4D-QSAR studies of coumarin derivatives as HIV-1 integrase 3′-processing inhibitors

4D-QSAR, ADMET properties, and molecular dynamics simulations for designing N-substituted urea/thioureas as human glutaminyl cyclase inhibitors

Human glutaminyl cyclase (hQC) inhibitors have great potential to be used as anti- Alzheimer's disease (AD) agents by reducing the toxic pyroform of β-amyloid in the brains of AD patients. The four-dimensional quantitative structure activity relationship (4D-QSAR) model of N-substituted urea/thioureas was established with satisfying predictive ability and statistical reliability (Q2 = 0.521, R2 = 0.933, R2prep = 0.619). By utilizing the developed 4D-QSAR model, a set of new N-substituted urea/thioureas was designed and evaluated for their Absorption Distribution Metabolism Excretion and Toxicity (ADMET) properties. The results of molecular dynamics (MD) simulations, Principal component analysis (PCA), free energy landscape (FEL), dynamic cross-correlation matrix (DCCM) and molecular mechanics generalized Born Poisson-Boltzmann surface area (MM-PBSA) free energy calculations, revealed that the designed compounds were remained stable in protein binding pocket and compounds b ∼ f (-35.1 to -44.55 kcal/mol) showed higher binding free energy than that of compound 14 (-33.51 kcal/mol). The findings of this work will be a theoretical foundation for further research and experimental validation of urea/thiourea derivatives as hQC inhibitors.

4D-QSAR Molecular Modeling and Analysis of Flavonoid Derivatives as Acetylcholinesterase Inhibitors

Flavonoids are potential strikingly natural compounds with antioxidant activity and acetylcholinesterase (AChE) inhibitory activity for treating Alzheimer's disease (AD). In present study, in line with our interests in flavonoid derivatives as AChE inhibitors, a four-dimensional quantitative structure-activity relationship (4D-QSAR) molecular model was proposed. The data required to perform 4D-QSAR analysis includes 52 compounds reported in the literature, usually analogs, and their measured biological activities in a common assay. The model was generated by a complete set of 4D-QSAR program which was written by our group. The best model was found after trying multiple experiments. It had a good predictive ability with the cross-validation correlation coefficient Q² = 0.77, the internal validation correlation coefficient R² = 0.954, and the external validation correlation coefficient R²_pred = 0.715. The molecular docking analysis was also carried out to understand exceedingly the interactions between flavonoids and the AChE targets, which was in good agreement with the 4D-QSAR model. Based on the information provided by the 4D-QSAR model and molecular docking analysis, the idea for optimizing the structures of flavonoids as AChE inhibitors was put forward which maybe provide theoretical guidance for the research and development of new AChE inhibitors.

Classification and Design of HIV-1 Integrase Inhibitors Based on Machine Learning

A key enzyme in human immunodeficiency virus type 1 (HIV-1) life cycle, integrase (IN) aids the integration of viral DNA into the host DNA, which has become an ideal target for the development of anti-HIV drugs. A total of 1785 potential HIV-1 IN inhibitors were collected from the databases of ChEMBL, Binding Database, DrugBank, and PubMed, as well as from 40 references. The database was divided into the training set and test set by random sampling. By exploring the correlation between molecular descriptors and inhibitory activity, it is found that the classification and specific activity data of inhibitors can be more accurately predicted by the combination of molecular descriptors and molecular fingerprints. The calculation of molecular fingerprint descriptor provides the additional substructure information to improve the prediction ability. Based on the training set, two machine learning methods, the recursive partition (RP) and naive Bayes (NB) models, were used to build the classifiers of HIV-1 IN inhibitors. Through the test set verification, the RP technique accurately predicted 82.5% inhibitors and 86.3% noninhibitors. The NB model predicted 88.3% inhibitors and 87.2% noninhibitors with correlation coefficient of 85.2%. The results show that the prediction performance of NB model is slightly better than that of RP, and the key molecular segments are also obtained. Additionally, CoMFA and CoMSIA models with good activity prediction ability both were constructed by exploring the structure-activity relationship, which is helpful for the design and optimization of HIV-1 IN inhibitors.

