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Siddiqui NF, Vishwakarma P, Thakur S, Jadhav HR. Bioactivity predictions and virtual screening using machine learning predictive model. J Biomol Struct Dyn 2024:1-20. [PMID: 38217308 DOI: 10.1080/07391102.2023.2300132] [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: 09/20/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Recently, there has been significant attention on machine learning algorithms for predictive modeling. Prediction models for enzyme inhibitors are limited, and it is essential to account for chemical biases while developing them. The lack of repeatability in available models and chemical bias issues constrain drug discovery and development. A new prediction model for enzyme inhibitors has been developed, and the model efficacy was checked using Dipeptidyl peptidase 4 (DPP-4) inhibitors. A Python script was prepared and can be provided for personal use upon request. Among various machine learning algorithms, it was found that Random Forest offers the best accuracy. Two models were compared, one with diverse training and test data and the other with a random split. It was concluded that machine learning predictive models based on the Murcko scaffold can address chemical bias concerns. In-silico screening of the Drug Bank database identified two molecules against DPP-4, which are previously proven hit molecules. The approach was further validated through molecular docking studies and molecular dynamics simulations, demonstrating the credibility and relevance of the developed model for future investigations and potential translation into clinical applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Noor Fatima Siddiqui
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Pinky Vishwakarma
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Shikha Thakur
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Hemant R Jadhav
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
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Saini K, Sharma S, Khan Y. DPP-4 inhibitors for treating T2DM - hype or hope? an analysis based on the current literature. Front Mol Biosci 2023; 10:1130625. [PMID: 37287751 PMCID: PMC10242023 DOI: 10.3389/fmolb.2023.1130625] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
DPP-4 inhibition is an interesting line of therapy for treating Type 2 Diabetes Mellitus (T2DM) and is based on promoting the incretin effect. Here, the authors have presented a brief appraisal of DPP-4 inhibitors, their modes of action, and the clinical efficiency of currently available drugs based on DPP-4 inhibitors. The safety profiles as well as future directions including their potential application in improving COVID-19 patient outcomes have also been discussed in detail. This review also highlights the existing queries and evidence gaps in DPP-4 inhibitor research. Authors have concluded that the excitement surrounding DPP-4 inhibitors is justified because in addition to controlling blood glucose level, they are good at managing risk factors associated with diabetes.
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Natural Compounds as DPP-4 Inhibitors: 3D-Similarity Search, ADME Toxicity, and Molecular Docking Approaches. Symmetry (Basel) 2022. [DOI: 10.3390/sym14091842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Type 2 diabetes mellitus is one of the most common diseases of the 21st century, caused by a sedentary lifestyle, poor diet, high blood pressure, family history, and obesity. To date, there are no known complete cures for type 2 diabetes. To identify bioactive natural products (NPs) to manage type 2 diabetes, the NPs from the ZINC15 database (ZINC-NPs DB) were screened using a 3D shape similarity search, molecular docking approaches, and ADMETox approaches. Frequently, in silico studies result in asymmetric structures as “hit” molecules. Therefore, the asymmetrical FDA-approved diabetes drugs linagliptin (8-[(3R)-3-aminopiperidin-1-yl]-7-but-2-ynyl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]purine-2,6-dione), sitagliptin ((3R)-3-amino-1-[3-(trifluoromethyl)-6,8-dihydro-5H-[1,2,4]triazolo[4,3-a]pyrazin-7-yl]-4-(2,4,5-trifluorophenyl)butan-1-one), and alogliptin (2-[[6-[(3R)-3-aminopiperidin-1-yl]-3-methyl-2,4-dioxopyrimidin-1-yl]methyl]benzonitrile) were used as queries to virtually screen the ZINC-NPs DB and detect novel potential dipeptidyl peptidase-4 (DPP-4) inhibitors. The most promising NPs, characterized by the best sets of similarity and ADMETox features, were used during the molecular docking stage. The results highlight that 11 asymmetrical NPs out of 224,205 NPs are potential DPP-4 candidates from natural sources and deserve consideration for further in vitro/in vivo tests.
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Silybin induces endothelium-dependent vasodilation via TRPV4 channels in mouse mesenteric arteries. Hypertens Res 2022; 45:1954-1963. [PMID: 36056206 DOI: 10.1038/s41440-022-01000-4] [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: 03/24/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 11/08/2022]
Abstract
Silybin is a flavonolignan extracted from the seeds of Silybum marianum that has been used as a dietary supplement for treating hepatic diseases and components of metabolic syndrome such as diabetes, obesity and hypertension. Transient receptor potential vanilloid 4 (TRPV4) channels are Ca2+-permeable, nonselective cation channels that regulate vascular endothelial function and blood flow. However, the relationship between silybin and TRPV4 channels in small mesenteric arteries remains unknown. In our study, we carried out a molecular docking experiment by using Discovery Studio v3.5 to predict the binding of silybin to TRPV4. Activation of TRPV4 with silybin was detected via intracellular Ca2+ concentration ([Ca2+]i) measurement and patch clamp experiments. The molecular docking results showed that silybin was likely to bind to the ankyrin repeat domain of TPRV4. [Ca2+]i measurements in mesenteric arterial endothelial cells (MAECs) and TRPV4-overexpressing HEK293 (TRPV4-HEK293) cells demonstrated that silybin induced Ca2+ influx by activating TRPV4 channels. The patch clamp experiments indicated that in TRPV4-HEK293 cells, silybin induced TRPV4-mediated cation currents. In addition, in high-salt-induced hypertensive mice, oral administration of silybin decreased systolic blood pressure (SBP) and significantly improved the arterial dilatory response to acetylcholine. Our findings provide the first evidence that silybin could induce mesenteric endothelium-dependent vasodilation and reduce blood pressure in high-salt-induced hypertensive mice via TRPV4 channels, thereby revealing the potential effect of silybin on preventing endothelial dysfunction-related cardiovascular diseases.
