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Nimal S, Kumbhar N, Saruchi, Rathore S, Naik N, Paymal S, Gacche RN. Apigenin and its combination with Vorinostat induces apoptotic-mediated cell death in TNBC by modulating the epigenetic and apoptotic regulators and related miRNAs. Sci Rep 2024; 14:9540. [PMID: 38664447 PMCID: PMC11045774 DOI: 10.1038/s41598-024-60395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is a metastatic disease and a formidable treatment challenge as it does not respond to existing therapies. Epigenetic regulators play a crucial role in the progression and metastasis by modulating the expression of anti-apoptotic, pro-apoptotic markers and related miRNAs in TNBC cells. We have investigated the anti-TNBC potential of dietary flavonoid 'Apigenin' and its combination with Vorinostat on MDA-MB-231 cells. At Apigenin generated ROS, inhibited cell migration, arrested the cell cycle at subG0/G1 phases, and induced apoptotic-mediated cell death. Apigenin reduced the expression of the class-I HDACs at the transcriptomic and proteomic levels. In the immunoblotting study, Apigenin has upregulated pro-apoptotic markers and downregulated anti-apoptotic proteins. Apigenin inhibited the enzymatic activity of HDAC/DNMT and increased HAT activity. Apigenin has manifested its effect on miRNA expression by upregulating the tumor-suppressor miR-200b and downregulation oncomiR-21. Combination study reduced the growth of TNBC cells synergistically by modulating the expression of epigenetic and apoptotic regulators. Molecular docking and MD simulations explored the mechanism of catalytic inhibition of HDAC1 and HDAC3 and supported the in-vitro studies. The overall studies demonstrated an anti-TNBC potential of Apigenin and may help to design an effective strategy to treat metastatic phenotype of TNBC.
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Affiliation(s)
- Snehal Nimal
- Department of Biotechnology, Savitribai Phule Pune University (SPPU), Pune, 411007, Maharashtra (MS), India
| | - Navanath Kumbhar
- Department of Biotechnology, Savitribai Phule Pune University (SPPU), Pune, 411007, Maharashtra (MS), India
- Medical Information Management, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (MS), India
| | - Saruchi
- Department of Biotechnology, Savitribai Phule Pune University (SPPU), Pune, 411007, Maharashtra (MS), India
| | - Shriya Rathore
- Department of Biotechnology, Savitribai Phule Pune University (SPPU), Pune, 411007, Maharashtra (MS), India
| | - Nitin Naik
- Department of Microbiology, Shivaji University, Kolhapur, 416004, Maharashtra (MS), India
| | - Sneha Paymal
- Department of Microbiology, Shivaji University, Kolhapur, 416004, Maharashtra (MS), India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University (SPPU), Pune, 411007, Maharashtra (MS), India.
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Samizo S, Kaneko H. Predictive Modeling of HMG-CoA Reductase Inhibitory Activity and Design of New HMG-CoA Reductase Inhibitors. ACS OMEGA 2023; 8:27247-27255. [PMID: 37546661 PMCID: PMC10399166 DOI: 10.1021/acsomega.3c02567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023]
Abstract
As blood cholesterol increases, it accumulates in the intima of blood vessels, elevating the risk of atherosclerosis and coronary artery disease. Drugs that inhibit enzymes essential for cholesterol synthesis are effective in improving blood cholesterol levels. Statins are used to treat hypercholesterolemia as they inhibit 3-hydroxyl-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR), the rate-limiting enzyme in cholesterol synthesis. Statins are known to exert their effects by translocating to the liver, where they are taken up by the organic anion transporting polypeptide 1B1 (OATP1B1). Therefore, we hypothesized that a compound with high HMGR inhibitory activity and high affinity for OATP1B1 would be an excellent new therapeutic agent for hypercholesterolemia with increased liver selectivity and fewer side effects. In this study, we developed two models for predicting HMGR inhibitory activity and OATP1B1 affinity to propose the chemical structure of a new therapeutic agent for hypercholesterolemia with both high inhibitory activity and high liver selectivity. HMGR inhibitory activity and OATP1B1 affinity prediction models were constructed with high prediction accuracy for the test data: r2 = 0.772 and 0.768, respectively. New chemical structures were then input into these models to search for candidate compounds. We found compounds with higher HMGR inhibitory activity and OATP1B1 affinity than rosuvastatin, the most recently developed statin drug, and compounds that did not have a common structure of statins with high HMGR inhibitory activity.
