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Wang C, Zheng L, Udenigwe CC, Lin L, Zhao M. Molecular Mechanistic Insights into Dipeptidyl Peptidase-IV Inhibitory Peptides to Decipher the Structural Basis of Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11230-11240. [PMID: 38709903 DOI: 10.1021/acs.jafc.3c08791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Dipeptidyl peptidase-IV (DPP-IV) inhibiting peptides have attracted increased attention because of their possible beneficial effects on glycemic homeostasis. However, the structural basis underpinning their activities has not been well understood. This study combined computational and in vitro investigations to explore the structural basis of DPP-IV inhibitory peptides. We first superimposed the Xaa-Pro-type peptide-like structures from several crystal structures of DPP-IV ligand-protein complexes to analyze the recognition interactions of DPP-IV to peptides. Thereafter, a small set of Xaa-Pro-type peptides was designed to explore the effect of key interactions on inhibitory activity. The intramolecular interaction of Xaa-Pro-type peptides at the first and third positions from the N-terminus was pivotal to their inhibitory activities. Residue interactions between DPP-IV and residues of the peptides at the fourth and fifth positions of the N-terminus contributed significantly to the inhibitory effect of Xaa-Pro-type tetrapeptides and pentapeptides. Based on the interaction descriptors, quantitative structure-activity relationship (QSAR) studies with the DPP-IV inhibitory peptides resulted in valid models with high R2 values (0.90 for tripeptides; 0.91 for tetrapeptides and pentapeptides) and Q2 values (0.33 for tripeptides; 0.68 for tetrapeptides and pentapeptides). Taken together, the structural information on DPP-IV and peptides in this study facilitated the development of novel DPP-IV inhibitory peptides.
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Affiliation(s)
- Chenyang Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Lin Zheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou 521000, China
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Lianzhu Lin
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou 521000, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou 521000, China
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2
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Singhal S, Manikrao Patil V, Verma S, Masand N. Recent advances and structure-activity relationship studies of DPP-4 inhibitors as anti-diabetic agents. Bioorg Chem 2024; 146:107277. [PMID: 38493634 DOI: 10.1016/j.bioorg.2024.107277] [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: 11/22/2023] [Revised: 02/02/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Abstract
Diabetes mellitus (DM) is one of the largest public health problems worldwide and in the last decades various therapeutic targets have been investigated. For the treatment of type-2 DM (T2DM), dipeptidyl peptidase-4 (DPP-4) is one of the well reported target and has established safety in terms of cardiovascular complexicity. Preclinical and clinical studies using DPP-4 inhibitors have demonstrated its safety and effectiveness and have lesser risk of associated hypoglycaemic effect making it suitable for elderly patients. FDA has approved a number of structurally diverse DPP-4 inhibitors for clinical use. The present manuscript aims to focus on the well reported hybrid and non-hybrid analogues and their structural activity relationship (SAR) studies. It aims to provide structural insights for this class of compounds pertaining to favourable applicability of selective DPP-4 inhibitors in the treatment of T2DM.
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Affiliation(s)
- Shipra Singhal
- Department of Pharmaceutical Chemistry, KIET School of Pharmacy, KIET Group of Institutions, Delhi NCR, Ghaziabad, Uttar Pradesh, India
| | - Vaishali Manikrao Patil
- Charak School of Pharmacy, Chaudhary Charan Singh (CCS) University, Meerut, Uttar Pradesh, India; Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia.
| | - Saroj Verma
- Department of Pharmacy, School of Medical and Allied Sciences, K. R. Mangalam University, Gurugram, India
| | - Neeraj Masand
- Department of Pharmacy, Lala Lajpat Rai Memorial Medical College, Meerut, Uttar Pradesh, India
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3
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Wu Y, Zhang J, Zhu R, Zhang H, Li D, Li H, Tang H, Chen L, Peng X, Xu X, Zhao K. Mechanistic Study of Novel Dipeptidyl Peptidase IV Inhibitory Peptides from Goat's Milk Based on Peptidomics and In Silico Analysis. Foods 2024; 13:1194. [PMID: 38672866 PMCID: PMC11049645 DOI: 10.3390/foods13081194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Two novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides (YPF and LLLP) were discovered from goat milk protein by peptidomics, in silico analysis, and in vitro assessment. A total of 698 peptides (<23 AA) were successfully identified by LC-MS/MS from goat milk hydrolysates (hydrolyzed by papaian plus proteinase K). Then, 105 potential DPP-IV inhibitory peptides were screened using PeptideRanker, the ToxinPred tool, Libdock, iDPPIV-SCM, and sequence characteristics. After ADME, physicochemical property evaluation, and a literature search, 12 candidates were efficiently selected and synthesized in vitro for functional validation. Two peptides (YPF and LLLP) were found to exert relatively high in vitro chemical system (IC50 = 368.54 ± 12.97 μM and 213.99 ± 0.64 μM) and in situ (IC50 = 159.46 ± 17.40 μM and 154.96 ± 8.41 μM) DPP-IV inhibitory capacities, and their inhibitory mechanisms were further explored by molecular docking. Our study showed that the formation of strong non-bonding interactions with the core residues from the pocket of DPP-IV (such as ARG358, PHE357, GLU205, TYR662, TYR547, and TYR666) might primarily account for the DPP-IV inhibitory activity of two identified peptides. Overall, the two novel DPP-IV inhibitory peptides rapidly identified in this study can be used as functional food ingredients for the control of diabetes.