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Li TT, Peng C, Wang JQ, Xu ZJ, Su MB, Li J, Zhu WL, Li JY. Distal mutation V486M disrupts the catalytic activity of DPP4 by affecting the flap of the propeller domain. Acta Pharmacol Sin 2022; 43:2147-2155. [PMID: 34907358 PMCID: PMC8669218 DOI: 10.1038/s41401-021-00818-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/06/2021] [Indexed: 12/13/2022] Open
Abstract
Dipeptidyl peptidase-4 (DPP4) plays a crucial role in regulating the bioactivity of glucagon-like peptide-1 (GLP-1) that enhances insulin secretion and pancreatic β-cell proliferation, making it a therapeutic target for type 2 diabetes. Although the crystal structure of DPP4 has been determined, its structure-function mechanism is largely unknown. Here, we examined the biochemical properties of sporadic human DPP4 mutations distal from its catalytic site, among which V486M ablates DPP4 dimerization and causes loss of enzymatic activity. Unbiased molecular dynamics simulations revealed that the distal V486M mutation induces a local conformational collapse in a β-propeller loop (residues 234-260, defined as the flap) and disrupts the dimerization of DPP4. The "open/closed" conformational transitions of the flap whereby capping the active site, are involved in the enzymatic activity of DPP4. Further site-directed mutagenesis guided by theoretical predictions verified the importance of the conformational dynamics of the flap for the enzymatic activity of DPP4. Therefore, the current studies that combined theoretical modeling and experimental identification, provide important insights into the biological function of DPP4 and allow for the evaluation of directed DPP4 genetic mutations before initiating clinical applications and drug development.
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Affiliation(s)
- Teng-teng Li
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, the National Drug Screening Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Cheng Peng
- grid.9227.e0000000119573309CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ji-qiu Wang
- grid.16821.3c0000 0004 0368 8293Department of Endocrinology and Metabolism, China National Research Center for Metabolic Diseases, National Key Laboratory for Medical Genomes, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200025 China
| | - Zhi-jian Xu
- grid.9227.e0000000119573309CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ming-bo Su
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, the National Drug Screening Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Jia Li
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, the National Drug Screening Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Wei-liang Zhu
- grid.9227.e0000000119573309CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jing-ya Li
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, the National Drug Screening Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
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Computational Study of Asian Propolis Compounds as Potential Anti-Type 2 Diabetes Mellitus Agents by Using Inverse Virtual Screening with the DIA-DB Web Server, Tanimoto Similarity Analysis, and Molecular Dynamic Simulation. Molecules 2022; 27:molecules27133972. [PMID: 35807241 PMCID: PMC9268573 DOI: 10.3390/molecules27133972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
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Antioxidant and Antihyperglycemic Effects of Ephedra foeminea Aqueous Extract in Streptozotocin-Induced Diabetic Rats. Nutrients 2022; 14:nu14112338. [PMID: 35684137 PMCID: PMC9182796 DOI: 10.3390/nu14112338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Ephedra foeminea is known in Jordan as Alanda and traditionally. It is used to treat respiratory symptoms such as asthma and skin rashes as an infusion in boiling water. The purpose of this study was to determine the antidiabetic property of Ephedra foeminea aqueous extract in streptozotocin-induced diabetic rats. Methods: The aqueous extract of Ephedra foeminea plant was used to determine the potential of its efficacy in the treatment of diabetes, and this extract was tested on diabetic rats as a model. The chemical composition of Ephedra foeminea aqueous extract was determined using liquid chromatography–mass spectrometry (LC-MS). Antioxidant activity was assessed using two classical assays (ABTS and DPPH). Results: The most abundant compounds in the Ephedra foeminea extract were limonene (6.3%), kaempferol (6.2%), stearic acid (5.9%), β-sitosterol (5.5%), thiamine (4.1%), riboflavin (3.1%), naringenin (2.8%), kaempferol-3-rhamnoside (2.3%), quercetin (2.2%), and ferulic acid (2.0%). The antioxidant activity of Ephedra foeminea aqueous extract was remarkable, as evidenced by radical scavenging capacities of 12.28 mg Trolox/g in ABTS and 72.8 mg GAE/g in DPPH. In comparison to control, induced diabetic rats treated with Ephedra foeminea extract showed significant improvement in blood glucose levels, lipid profile, liver, and kidney functions. Interleukin 1 and glutathione peroxidase levels in the spleen, pancreas, kidney, and liver of induced diabetic rats treated with Ephedra foeminea extract were significantly lower than in untreated diabetic rats. Conclusions: Ephedra foeminea aqueous extract appears to protect diabetic rats against oxidative stress and improve blood parameters. In addition, it has antioxidant properties that might be very beneficial medicinally.
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QSAR, Docking, and Molecular Dynamics Simulation Studies of Sigmacidins as Antimicrobials against Streptococci. Int J Mol Sci 2022; 23:ijms23084085. [PMID: 35456906 PMCID: PMC9025105 DOI: 10.3390/ijms23084085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/02/2022] Open
Abstract
Streptococci are a family of bacterial species significantly affecting human health. In addition, environmental Streptococci represent one of the major causes of diverse livestock diseases. Due to antimicrobial resistance, there is an urgent need for novel antimicrobial agent discovery against Streptococci. We discovered a class of benzoic acid derivatives named sigmacidins inhibiting the bacterial RNA polymerase-σ factor interaction and demonstrating excellent antimicrobial activity against Streptococci. In this work, a combinational computer approach was applied to gain insight into the structural basis and mechanism of action of sigmacidins as antimicrobials against Streptococcus pneumoniae. Both two- and three-dimensional quantitative structure-active relationships (2D and 3D QSAR) of sigmacidins displayed good predictive ability. Moreover, molecular docking and molecular dynamics simulation studies disclosed possible contacts between the inhibitors and the protein. The results obtained in this study provided understanding and new directions to the further optimizations of sigmacidins as novel antimicrobials.