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Nartea R, Mitoiu BI, Ghiorghiu I. The Link between Magnesium Supplements and Statin Medication in Dyslipidemic Patients. Curr Issues Mol Biol 2023; 45:3146-3167. [PMID: 37185729 PMCID: PMC10136538 DOI: 10.3390/cimb45040205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 05/17/2023] Open
Abstract
Many investigations have discovered a connection between statins and magnesium supplements. On one hand, increasing research suggests that chronic hypomagnesemia may be an important factor in the etiology of some metabolic illnesses, including obesity and overweight, insulin resistance and type 2 diabetes mellitus, hypertension, alterations in lipid metabolism, and low-grade inflammation. Chronic metabolic problems seem to be prevented by a high Mg intake combined with diet and/or supplements. On the other hand, it is known that statins lower the frequency of cardiac events, stroke, and mortality, not by lowering LDL-C, but by the capacity to reduce mevalonate formation. That will enhance endothelial function, inhibit vascular smooth muscle cell proliferation and migration and encourage macrophages to promote plaque stability and regression while reducing inflammation. Taking these factors into consideration, we did an extensive analysis of the relevant literature, comparing the effects of Mg2 and statin medications on lipoproteins and, implicitly, on the key enzymes involved in cholesterol metabolism.
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Affiliation(s)
- Roxana Nartea
- Clinical Department 9, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- National Institute for Rehabilitation, Physical Medicine and Balneoclimatology, 030079 Bucharest, Romania
| | - Brindusa Ilinca Mitoiu
- Clinical Department 9, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Agrippa Ionescu Clinical Emergency Hospital, 077016 Bucharest, Romania
| | - Ioana Ghiorghiu
- Clinical Department 9, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- National Institute for Rehabilitation, Physical Medicine and Balneoclimatology, 030079 Bucharest, Romania
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Madrigal-Aguilar DA, Gonzalez-Silva A, Rosales-Acosta B, Bautista-Crescencio C, Ortiz-Álvarez J, Escalante CH, Sánchez-Navarrete J, Hernández-Rodríguez C, Chamorro-Cevallos G, Tamariz J, Villa-Tanaca L. Antifungal Activity of Fibrate-Based Compounds and Substituted Pyrroles That Inhibit the Enzyme 3-Hydroxy-methyl-glutaryl-CoA Reductase of Candida glabrata (CgHMGR), Thus Decreasing Yeast Viability and Ergosterol Synthesis. Microbiol Spectr 2022; 10:e0164221. [PMID: 35377226 PMCID: PMC9045318 DOI: 10.1128/spectrum.01642-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Due to the emergence of multidrug-resistant strains of yeasts belonging to the Candida genus, there is an urgent need to discover antifungal agents directed at alternative molecular targets. The aim of the current study was to evaluate the capacity of three different series of synthetic compounds to inhibit the Candida glabrata enzyme denominated 3-hydroxy-methyl-glutaryl-CoA reductase and thus affect ergosterol synthesis and yeast viability. Compounds 1c (α-asarone-related) and 5b (with a pyrrolic core) were selected as the best antifungal candidates among over 20 synthetic compounds studied. Both inhibited the growth of fluconazole-resistant and fluconazole-susceptible C. glabrata strains. A yeast growth rescue experiment based on the addition of exogenous ergosterol showed that the compounds act by inhibiting the mevalonate synthesis pathway. A greater recovery of yeast growth occurred for the C. glabrata 43 fluconazole-resistant (versus fluconazole-susceptible) strain and after treatment with 1c (versus 5b). Given that the compounds decreased the concentration of ergosterol in the yeast strains, they probably target ergosterol synthesis. According to the docking analysis, the inhibitory effect of 1c and 5b could possibly be mediated by their interaction with the amino acid residues of the catalytic site of the enzyme. Since 1c displayed higher binding energy than α-asarone and 5b, it is the best candidate for further research, which should include structural modifications to increase its specificity and potency. The derivatives could then be examined with in vivo animal models using a therapeutic dose. IMPORTANCE Within the context of the COVID-19 pandemic, there is currently an epidemiological alert in health care services due to outbreaks of Candida auris, Candida glabrata, and other fungal species multiresistant to conventional antifungals. Therefore, it is important to propose alternative molecular targets, as well as new antifungals. The three series of synthetic compounds herein designed and synthesized are inhibitors of ergosterol synthesis in yeasts. Of the more than 20 compounds studied, two were selected as the best antifungal candidates. These compounds were able to inhibit the growth and synthesis of ergosterol in C. glabrata strains, whether susceptible or resistant to fluconazole. The rational design of antifungal compounds derived from clinical drugs (statins, fibrates, etc.) has many advantages. Future studies are needed to modify the structure of the two present test compounds to obtain safer and less toxic antifungals. Moreover, it is important to carry out a more in-depth mechanistic approach.
