen bond receptors and 2 conjugated aromatic rings， which could better distinguish active and inactive molecules. The predicted value of pIC50 fitted the experimental value best （the correlation coefficient was 0.665 3）， and it had good predictive ability and high reliability. Finally， 9 potential eEF2K inhibitor molecules were obtained through virtual screening （pIC50 ranged from 1.074 to 1.185， and Dcoking-score of protein-molecule interaction ranged from －9.730 to －7.467）. Pro268， Asp267， Gln171， Phe121 and Glu212 may be the key amino acids for the interaction between eEF2K inhibitors and target proteins， including hydrogen bonds， salt bridges and hydrophobicity. These 9 molecules are expected to be the lead compounds for the development of eEF2K inhibitors.

Network pharmacology-based analysis of Chinese herbal Naodesheng formula for application to Alzheimer's disease / 中国天然药物

Naodesheng (NDS) formula, which consists of Rhizoma Chuanxiong, Lobed Kudzuvine, Carthamus tinctorius, Radix Notoginseng, and Crataegus pinnatifida, is widely applied for the treatment of cardio/cerebrovascular ischemic diseases, ischemic stroke, and sequelae of cerebral hemorrhage, etc. At present, the studies on NDS formula for Alzheimer's disease (AD) only focus on single component of this prescription, and there is no report about the synergistic mechanism of the constituents in NDS formula for the potential treatment of dementia. Therefore, the present study aimed to predict the potential targets and uncover the mechanisms of NDS formula for the treatment of AD. Firstly, we collected the constituents in NDS formula and key targets toward AD. Then, drug-likeness, oral bioavailability, and blood-brain barrier permeability were evaluated to find drug-like and lead-like constituents for treatment of central nervous system diseases. By combining the advantages of machine learning, molecular docking, and pharmacophore mapping, we attempted to predict the targets of constituents and find potential multi-target compounds from NDS formula. Finally, we built constituent-target network, constituent-target-target network and target-biological pathway network to study the network pharmacology of the constituents in NDS formula. To the best of our knowledge, this represented the first to study the mechanism of NDS formula for potential efficacy for AD treatment by means of the virtual screening and network pharmacology methods.

Network pharmacology-based analysis of Chinese herbal Naodesheng formula for application to Alzheimer's disease / 中国天然药物

Naodesheng (NDS) formula, which consists of Rhizoma Chuanxiong, Lobed Kudzuvine, Carthamus tinctorius, Radix Notoginseng, and Crataegus pinnatifida, is widely applied for the treatment of cardio/cerebrovascular ischemic diseases, ischemic stroke, and sequelae of cerebral hemorrhage, etc. At present, the studies on NDS formula for Alzheimer's disease (AD) only focus on single component of this prescription, and there is no report about the synergistic mechanism of the constituents in NDS formula for the potential treatment of dementia. Therefore, the present study aimed to predict the potential targets and uncover the mechanisms of NDS formula for the treatment of AD. Firstly, we collected the constituents in NDS formula and key targets toward AD. Then, drug-likeness, oral bioavailability, and blood-brain barrier permeability were evaluated to find drug-like and lead-like constituents for treatment of central nervous system diseases. By combining the advantages of machine learning, molecular docking, and pharmacophore mapping, we attempted to predict the targets of constituents and find potential multi-target compounds from NDS formula. Finally, we built constituent-target network, constituent-target-target network and target-biological pathway network to study the network pharmacology of the constituents in NDS formula. To the best of our knowledge, this represented the first to study the mechanism of NDS formula for potential efficacy for AD treatment by means of the virtual screening and network pharmacology methods.

Multi-target drug design strategy and its research progress / 药学学报

Currently, single-target drugs are often difficult to achieve the desired results in the treatment of multifactorial diseases such as tumors, cardiovascular and endocrine diseases, and may also cause toxicity. Multi-target drugs can improve the efficacy, reduce side effect and drug resistance by regulating multiple links of the disease, showing good prospects for the application. The main aim of this article is to review the strategies of designing multi-target directed ligands (MTDLs) (including conjugated-pharmacophore, fused-pharmacophore and merged-pharmacophore) and the research progress in recent years. The existing problems and challenges of multi-target drugs are also discussed, to provide new ideas for the study of multi-target drugs.