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Bisht P, Gautam P, Bhattacharya A, Singh R, Verma SK. Designing of xanthine-based DPP-4 inhibitors: a structure-guided alignment dependent Multifacet 3D-QSAR modeling, and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-25. [PMID: 38783776 DOI: 10.1080/07391102.2024.2329787] [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: 05/24/2023] [Accepted: 03/06/2024] [Indexed: 05/25/2024]
Abstract
The DPP-4 enzyme degrades incretin hormones GLP-1 and GIP. DPP-4 inhibitors are found effective in the prevention of the degradation of incretins. Xanthine scaffold-bearing molecules are reported as potential DPP-4 inhibitors for treating type 2 diabetes mellitus, e.g. the marketed drug linagliptin. In this work, structure-guided alignment-dependent atom- and Gaussian field-based 3D-QSAR have been performed on a dataset of 75 molecules. The robustness and predictive ability of the developed multifacet 3D-QSAR models were validated on different statistical parameters and found to be statistically fit. The favorable and unfavorable pharmacophoric features were mapped for each multifacet 3D-QSAR model based on three alignment sets (1-3). A five-point common pharmacophore hypothesis was generated separately for each set of alignments. The molecular dynamics simulations (up to 100 ns) were performed for the potent molecule from each alignment set (Compounds 12, 40 and 57) compared to reference standard linagliptin to study the binding energy and stability of target-ligand complexes. The MM-PBSA calculations revealed that the binding free energy and stability of compounds 12 (-40.324 ± 17.876 kJ/mol), 40 (-80.543 ± 21.782 kJ/mol) and 57 (-50.202 ± 16.055 kJ/mol) were better than the reference drug linagliptin (-20.390 ± 63.200 kJ/mol). The generated contour maps from structure-guided alignment-dependent multifacet 3D-QSAR models offer information about the structure-activity relationship (SAR) and ligand-target binding energy and stability data from MD simulation may be utilized to design and develop target selective xanthine-based novel DPP-4 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priya Bisht
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Priyadarshi Gautam
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Arka Bhattacharya
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
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2
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Chen X, Xue B, Wahab S, Sultan A, Khalid M, Yang S. Structure-based molecular docking and molecular dynamics simulations study for the identification of dipeptidyl peptidase 4 inhibitors in type 2 diabetes. J Biomol Struct Dyn 2023:1-14. [PMID: 38100564 DOI: 10.1080/07391102.2023.2291831] [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: 03/24/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023]
Abstract
Inhibition of dipeptidyl peptidase-4 (DPP4) activity has emerged as a promising therapeutic approach for the treatment of type 2 diabetes mellitus (T2DM). Bioinformatics-driven approaches have emerged as crucial tools in drug discovery. Molecular docking and molecular dynamics (MD) simulations are effective tools in drug discovery, as they reduce the time and cost associated with experimental screening. In this study, we employed structure-assisted in-silico methods, including molecular docking and MD simulations, to identify SRT2183, a small molecule that may potentially inhibit the activity of DPP4 enzyme. The interaction between the small molecule "SRT2183" and DPP4 exhibited a binding affinity of -9.9 Kcal/Mol, leading to the formation of hydrogen bonds with the amino acid residues MET348, SER376, and THR351 of DPP4. The MD simulations over a period of 100 ns indicated stable protein-ligand interactions, with no significant conformational rearrangements observed within the simulated timeframe. In conclusion, our results suggest that the small molecule SRT2183 may have the potential to inhibit the DPP4 enzyme and pave the way for the therapeutics of T2DM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Chen