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Hadidi S, Majnooni M, Kazemi F, Mojarrab M, Bahrami G, Miraghaei S. The alkaloids of Isatis indigotica as promising candidates against COVID-19: A molecular docking simulation for drug development. JOURNAL OF REPORTS IN PHARMACEUTICAL SCIENCES 2022. [DOI: 10.4103/jrptps.jrptps_113_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Wilson CG, Aarons L, Augustijns P, Brouwers J, Darwich AS, De Waal T, Garbacz G, Hansmann S, Hoc D, Ivanova A, Koziolek M, Reppas C, Schick P, Vertzoni M, García-Horsman JA. Integration of advanced methods and models to study drug absorption and related processes: An UNGAP perspective. Eur J Pharm Sci 2021; 172:106100. [PMID: 34936937 DOI: 10.1016/j.ejps.2021.106100] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023]
Abstract
This collection of contributions from the European Network on Understanding Gastrointestinal Absorption-related Processes (UNGAP) community assembly aims to provide information on some of the current and newer methods employed to study the behaviour of medicines. It is the product of interactions in the immediate pre-Covid period when UNGAP members were able to meet and set up workshops and to discuss progress across the disciplines. UNGAP activities are divided into work packages that cover special treatment populations, absorption processes in different regions of the gut, the development of advanced formulations and the integration of food and pharmaceutical scientists in the food-drug interface. This involves both new and established technical approaches in which we have attempted to define best practice and highlight areas where further research is needed. Over the last months we have been able to reflect on some of the key innovative approaches which we were tasked with mapping, including theoretical, in silico, in vitro, in vivo and ex vivo, preclinical and clinical approaches. This is the product of some of us in a snapshot of where UNGAP has travelled and what aspects of innovative technologies are important. It is not a comprehensive review of all methods used in research to study drug dissolution and absorption, but provides an ample panorama of current and advanced methods generally and potentially useful in this area. This collection starts from a consideration of advances in a priori approaches: an understanding of the molecular properties of the compound to predict biological characteristics relevant to absorption. The next four sections discuss a major activity in the UNGAP initiative, the pursuit of more representative conditions to study lumenal dissolution of drug formulations developed independently by academic teams. They are important because they illustrate examples of in vitro simulation systems that have begun to provide a useful understanding of formulation behaviour in the upper GI tract for industry. The Leuven team highlights the importance of the physiology of the digestive tract, as they describe the relevance of gastric and intestinal fluids on the behaviour of drugs along the tract. This provides the introduction to microdosing as an early tool to study drug disposition. Microdosing in oncology is starting to use gamma-emitting tracers, which provides a link through SPECT to the next section on nuclear medicine. The last two papers link the modelling approaches used by the pharmaceutical industry, in silico to Pop-PK linking to Darwich and Aarons, who provide discussion on pharmacometric modelling, completing the loop of molecule to man.
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Affiliation(s)
- Clive G Wilson
- Strathclyde Institute of Pharmacy & Biomedical Sciences, Glasgow, U.K.
| | | | | | | | | | | | | | | | | | | | - Mirko Koziolek
- NCE Formulation Sciences, Abbvie Deutschland GmbH & Co. KG, Germany
| | | | - Philipp Schick
- Department of Biopharmaceutics and Pharmaceutical Technology, Center of Drug Absorption and Transport, University of Greifswald, Germany
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Characteristics of Food Protein-Derived Antidiabetic Bioactive Peptides: A Literature Update. Int J Mol Sci 2021; 22:ijms22179508. [PMID: 34502417 PMCID: PMC8431147 DOI: 10.3390/ijms22179508] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022] Open
Abstract
Diabetes, a glucose metabolic disorder, is considered one of the biggest challenges associated with a complex complication of health crises in the modern lifestyle. Inhibition or reduction of the dipeptidyl peptidase IV (DPP-IV), alpha-glucosidase, and protein-tyrosine phosphatase 1B (PTP-1B) enzyme activities or expressions are notably considered as the promising therapeutic strategies for the management of type 2 diabetes (T2D). Various food protein-derived antidiabetic bioactive peptides have been isolated and verified. This review provides an overview of the DPP-IV, PTP-1B, and α-glucosidase inhibitors, and updates on the methods for the discovery of DPP-IV inhibitory peptides released from food-protein hydrolysate. The finding of novel bioactive peptides involves studies about the strategy of separation fractionation, the identification of peptide sequences, and the evaluation of peptide characteristics in vitro, in silico, in situ, and in vivo. The potential of bioactive peptides suggests useful applications in the prevention and management of diabetes. Furthermore, evidence of clinical studies is necessary for the validation of these peptides’ efficiencies before commercial applications.
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Kumar SB, Krishna S, Pradeep S, Mathews DE, Pattabiraman R, Murahari M, Murthy TPK. Screening of natural compounds from Cyperus rotundus Linn against SARS-CoV-2 main protease (M pro): An integrated computational approach. Comput Biol Med 2021; 134:104524. [PMID: 34090015 PMCID: PMC8164362 DOI: 10.1016/j.compbiomed.2021.104524] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/22/2021] [Accepted: 05/22/2021] [Indexed: 01/10/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a viral respiratory disease that has been spreading across the globe. The World Health Organization (WHO) declared it as a public health emergency. The treatment of COVID-19 has been hampered due to the lack of effective therapeutic efforts. Main Protease (Mpro) is a key enzyme in the viral replication cycle and its non-specificity to human protease makes it a potential drug target. Cyperus rotundus Linn, which belongs to the Cyperaceae family, is a traditional herbal medicine that has been widely studied for its antiviral properties. In this study, a computational approach was used to screen natural compounds from C. rotundus Linn using BIOVIA Discovery Suite and novel potential molecules against Mpro of SARS-CoV-2 were predicted. Molecular docking was performed using LibDock protocol and selected ligands were further subjected to docking analysis by CDOCKER. The docking scores of the selected ligands were compared with standard antiretroviral drugs such as lopinavir and ritonavir to assess their binding potentials. Interaction pharmacophore analysis was then performed for the compounds exhibiting good binding scores to evaluate their protein–ligand interactions. The selected protein–ligand complexes were subjected to molecular dynamics simulation for 50 ns. Results of binding free energy analysis revealed that two compounds—β-amyrin and stigmasta-5,22-dien-3-ol—exhibited the best binding interactions and stability. Finally, absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were performed to understand the pharmacokinetic properties and safety profile of the compounds. The overall results indicate that the phytochemicals from Cyperus rotundus Linn, namely β-amyrin and stigmasta-5,22-dien-3-ol, can be screened as potential inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- S Birendra Kumar
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India
| | - Swati Krishna
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India
| | - Sneha Pradeep
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India
| | - Divya Elsa Mathews
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India
| | - Ramya Pattabiraman
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India
| | - Manikanta Murahari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bengaluru, 560054, Karnataka, India.