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Affiliation(s)
- Damián A. Madrigal-Aguilar
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Adilene Gonzalez-Silva
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Blanca Rosales-Acosta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Celia Bautista-Crescencio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jossué Ortiz-Álvarez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Carlos H. Escalante
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Germán Chamorro-Cevallos
- Departamento de Farmacia, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Joaquín Tamariz
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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Fatoki TH. Effect of pH on structural dynamics of HMG-CoA reductase and binding affinity to β-sitosterol. J Biomol Struct Dyn 2022:1-7. [PMID: 35470784 DOI: 10.1080/07391102.2022.2067240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR; EC 1.1.1.34) catalyzes the conversion of (3S)-hydroxy-3-methylglutaryl-CoA (HMG-CoA) to mevalonic acid, which has been defined as the rate-limiting step in the synthesis of cholesterol and other isoprenoids, thus playing a critical role in cellular cholesterol homeostasis. In this study, the effect of changing pH on the structural dynamics and binding affinity of HMGCR were investigated by molecular dynamics simulation using OpenMM, and molecular docking using Autodock Vina. The results pinpoint pH 8.0 for optimum structural stability/activity of HMGCR, and the insightful relationships between pH, structural dynamics radius of gyration (Rg) or root mean square deviation (RMSD), and binding affinity of HMGCR. This method will be useful to predict the pH for the uncharacterized human proteins, toward biomedical and biotechnological applicationsCommunicated by Ramaswamy H. Sarma.
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6
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Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Sci Rep 2022; 12:1712. [PMID: 35110603 PMCID: PMC8810932 DOI: 10.1038/s41598-022-05698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 02/08/2023] Open
Abstract
In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model ‘Hypo 1’ showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
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Marine-derived polygalactofucan and its β-2-deoxy-amino-substituted glucopyranan composite attenuate 3-hydroxy-3-methylglutaryl-CoA reductase: prospective natural anti-dyslipidemic leads. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02482-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hanna CB, Yao S, Martin M, Schönbrunn E, Georg GI, Jensen JT, Cuellar RAD. Identification and Screening of Selective WEE2 Inhibitors to Develop Non-Hormonal Contraceptives that Specifically Target Meiosis. ChemistrySelect 2019; 4:13363-13369. [PMID: 32190728 PMCID: PMC7079731 DOI: 10.1002/slct.201903696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022]
Abstract
We used a progressive elimination strategy to identify oocyte-specific WEE2 kinase inhibitors for potential non-hormonal contraceptives that target meiosis. Beginning with an in-house library of over 300,000 compounds, virtual high throughput screening identified 57 WEE2 inhibitors with preferential predicted binding over the somatic variant WEE1. Seven compounds were further evaluated in vitro by enzyme-linked immunosorbent assay to measure biochemical inhibition on WEE1 and WEE2 phosphorylation of CDK1. To assess specificity, we evaluated WEE2-mediated inhibition of meiosis using in vitro oocyte fertilization, and WEE1-mediated inhibition of mitosis using a somatic cell proliferation assay. Our results from these assays identified three candidates for further development: 6-(2,6-dichlorophenyl)-2-((4-(2-(diethylamino)ethoxy) phenyl)amino)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one (2), 6-(2,6-dichlorophenyl)-8-methyl-2-((4-morpholinophenyl) amino)pyrido[2,3-d]pyrimidin-7(8H)-one (12), and 3-((6-(2,6-dichlorophenyl)-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino)benzoic acid (16).
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Affiliation(s)
- Carol B Hanna
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 Northwest 185 Avenue, Beaverton, OR 97006 (USA)
| | - Shan Yao
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 Northwest 185 Avenue, Beaverton, OR 97006 (USA)
| | - Mat Martin
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612 (USA)
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612 (USA)
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street Southeast, Minneapolis, MN 55414 (USA)
| | - Jeffrey T Jensen
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 Northwest 185 Avenue, Beaverton, OR 97006 (USA)
- Department of Obstetrics & Gynecology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239 (USA)
| | - Rebecca A D Cuellar
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street Southeast, Minneapolis, MN 55414 (USA)
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Gulcan HO, Yigitkan S, Orhan IE. The Natural Products as Hydroxymethylglutaryl-Coa Reductase Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181112144353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
High cholesterol and triglyceride levels are mainly related to further generation of lifethreating
metabolism disorders including cardiovascular system diseases. Therefore,
hypercholesterolemia (i.e., also referred to as hyperlipoproteinemia) is a serious disease state, which
must be controlled. Currently, the treatment of hypercholesterolemia is mainly achieved through the
employment of statins in the clinic, although there are alternative drugs (e.g., ezetimibe,
cholestyramine). In fact, the original statins are natural products directly obtained from fungi-like
molds and mushrooms and they are potent inhibitors of hydroxymethylglutaryl-CoA reductase, the
key enzyme in the biosynthesis of cholesterol. This review focuses on the first identification of
natural statins, their synthetic and semi-synthetic analogues, and the validation of
hydroxymethylglutaryl-CoA reductase as a target in the treatment of hypercholesterolemia.