- School of Management, Guangzhou College of Technology and Business, Guangzhou, China
| | - Bin Xue
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Armiya Sultan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Song Yang
- Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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3
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Shah BM, Modi P, Trivedi P. Recent Medicinal Chemistry Approach for the Development of Dipeptidyl Peptidase IV Inhibitors. Curr Med Chem 2021; 28:3595-3621. [PMID: 33045957 DOI: 10.2174/0929867327666201012153255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Diabetes, a metabolic disease, occurs due to a decreased or no effect of insulin on the blood glucose level. The current oral medications stimulate insulin release, increase glucose absorption and its utilization, and decrease hepatic glucose output. Two major incretin hormones like Glucose-dependent insulinotropic polypeptide (GIP) and glucagonlike peptide - 1 (GLP-1) stimulate insulin release after a meal, but their action is inhibited by enzyme dipeptidyl peptidase- IV. OBJECTIVE The activity of endogenous GLP-1 and GIP prolongs and extends with DPP IV inhibitors, which are responsible for the stimulation of insulin secretion and regulation of blood glucose level. DPP IV inhibitors have shown effectiveness and endurability with a neutral effect on weight as well as less chances of hypoglycemia in the management of type 2 diabetes. These journeys started from Sitagliptin (marketed in 2006) to Evogliptin (marketed in 2015, Korea). CONCLUSION Treatment of type 2 diabetes includes lifestyle changes, oral medications, and insulin. Newer and superior therapies are needed more than currently prescribed drugs. Various heterocyclic derivatives have been tried, but due to masking of DASH proteins, CYP enzymes, and hERG channel, they showed side effects. Based on these, the study has been focused on the development of safe, influential, selective, and long-lasting inhibitors of DPP IV.
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Affiliation(s)
- Bhumi M Shah
- Department of Pharmaceutical Chemistry, K.B. Institute of Pharmaceutical Education and Research, Gandhinagar, Gujarat 382023, India
| | - Palmi Modi
- Department of Pharmaceutical Chemistry, L.J. Institutes of Pharmacy, Sarkhej, Ahmedabad, Gujarat 382210, India
| | - Priti Trivedi
- Department of Pharmaceutical Chemistry, K.B. Institute of Pharmaceutical Education and Research, Gandhinagar, Gujarat 382023, India
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Dowarah J, Singh VP. Anti-diabetic drugs recent approaches and advancements. Bioorg Med Chem 2020; 28:115263. [PMID: 32008883 DOI: 10.1016/j.bmc.2019.115263] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/20/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Diabetes is one of the major diseases worldwide and is the third leading cause of death in the United States. Anti-diabetic drugs are used in the treatment of diabetes mellitus to control glucose levels in the blood. Most of the drugs are administered orally, except for a few of them, such as insulin, exenatide, and pramlintide. In this review, we are going to discuss seven major types of anti-diabetic drugs: Peroxisome proliferator-activated receptor (PPAR) agonist, protein tyrosine phosphatase 1B (PTP1B) inhibitors, aldose reductase inhibitors, α-glucosidase inhibitors, dipeptidyl peptidase IV (DPP-4) inhibitors, G protein-coupled receptor (GPCR) agonists and sodium-glucose co-transporter (SGLT) inhibitors. Here, we are also discussing some of the recently reported anti-diabetic agents with its multi-target pharmacological actions. This review summarises recent approaches and advancement in anti-diabetes treatment concerning characteristics, structure-activity relationships, functional mechanisms, expression regulation, and applications in medicine.
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Affiliation(s)
- Jayanta Dowarah
- Department of Chemistry, Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India
| | - Ved Prakash Singh
- Department of Chemistry, Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India.