| | - T P Krishna Murthy
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, 560054, Karnataka, India.
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Ram H, Kumar P, Purohit A, Kashyap P, Kumar S, Kumar S, Singh G, Alqarawi AA, Hashem A, Abd-Allah EF, Al-Arjani ABF, Singh BP. Improvements in HOMA indices and pancreatic endocrinal tissues in type 2-diabetic rats by DPP-4 inhibition and antioxidant potential of an ethanol fruit extract of Withania coagulans. Nutr Metab (Lond) 2021; 18:43. [PMID: 33882957 PMCID: PMC8059290 DOI: 10.1186/s12986-021-00547-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/20/2021] [Indexed: 01/12/2023] Open
Abstract
CONTEXT Withania coagulans (Stocks) Dunal fruits are used in the therapeutics of several ailments due to possessing of potent phytoconstituents which is also used traditionally for curing the diabetes. OBJECTIVE The present study was assessing the amelioration potential of the phytochemicals of an ethanol fruit extract of W. coagulans (Stocks) Dunal in the HOMA (Homeostatic model assessment) indices and pancreatic endocrinal tissues by inhibition of DPP-4 and antioxidants activities. MATERIAL AND METHODS The identification of phytoconstituents of the test extract was performed by LCMS. Further, assessments of in-vitro, in-vivo and in-silico were achieved by following standard methods. In-vivo studies were conducted on type-2 diabetic rats. RESULTS The chosen extract inhibited DPP-4 activity by 63.2% in an in vitro assay as well as significantly inhibit serum DPP-4 levels. Accordingly, the administration of the ethanol fruit extract resulted in a significant (P ≤ 0.001) alterations in the lipid profile, antioxidant levels, and HOMA indices. Moreover, pancreatic endocrinal tissues (islet of Langerhans) appeared to have the restoration of normal histoarchitecture as evidenced by increased cellular mass. Molecular docking (Protein-ligands) of identified phytoconstituents with DPP-4 (target enzyme) shown incredibly low binding energy (Kcal/mol) as required for ideal interactions. ADMET analysis of the pharmacokinetics of the identified phytoconstituents indicated an ideal profile as per Lipinski laws. CONCLUSION It can be concluded that the phytoconstituents of an ethanol fruit extract of W. coagulans have the potential to inhibit DPP-4 which result in improved glucose homeostasis and restoration of pancreatic endocrinal tissues in type-2 diabetic rats.
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Affiliation(s)
- Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India.
| | - Pramod Kumar
- Department of Zoology, Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Ashok Purohit
- Department of Zoology, Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Priya Kashyap
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, India
| | - Suresh Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, India
| | - Shivani Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi, India
| | - Garima Singh
- Department of Botany, Pachhunga University College, Aizawl, Mizoram, 796001, India
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Elsayed Fathi Abd-Allah
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, 12511, Egypt
| | - Al-Bandari Fahad Al-Arjani
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Bhim Pratap Singh
- Department of Agriculture and Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Sonepat, 131028, Haryana, India.
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Mahrosh HS, Mehmood R, Bukhari SA, Afzal G, Arif R. Investigation of Hypoglycemic Peptides Derived from Conserved Regions of adMc1 to Reveal Their Antidiabetic Activities. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5550180. [PMID: 33763471 PMCID: PMC7963905 DOI: 10.1155/2021/5550180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
Diabetes mellitus is the most common chronic disorder and leading cause of renal, neurological, and gastrointestinal manifestations in developed and developing countries. Despite of many drugs and combinational therapies, the complications of diabetes are still listed due to severe consequences of those drugs. In past few years, plant-derived drugs draw special attention due to their higher efficacy and fewer side-effects. Momordica charantia also known as bitter melon is referred as an antidiabetic and hypoglycemic plant in native populations of Asia and East Africa. In current study, an in silico approach was used to evaluate the interactions and binding patterns of plant-derived peptides devised from a hypoglycemic protein adMc1 of M. charantia as potential inhibitor of DPP-IV, SGLT1, and GLUT2 receptor proteins. The study has described a novel approach to investigate hypoglycemic peptides to cure diabetes. A total of eighty tetra-, penta-, and hexapeptides were devised from conserved regions of adMc1 homologs. The molecular docking approach using MOE software was employed to reveal inhibiting potentials of devised peptides against three selected proteins. Out of 30 shortlisted ligands six peptides (i.e. SMCG, DECC, TTIT, RTTI, ARNL and TVEV) accomplished the criteria of being good drug candidates against selected receptor proteins following the drugability assessment test. The overall results are acceptable on the basis of ADMET profiling for being good drug candidates against selected proteins.