Coumarin-based derivatives with potential anti-HIV activity

Acquired immunodeficiency syndrome (AIDS), as a result of human immunodeficiency virus (HIV) infection which leads to severe suppression of immune functions, is an enormous world-wide health threat. The anti-HIV agents are critical for the HIV/AIDS therapy, but the generation of viral mutants and the severe side effects of the anti-HIV agents pose serious hurdles in the treatment of HIV infection, and creat an urgent need to develop novel anti-HIV agents. The plant-derived compounds possess structural and mechanistic diversity, and among them, coumarin-based derivatives have the potential to inhibit different stages in the HIV replication cycle, inclusive of virus-host cell attachment, cell membrane fusion, integration, assembly besides the conventional target like inhibition of the reverse transcriptase, protease, and integrase. Moreover, (+)-calanolide A, a coumarin-based natural product, is a potential anti-HIV agent. Thus, coumarin-based derivatives are useful scaffolds for the development of anti-HIV agents. This review article describes the recent progress in the discovery, structural modification, and structure-activity relationship studies of potent anti-HIV coumarin-based derivatives including natural coumarin compounds, synthetic hybrids, dimers, and other synthetic derivatives covering articles published between 2000 and 2020.

Chromenone derivatives as a versatile scaffold with dual mode of inhibition of HIV-1 reverse transcriptase-associated Ribonuclease H function and integrase activity

A number of compounds targeting different processes of the Human Immunodeficiency Virus type 1 (HIV-1) life cycle have been developed in the continuing fight against AIDS. Coumarin-based molecules already proved to act as HIV-1 Protease (PR) or Integrase (IN) inhibitors and also to target HIV-1 reverse transcriptase (RT), blocking the DNA-dependent DNA-polymerase activity or the RNA-dependent DNA-polymerase activity working as common NNRTIs. In the present study, with the aim to exploit a coumarin-based scaffold to achieve the inhibition of multiple viral coded enzymatic functions, novel 4-hydroxy-2H, 5H-pyrano (3, 2-c) chromene-2, 5-dione derivatives were synthesized. The modeling studies calculated the theoretical binding affinity of the synthesized compounds on both HIV-1 IN and RT-associated Ribonuclease H (RNase H) active sites, which was confirmed by biological assays. Our results provide a basis for the identification of dual HIV-1 IN and RT RNase H inhibitors compounds.

Pharmacological and Nutritional Effects of Natural Coumarins and Their Structure-Activity Relationships

Coumarins are fused benzene and pyrone ring systems with a wide spectrum of bioactivities, including antitumor, anti-inflammation, antiviral, and antibacterial effects. In this paper, the current development of coumarin-based drugs is introduced, and their structure-activity relationship is discussed by reviewing the relevant literature published in the past 20 years. Coumarin molecules can be customized by the target site to prevent systemic side effects by virtue of structural modification. The ortho-phenolic hydroxyl on the benzene ring has remarkable antioxidant and antitumor activities. Coumarins with aryl groups at the C-4 position have good activities in anti-HIV, antitumor, anti-inflammation, and analgesia. C-3 phenylcoumarins have strong anti-HIV and antioxidant effects. Tetracycline pyranocoumarins can significantly inhibit HIV; osthol structural analogues have antimicrobial activity. Praeruptorin C and its derivatives play an important role in lowering blood pressure and dilating coronary arteries, and khellactone derivatives have significant inhibitory effects on AIDS, cancer, and cardiovascular diseases. It is concluded that the specific site on the core structure of coumarin exhibits one or more activities due to the electronic or steric effects of the substituents. This review is intended to be conducive to rational design and development of more active and less toxic agents with a coumarin scaffold.