Furthermore, other natural products that have been shown to possess the potential to inhibit
hydroxymethylglutaryl-CoA reductase are also reviewed with respect to their chemical structures.
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Affiliation(s)
- Hayrettin Ozan Gulcan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, TRNC, via Mersin 10, Turkey
| | - Serkan Yigitkan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Dicle University, 06330 Diyarbakir, Turkey
| | - Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Ankara, Turkey
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10
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Sun Z, Wang X, Zhang JZ. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Pharmacodynamics and potential synergistic effects of Mai-Luo-Ning injection on cardiovascular protection, based on molecular docking. Chin J Nat Med 2015; 13:815-822. [PMID: 26614456 DOI: 10.1016/s1875-5364(15)30085-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/20/2022]
Abstract
As a computer-assisted approach, molecular docking has been universally applied in drug research and development and plays an important role in the investigation and evaluation of herbal medicines. Herein, the method was used to estimate the pharmacodynamics of Mai-Luo-Ning injection, a traditional Chinese compound herbal prescription. Through investigating the interactions between several important proteins in cardiovascular system and characteristic components of the formula, its effect on cardiovascular protection was evaluated. Results showed the differences in the interactions between each component and the selected target proteins and revealed the possible mechanisms for synergistic effects of various characteristic components on cardiovascular protection. The study provided scientific evidence supporting the mechanistic study of the interactions among multi-components and targets, offering a general approach to investigating the pharmacodynamics of complicated materials in compound herbal prescriptions.
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Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling. Acta Pharmacol Sin 2015; 36:998-1012. [PMID: 26051108 DOI: 10.1038/aps.2015.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/27/2015] [Indexed: 01/04/2023] Open
Abstract
AIM Recent evidence suggests that aldo-keto reductase family 1 B10 (AKR1B10) may be a potential diagnostic or prognostic marker of human tumors, and that AKR1B10 inhibitors offer a promising choice for treatment of many types of human cancers. The aim of this study was to identify novel chemical scaffolds of AKR1B10 inhibitors using in silico approaches. METHODS The 3D QSAR pharmacophore models were generated using HypoGen. A validated pharmacophore model was selected for virtual screening of 4 chemical databases. The best mapped compounds were assessed for their drug-like properties. The binding orientations of the resulting compounds were predicted by molecular docking. Density functional theory calculations were carried out using B3LYP. The stability of the protein-ligand complexes and the final binding modes of the hit compounds were analyzed using 10 ns molecular dynamics (MD) simulations. RESULTS The best pharmacophore model (Hypo 1) showed the highest correlation coefficient (0.979), lowest total cost (102.89) and least RMSD value (0.59). Hypo 1 consisted of one hydrogen-bond acceptor, one hydrogen-bond donor, one ring aromatic and one hydrophobic feature. This model was validated by Fischer's randomization and 40 test set compounds. Virtual screening of chemical databases and the docking studies resulted in 30 representative compounds. Frontier orbital analysis confirmed that only 3 compounds had sufficiently low energy band gaps. MD simulations revealed the binding modes of the 3 hit compounds: all of them showed a large number of hydrogen bonds and hydrophobic interactions with the active site and specificity pocket residues of AKR1B10. CONCLUSION Three compounds with new structural scaffolds have been identified, which have stronger binding affinities for AKR1B10 than known inhibitors.
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Zeng L, Yan J, Luo L, Zhang D. Effects of Pu-erh tea aqueous extract (PTAE) on blood lipid metabolism enzymes. Food Funct 2015; 6:2008-16. [DOI: 10.1039/c5fo00362h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Effects of Pu-erh tea aqueous extract (PTAE) on blood lipid metabolism enzymes (e.g.HMGR) are assayedin vitro.
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Affiliation(s)
- Liang Zeng
- College of Food Science
- Southwest University
- Chongqing
- China
- TAETEA Group Postdoctoral Research Station
| | - Jingna Yan
- College of Food Science
- Southwest University
- Chongqing
- China
| | - Liyong Luo
- College of Food Science
- Southwest University
- Chongqing
- China
| | - Dongying Zhang
- College of Longrun Pu-erh Tea
- Yunnan Agricultural University
- Kunming
- China
- TAETEA Group Postdoctoral Research Station
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