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Affiliation(s)
| | - Rizwan Mehmood
- Department of Biochemistry, Government College University Faisalabad, Pakistan
| | | | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Rawaba Arif
- Department of Biochemistry, Government College University Faisalabad, Pakistan
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15
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Chen TH, Fu YS, Chen SP, Fuh YM, Chang C, Weng CF. Garcinia linii extracts exert the mediation of anti-diabetic molecular targets on anti-hyperglycemia. Biomed Pharmacother 2021; 134:111151. [DOI: 10.1016/j.biopha.2020.111151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
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Iheagwam FN, Rotimi SO. Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants. SCIENTIFICA 2020; 2020:1878410. [PMID: 32963884 PMCID: PMC7492903 DOI: 10.1155/2020/1878410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/13/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic, which started in Wuhan, China, has spread rapidly over the world with no known antiviral therapy or vaccine. Interestingly, traditional Chinese medicine helped in flattening the pandemic curve in China. In this study, molecules from African medicinal plants were analysed as potential candidates against multiple SARS-CoV-2 therapeutic targets. Sixty-five molecules from the ZINC database subset (AfroDb Natural Products) were virtually screened with some reported repurposed therapeutics against six SARS-CoV-2 and two human targets. Molecular docking, druglikeness, absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the best hits were further simulated. Of the 65 compounds, only three, namely, 3-galloylcatechin, proanthocyanidin B1, and luteolin 7-galactoside found in almond (Terminalia catappa), grape (Vitis vinifera), and common verbena (Verbena officinalis), were able to bind to all eight targets better than the reported repurposed drugs. The findings suggest these molecules may play a role as therapeutic leads in tackling this pandemic due to their multitarget activity.
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Affiliation(s)
- Franklyn Nonso Iheagwam
- Department of Biochemistry, College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
- Covenant University Public Health and Wellness Research Cluster (CUPHWERC), College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
| | - Solomon Oladapo Rotimi
- Department of Biochemistry, College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
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A Review of the Ephedra genus: Distribution, Ecology, Ethnobotany, Phytochemistry and Pharmacological Properties. Molecules 2020; 25:molecules25143283. [PMID: 32698308 PMCID: PMC7397145 DOI: 10.3390/molecules25143283] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022] Open
Abstract
Ephedra is one of the largest genera of the Ephedraceae family, which is distributed in arid and semiarid regions of the world. In the traditional medicine from several countries some species from the genus are commonly used to treat asthma, cold, flu, chills, fever, headache, nasal congestion, and cough. The chemical constituents of Ephedra species have been of research interest for decades due to their contents of ephedrine-type alkaloids and its pharmacological properties. Other chemical constituents such as phenolic and amino acid derivatives also have resulted attractive and have provided evidence-based supporting of the ethnomedical uses of the Ephedra species. In recent years, research has been expanded to explore the endophytic fungal diversity associated to Ephedra species, as well as, the chemical constituents derived from these fungi and their pharmacological bioprospecting. Two additional aspects that illustrate the chemical diversity of Ephedra genus are the chemotaxonomy approaches and the use of ephedrine-type alkaloids as building blocks in organic synthesis. American Ephedra species, especially those that exist in Mexico, are considered to lack ephedrine type alkaloids. In this sense, the phytochemical study of Mexican Ephedra species is a promising area of research to corroborate their ephedrine-type alkaloids content and, in turn, discover new chemical compounds with potential biological activity. Therefore, the present review represents a key compilation of all the relevant information for the Ephedra genus, in particular the American species, the species distribution, their ecological interactions, its ethnobotany, its phytochemistry and their pharmacological activities and toxicities, in order to promote clear directions for future research.
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Yang Y, Shi CY, Xie J, Dai JH, He SL, Tian Y. Identification of Potential Dipeptidyl Peptidase (DPP)-IV Inhibitors among Moringa oleifera Phytochemicals by Virtual Screening, Molecular Docking Analysis, ADME/T-Based Prediction, and In Vitro Analyses. Molecules 2020; 25:molecules25010189. [PMID: 31906524 PMCID: PMC6983023 DOI: 10.3390/molecules25010189] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
Moringa oleifera Lam. (MO) is called the “Miracle Tree” because of its extensive pharmacological activity. In addition to being an important food, it has also been used for a long time in traditional medicine in Asia for the treatment of chronic diseases such as diabetes and obesity. In this study, by constructing a library of MO phytochemical structures and using Discovery Studio software, compounds were subjected to virtual screening and molecular docking experiments related to their inhibition of dipeptidyl peptidase (DPP-IV), an important target for the treatment of type 2 diabetes. After the four-step screening process, involving screening for drug-like compounds, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADME/T) of pharmacokinetic properties, LibDock heatmap matching analysis, and CDOCKER molecular docking analysis, three MO components that were candidate DPP-IV inhibitors were identified and their docking modes were analyzed. In vitro activity verification showed that all three MO components had certain DPP-IV inhibitory activities, of which O-Ethyl-4-[(α-l-rhamnosyloxy)-benzyl] carbamate (compound 1) had the highest activity (half-maximal inhibitory concentration [IC50] = 798 nM). This study provides a reference for exploring the molecular mechanisms underlying the anti-diabetic activity of MO. The obtained DPP-IV inhibitors could be used for structural optimization and in-depth in vivo evaluation.
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Affiliation(s)
- Yang Yang
- College of Science, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Key Laboratory of Biomass Big Data, Yunnan Agricultural University, Kunming 650201, China;
| | - Chong-Yin Shi
- Institute of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.-Y.S.); (J.-H.D.)
| | - Jing Xie
- Yunnan Key Laboratory of Biomass Big Data, Yunnan Agricultural University, Kunming 650201, China;
| | - Jia-He Dai
- Institute of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.-Y.S.); (J.-H.D.)
| | - Shui-Lian He
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.-L.H.); (Y.T.)
| | - Yang Tian
- Yunnan Key Laboratory of Biomass Big Data, Yunnan Agricultural University, Kunming 650201, China;
- Institute of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.-Y.S.); (J.-H.D.)