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Wang K, Han L, Mustakis J, Li B, Magano J, Damon DB, Dion A, Maloney MT, Post R, Li R. Kinetic and Data-Driven Reaction Analysis for Pharmaceutical Process Development. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03578] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ke Wang
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lu Han
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jason Mustakis
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Bryan Li
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Javier Magano
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - David B. Damon
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Amelie Dion
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark T. Maloney
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ronald Post
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ruizhi Li
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
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Tomović K, Kocić G, Šmelcerović A. POTENTIAL DUAL MECHANISM OF HYPOURICEMICACTIVITY OF DPP-4 INHIBITORS WITH PURINE-BASED SCAFFOLD. ACTA MEDICA MEDIANAE 2019. [DOI: 10.5633/amm.2019.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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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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Li N, Wang LJ, Jiang B, Li XQ, Guo CL, Guo SJ, Shi DY. Recent progress of the development of dipeptidyl peptidase-4 inhibitors for the treatment of type 2 diabetes mellitus. Eur J Med Chem 2018; 151:145-157. [PMID: 29609120 DOI: 10.1016/j.ejmech.2018.03.041] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Diabetes is a fast growing chronic metabolic disorder around the world. Dipeptidyl peptidase-4 (DPP-4) is a new promising target during type 2 diabetes glycemic control. Thus, a number of potent DPP-4 inhibitors were developed and play a rapidly evolving role in the management of type 2 diabetes in recent years. This article reviews the development of synthetic and natural DPP-4 inhibitors from 2012 to 2017 and provides their physico-chemical properties, biological activities against DPP-4 and selectivity over dipeptidyl peptidase-8/9. Moreover, the glucose-lowering mechanisms and the active site of DPP-4 are also discussed. We also discuss strategies and structure-activity relationships for identifying potent DPP-4 inhibitors, which will provide useful information for developing potent DPP-4 drugs as type 2 diabtes treatments.
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Affiliation(s)
- Ning Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Li-Jun Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Bo Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Xiang-Qian Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Chuan-Long Guo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Shu-Ju Guo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China
| | - Da-Yong Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, China.
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9
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Lee D, Lee S, Liu KH, Bae JS, Baek DJ, Lee T. Solid-Phase Synthesis of 1,3,7,8-Tetrasubstituted Xanthine Derivatives on Traceless Solid Support. ACS COMBINATORIAL SCIENCE 2016; 18:70-4. [PMID: 26616892 DOI: 10.1021/acscombsci.5b00148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traceless solid-phase synthesis of 1,3,7,8-tetrasubstituted xanthine (1,3,7,8-tetrasubstituted 1H-purine-2,6(3H,7H)-dione) derivatives has been developed. The solid-phase synthetic route began on a solid supported N'-cyano-N-substituted carbamimidothioate, which was prepared from cyanamide, isothiocyanate, and Merrifield resin. After N-alkylation of carbamimidothioate resin with ethyl 2-bromoacetate, an imidazole ring is introduced by Thorpe-Ziegler-type cyclization. The resulting imidazole resin is converted to 1,3,7-trisubstituted xanthine resin using sequential reactions, such as Lewis acid-catalyzed urea formation, pyrimidine ring cyclization, and N-alkylation. After oxidation of sulfides to sulfones, traceless cleavage with amine or thiol nucleophiles afforded the desired 1,3,7,8-tetrasubstituted xanthines in good purities and overall yields (eight-steps; 36 examples). This efficient solid-phase synthesis enables the incorporation of four diversity points into the preparation of the 1,3,7,8-tetrasubstituted xanthines.
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Affiliation(s)
- Doohyun Lee
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
| | - Seungyeon Lee
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
| | - Kwang-Hyeon Liu
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
| | - Jong-Sup Bae
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
| | - Dong Jae Baek
- College
of Pharmacy, Natural Medicine Research Institute, Mokpo National University, 1666 Youngsan-ro, Muan-gun, Jeonnam 534-729, Korea
| | - Taeho Lee
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Korea
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Design, synthesis and biological evaluation of novel pyrazolo-pyrimidinones as DPP-IV inhibitors in diabetes. Bioorg Med Chem Lett 2015; 25:4428-33. [PMID: 26372650 DOI: 10.1016/j.bmcl.2015.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/19/2015] [Accepted: 09/07/2015] [Indexed: 01/19/2023]
Abstract
We report the design, synthesis, biological activity and docking studies of series of novel pyrazolo[3,4-d]pyrimidinones as DPP-IV inhibitors in diabetes. Molecules were synthesized and evaluated for their DPP-IV inhibition activity. Compounds 5e, 5k, 5o and 6a were found to be potent inhibitors of DPP-IV enzyme. Amongst all the synthesized compounds, 6-methyl-5-(4-methylpyridin-2-yl)-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one (5k) was found to be the most active based on in vitro DPP-IV studies and also exhibited promising in vivo blood glucose lowering activity in male Wistar rats.
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