- Correspondence: (S.-L.H.); (Y.T.)
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Iheagwam FN, Ogunlana OO, Chinedu SN. Model Optimization and In Silico Analysis of Potential Dipeptidyl Peptidase IV Antagonists from GC-MS Identified Compounds in Nauclea latifolia Leaf Extracts. Int J Mol Sci 2019; 20:ijms20235913. [PMID: 31775302 PMCID: PMC6929178 DOI: 10.3390/ijms20235913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Dipeptidyl peptidase IV (DPP-IV) is a pharmacotherapeutic target in type 2 diabetes. Inhibitors of this enzyme constitute a new class of drugs used in the treatment and management of type 2 diabetes. In this study, phytocompounds in Nauclea latifolia (NL) leaf extracts, identified using gas chromatography–mass spectroscopy (GC-MS), were tested for potential antagonists of DPP-IV via in silico techniques. Phytocompounds present in N. latifolia aqueous (NLA) and ethanol (NLE) leaf extracts were identified using GC–MS. DPP-IV model optimization and molecular docking of the identified compounds/standard inhibitors in the binding pocket was simulated. Drug-likeness, pharmacokinetic and pharmacodynamic properties of promising docked leads were also predicted. Results showed the presence of 50 phytocompounds in NL extracts of which only 2-O-p-methylphenyl-1-thio-β-d-glucoside, 3-tosylsedoheptulose, 4-benzyloxy-6-hydroxymethyl-tetrahydropyran-2,3,5-triol and vitamin E exhibited comparable or better binding iGEMDOCK and AutoDock Vina scores than the clinically prescribed standards. These four compounds exhibited promising drug-likeness as well as absorption, distribution, metabolism, excretion and toxicity (ADMET) properties suggesting their candidature as novel leads for developing DPP-IV inhibitors.
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Affiliation(s)
- Franklyn Nonso Iheagwam
- Department of Biochemistry, Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria; (O.O.O.); (S.N.C.)
- Covenant University Public Health and Wellness Research Cluster (CUPHWERC), Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria
- Correspondence: ; Tel.: +234-8163615298
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria; (O.O.O.); (S.N.C.)
- Covenant University Public Health and Wellness Research Cluster (CUPHWERC), Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria
| | - Shalom Nwodo Chinedu
- Department of Biochemistry, Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria; (O.O.O.); (S.N.C.)
- Covenant University Public Health and Wellness Research Cluster (CUPHWERC), Covenant University, PMB 1023, Ota 112212, Ogun State, Nigeria
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21
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Musoev A, Numonov S, You Z, Gao H. Discovery of Novel DPP-IV Inhibitors as Potential Candidates for the Treatment of Type 2 Diabetes mellitus Predicted by 3D QSAR Pharmacophore Models, Molecular Docking and de novo Evolution. Molecules 2019; 24:molecules24162870. [PMID: 31394858 PMCID: PMC6720998 DOI: 10.3390/molecules24162870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/31/2022] Open
Abstract
Dipeptidyl peptidase-IV (DPP-IV) rapidly breaks down the incretin hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic peptide (GIP). Thus, the use of DPP-IV inhibitors to retard the degradation of endogenous GLP-1 is a possible mode of therapy correcting the defect in incretin-related physiology. The aim of this study is to find a new small molecule and explore the inhibition activity to the DPP-IV enzyme using a computer aided simulation. In this study, the predicted compounds were suggested as potent anti-diabetic candidates. Chosen structures were applied following computational strategies: The generation of the three-dimensional quantitative structure-activity relationship (3D QSAR) pharmacophore models, virtual screening, molecular docking, and de novo Evolution. The method also validated by performing re-docking and cross-docking studies of seven protein systems for which crystal structures were available for all bound ligands. The molecular docking experiments of predicted compounds within the binding pocket of DPP-IV were conducted. By using 25 training set inhibitors, ten pharmacophore models were generated, among which hypo1 was the best pharmacophore model with the best predictive power on account of the highest cost difference (352.03), the lowest root mean squared deviation (RMSD) (2.234), and the best correlation coefficient (0.925). Hypo1 pharmacophore model was used for virtual screening. A total of 161 compounds including 120 from the databases, 25 from the training set, 16 from the test set were selected for molecular docking. Analyzing the amino acid residues of the ligand-receptor interaction, it can be concluded that Arg125, Glu205, Glu206, Tyr547, Tyr662, and Tyr666 are the main amino acid residues. The last step in this study was de novo Evolution that generated 11 novel compounds. The derivative dpp4_45_Evo_1 by all scores CDOCKER_ENERGY (CDOCKER, -41.79), LigScore1 (LScore1, 5.86), LigScore2 (LScore2, 7.07), PLP1 (-112.01), PLP2 (-105.77), PMF (-162.5)—have exceeded the control compound. Thus the most active compound among 11 derivative compounds is dpp4_45_Evo_1. Additionally, for derivatives dpp4_42_Evo_1, dpp4_43_Evo2, dpp4_46_Evo_4, and dpp4_47_Evo_2, significant upward shifts were recorded. The consensus score for the derivatives of dpp4_45_Evo_1 from 1 to 6, dpp4_43_Evo2 from 4 to 6, dpp4_46_Evo_4 from 1 to 6, and dpp4_47_Evo_2 from 0 to 6 were increased. Generally, predicted candidates can act as potent occurring DPP-IV inhibitors given their ability to bind directly to the active sites of DPP-IV. Our result described that the 6 re-docked and 27 cross-docked protein-ligand complexes showed RMSD values of less than 2 Å. Further investigation will result in the development of novel and potential antidiabetic drugs.
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Affiliation(s)
- Azizullo Musoev
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Sodik Numonov
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- Research Institution "Chinese-Tajik Innovation Center for Natural Products", Dushanbe 734063, Tajikistan
| | - Zhuhong You
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Hongwei Gao
- School of Life Science, Ludong University, Yantai 264025, China.
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Hussain H, Abbas G, Green IR, Ali I. Dipeptidyl peptidase IV inhibitors as a potential target for diabetes: patent review (2015-2018). Expert Opin Ther Pat 2019; 29:535-553. [PMID: 31203700 DOI: 10.1080/13543776.2019.1632290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Dipeptidyl peptidase 4 (DPP-4) belongs to the family of serine proteases and is involved in the degradation of GLP-1 and GIP hormones, which enhance the production and release of insulin. Targeting DPP-4 inhibitors is increasingly being considered as promising paradigms to treat type 2 diabetes mellitus and therefore DPP-4 inhibitors are being considered as promising antidiabetic drugs. AREAS COVERE This review provides an overview of published patents describing natural and synthetic DPP-4 inhibitors from January 2015 to December 2018. EXPERT OPINION A fair number of new synthetic and natural DPP-4 inhibitors have been reported in the last four years which describe the progress in the development of various heterocyclic scaffolds or heterocyclic hybrid compounds. As a result of this, many marketed DPP-4 inhibitors that have been approved by the appropriate governing bodies during the past decade, have been introduced as inhibitors. Molecular hybridization is an emerging idea in medicinal chemistry and therefore hybrid compounds of DPP-4 inhibitors with other DPP-4 inhibitors or with antidiabetic drugs should be formulated for a comprehensive evaluation. More detailed pharmacovigilance of DPP-4 inhibitors is required because this will address the pancreas-related adverse events as well as their impact on cardiovascular outcomes via long-term studies.
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Affiliation(s)
- Hidayat Hussain
- a Department of Bioorganic Chemistry , Leibniz Institute of Plant Biochemistry , Halle (Saale) , Germany
| | - Ghulam Abbas
- b Department of Biological Sciences and Chemistry , College of Arts and Sciences, University of Nizwa , Nizwa , Sultanate of Oman
| | - Ivan R Green
- c Department of Chemistry and Polymer Science , University of Stellenbosch , Matieland, Stellenbosch , South Africa
| | - Iftikhar Ali
- d Department of Chemistry , Karakoram International University , Gilgit, Gilgit-Baltistan , Pakistan
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Kalhotra P, Chittepu VCSR, Osorio-Revilla G, Gallardo-Velázquez T. Discovery of Galangin as a Potential DPP-4 Inhibitor That Improves Insulin-Stimulated Skeletal Muscle Glucose Uptake: A Combinational Therapy for Diabetes. Int J Mol Sci 2019; 20:ijms20051228. [PMID: 30862104 PMCID: PMC6429117 DOI: 10.3390/ijms20051228] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 12/30/2022] Open
Abstract
Dipeptidyl peptidase-4 (DPP-4) is a well-known therapeutic drug target proven to reduce blood glucose levels in diabetes mellitus, and clinically, DPP-4 inhibitors are used in combination with other anti-diabetic agents. However, side effects and skeletal muscle health are not considered in the treatment for diabetic patients. Recently, natural compounds have been proven to inhibit DPP-4 with fewer side effects. In this work, initially, molecular docking simulations revealed that a natural compound, Galangin, possess a binding energy of −24 KJ/mol and interaction residues SER 630 and TYR 547, that are responsible for potent DPP-4 inhibition. In vitro studies showed that galangin not only inhibits DPP-4 in a concentration-dependent manner but also regulates glucose levels, enabling the proliferation of rat L6 skeletal muscle cells. The combination of galangin with insulin benefits regulation of glucose levels significantly in comparison to galangin alone (p < 0.05). These findings suggest the beneficial effect of the use of galangin, both alone or in combination with insulin, to reduce glucose levels and improve skeletal muscle health in diabetes mellitus.
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Affiliation(s)
- Poonam Kalhotra
- Departamento de Biofísica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Veera C S R Chittepu
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu S/N, Col. Unidad Profesional Adolfo López Mateos, Zacatenco, CP. 07738 Ciudad de México, México.
| | - Guillermo Osorio-Revilla
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu S/N, Col. Unidad Profesional Adolfo López Mateos, Zacatenco, CP. 07738 Ciudad de México, México.
| | - Tzayhri Gallardo-Velázquez
- Departamento de Biofísica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
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Rohilla A, Gupta T, Pathak A, Akhtar MJ, Haider MR, Haider K, Shahar Yar M. Emergence of promising novel DPP-4 inhibitory heterocycles as anti-diabetic agents: A review. Arch Pharm (Weinheim) 2018; 351:e1800127. [PMID: 29878387 DOI: 10.1002/ardp.201800127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
Abstract
Diabetes has turned out to be an epidemic in the recent years all over the world, and today it has become a burden on the healthcare system. Over the years, with technological advancements, different classes of antidiabetic medications have emerged, like sulfonylureas, biguanides, alpha-glucosidase inhibitors, and thiazolidinediones, but these are often loaded with serious aftermaths like hypoglycemia, weight gain, cardiovascular and renal issues. Dipeptidyl peptidase-4 (DPP-4) inhibition is an exciting and new approach in the treatment of type-2 diabetes. DPP-4 inhibitors or "gliptins" are weight neutral, pose lesser risk of hypoglycemia, and provide a long-term post-meal glycemic control. In this review, an attempt has been made to investigate novel potential compounds that can be added to the existing list of anti-diabetic drugs.
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Affiliation(s)
- Ankit Rohilla
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Tanya Gupta
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Ankita Pathak
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Md J Akhtar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Md R Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Kashif Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Mohammad Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
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Plant dipeptidyl peptidase-IV inhibitors as antidiabetic agents: a brief review. Future Med Chem 2018; 10:1229-1239. [PMID: 29749760 DOI: 10.4155/fmc-2017-0235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Diabetes mellitus is an increasing public health problem in the world. Type 2 diabetes is the most common type of diabetes whose complications contribute to its high death rate. It seriously impacts healthcare systems and patients' quality of life. Therefore, effective measures and new treatment strategies are needed to solve this increasingly serious global problem. In recent years, inhibition of dipeptidyl peptidase IV (DPP-IV) has emerged as a new treatment option for Type 2 diabetes. This article reviews various plant DPP-IV inhibitors that showed inhibition toward enzyme as a major target for the management of Type 2 diabetes. These studies can contribute to the future development of DPP-IV inhibitors as drugs.
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High throughput screening against pantothenate synthetase identifies amide inhibitors against Mycobacterium tuberculosis and Staphylococcus aureus. In Silico Pharmacol 2018; 6:9. [PMID: 30607322 DOI: 10.1007/s40203-018-0046-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 04/10/2018] [Indexed: 01/14/2023] Open
Abstract
Abstract Pantothenate is a crucial enzyme for the synthesis of coenzyme A and acyl carrier protein in Mycobacterium tuberculosis and Staphylococcus aureus. It is indispensable for the growth and survival of these bacteria. Amides analogs are designed and have been used as inhibitors of pantothenate synthetase. Molecular docking approach has been used to design and predict the drug activity of molecule to the specific disease. In this work, more than hundred amides have been screened by Discovery Studio molecular docking programme to search best suitable molecule for the treatment of Mycobacterium tuberculosis. Pharmacophore generation has been done to recognize the binding modes of inhibitors in the receptor active site. To observe the stability and flexibility of inhibitors molecular dynamics (MD) simulation has been done; Lipinski's rule of five protocols is followed to screen drug likeness and ADMET (absorption, distribution, metabolism, excretion and toxicity) filtration is also used to value toxicity. DFT computation of optimized geometry and derivation of MOs has been used to correlate the drug likeness. The small difference in energy between HOMO and LUMO may help to activate the drug in the protein environment quickly. 2-Hydroxy-5-[(E)-2-{4-[(prop-2-enamido)sulfonyl]phenyl}diazen-1-yl]benzoic acid (M1) shows best theoretical efficiency against Mycobacterium tuberculosis (MTB) pantothenate synthetase and so does 2-hydroxy-5-[(E)-2-{4-[(2-phenylacetamido)sulfonyl]phenyl}diazen-1-yl]benzoic acid (M2) against Staphylococcus aureus pantothenate synthetase. These compounds also bind to Adenine-Thymine region of tuberculosis DNA. Graphical abstract
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Jin WY, Ma Y, Li WY, Li HL, Wang RL. Scaffold-based novel SHP2 allosteric inhibitors design using Receptor-Ligand pharmacophore model, virtual screening and molecular dynamics. Comput Biol Chem 2018; 73:179-188. [DOI: 10.1016/j.compbiolchem.2018.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 12/20/2022]
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Ma Y, Li HL, Chen XB, Jin WY, Zhou H, Ma Y, Wang RL. 3D QSAR Pharmacophore Based Virtual Screening for Identification of Potential Inhibitors for CDC25B. Comput Biol Chem 2018; 73:1-12. [PMID: 29413811 DOI: 10.1016/j.compbiolchem.2018.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/06/2018] [Accepted: 01/17/2018] [Indexed: 11/19/2022]
Abstract
Owing to its fundamental roles in cell cycle phases, the cell division cycle 25B (CDC25B) was broadly considered as potent clinical drug target for cancers. In this study, 3D QSAR pharmacophore models for CDC25B inhibitors were developed by the module of Hypogen. Three methods (cost analysis, test set prediction, and Fisher's test) were applied to validate that the models could be used to predict the biological activities of compounds. Subsequently, 26 compounds satisfied Lipinski's rule of five were obtained by the virtual screening of the Hypo-1-CDC25B against ZINC databases. It was then discovered that 9 identified molecules had better binding affinity than a known CDC25B inhibitors-compound 1 using docking studies. The molecular dynamics simulations showed that the compound had favorable conformations for binding to the CDC25B. Thus, our findings here would be helpful to discover potent lead compounds for the treatment of cancers.
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Affiliation(s)
- Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xiu-Bo Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China; Eye Hospital, Tianjin Medical University, School of Optometry and Ophthalmology, Tianjin Medical University, China
| | - Wen-Yan Jin
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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Rapid Identification of Dipeptidyl Peptidase-IV (DPP-IV) Inhibitory Peptides from Ruditapes philippinarum Hydrolysate. Molecules 2017; 22:molecules22101714. [PMID: 29027968 PMCID: PMC6151561 DOI: 10.3390/molecules22101714] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 01/08/2023] Open
Abstract
Dipeptidyl peptidase-IV (DPP-IV) inhibitory peptides were rapidly identified from Ruditapes philippinarum hydrolysate. The hydrolysate was fractionated by ethanol precipitation and preparative reverse phase high-performance liquid chromatography (RP-HPLC). The fraction which showed the highest DPP-IV inhibitory activity was then analyzed by a high-throughput nano-liquid chromatography electrospray ionization tandem mass spectrometry (nano-LC ESI-MS/MS) method, and the sequences of peptides were identified based on the MS/MS spectra against the Mollusca protein data from the UniProt database. In total, 50 peptides were identified. Furthermore, molecular docking was used to identify potential DPP-IV inhibitors from the identified peptides. Docking results suggested that four peptides: FAGDDAPR, LAPSTM, FAGDDAPRA, and FLMESH, could bind pockets of DPP-IV through hydrogen bonds, π-π bonds, and charge interactions. The four peptides were chemically synthesized and tested for DPP-IV inhibitory activity. The results showed that they possessed DPP-IV inhibitory activity with IC50 values of 168.72 μM, 140.82 μM, 393.30 μM, and >500 μM, respectively. These results indicate that R. philippinarum-derived peptides may have potential as functional food ingredients for the prevention of diabetes.
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