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Affiliation(s)
- Yulong Wu
- School of Public Health, Hangzhou Normal University, Hangzhou 311121, China; (Y.W.); (R.Z.)
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Jin Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Ruikai Zhu
- School of Public Health, Hangzhou Normal University, Hangzhou 311121, China; (Y.W.); (R.Z.)
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Hong Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710062, China
| | - Dapeng Li
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
- College of Life Science, Yantai University, Yantai 264005, China;
| | - Huanhuan Li
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Honggang Tang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Lihong Chen
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
| | - Xinyan Peng
- College of Life Science, Yantai University, Yantai 264005, China;
| | - Xianrong Xu
- School of Public Health, Hangzhou Normal University, Hangzhou 311121, China; (Y.W.); (R.Z.)
| | - Ke Zhao
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (H.Z.); (D.L.); (H.L.); (H.T.); (L.C.)
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Abdisa KB, Szerdahelyi E, Molnár MA, Friedrich L, Lakner Z, Koris A, Toth A, Nath A. Metabolic Syndrome and Biotherapeutic Activity of Dairy (Cow and Buffalo) Milk Proteins and Peptides: Fast Food-Induced Obesity Perspective-A Narrative Review. Biomolecules 2024; 14:478. [PMID: 38672494 PMCID: PMC11048494 DOI: 10.3390/biom14040478] [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: 01/02/2024] [Revised: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Metabolic syndrome (MS) is defined by the outcome of interconnected metabolic factors that directly increase the prevalence of obesity and other metabolic diseases. Currently, obesity is considered one of the most relevant topics of discussion because an epidemic heave of the incidence of obesity in both developing and underdeveloped countries has been reached. According to the World Obesity Atlas 2023 report, 38% of the world population are presently either obese or overweight. One of the causes of obesity is an imbalance of energy intake and energy expenditure, where nutritional imbalance due to consumption of high-calorie fast foods play a pivotal role. The dynamic interactions among different risk factors of obesity are highly complex; however, the underpinnings of hyperglycemia and dyslipidemia for obesity incidence are recognized. Fast foods, primarily composed of soluble carbohydrates, non-nutritive artificial sweeteners, saturated fats, and complexes of macronutrients (protein-carbohydrate, starch-lipid, starch-lipid-protein) provide high metabolic calories. Several experimental studies have pointed out that dairy proteins and peptides may modulate the activities of risk factors of obesity. To justify the results precisely, peptides from dairy milk proteins were synthesized under in vitro conditions and their contributions to biomarkers of obesity were assessed. Comprehensive information about the impact of proteins and peptides from dairy milks on fast food-induced obesity is presented in this narrative review article.
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Affiliation(s)
- Kenbon Beyene Abdisa
- Department of Food Process Engineering, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, HU-1118 Budapest, Hungary; (K.B.A.)
| | - Emőke Szerdahelyi
- Department of Nutrition, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, HU-1118 Budapest, Hungary;
| | - Máté András Molnár
- Department of Food Process Engineering, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, HU-1118 Budapest, Hungary; (K.B.A.)
| | - László Friedrich
- Department of Refrigeration and Livestock Product Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 43-45, HU-1118 Budapest, Hungary
| | - Zoltán Lakner
- Department of Agricultural Business and Economics, Institute of Agricultural and Food Economics, Hungarian University of Agriculture and Life Sciences, Villányi út 29-43, HU-1118 Budapest, Hungary
| | - András Koris
- Department of Food Process Engineering, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, HU-1118 Budapest, Hungary; (K.B.A.)
| | - Attila Toth
- Division of Clinical Physiology, Department of Cardiology, Faculty of Medicine, University of Debrecen, Móricz Zsigmond út 22, HU-4032 Debrecen, Hungary
| | - Arijit Nath
- Department of Food Process Engineering, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, HU-1118 Budapest, Hungary; (K.B.A.)
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5
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Zolg S, Donzelli L, Geiss-Friedlander R. N-terminal processing by dipeptidyl peptidase 9: Cut and Go! Biochimie 2024:S0300-9084(24)00052-X. [PMID: 38461970 DOI: 10.1016/j.biochi.2024.03.002] [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: 01/16/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Dipeptidyl peptidase 9 (DPP9) is an intracellular amino-dipeptidase with physiological roles in the immune system, DNA repair and mitochondria homeostasis, while its deregulation is linked to cancer progression and immune-associated defects. Through its rare ability to cleave a peptide bond following the imino-acid proline, DPP9 acts as a molecular switch that regulates key proteins, such as the tumor-suppressor BRCA2. In this review we will discuss key concepts underlying the outcomes of protein processing by DPP9, including substrate turn-over by the N-degron pathway. Additionally, we will review non-enzymatic roles and the regulation of DPP9 by discussing the interactome of this protease, which includes SUMO1, Filamin A, NLRP1 and CARD8.
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Affiliation(s)
- Samuel Zolg
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.
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6
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Antony P, Baby B, Jobe A, Vijayan R. Computational Modeling of the Interactions between DPP IV and Hemorphins. Int J Mol Sci 2024; 25:3059. [PMID: 38474306 DOI: 10.3390/ijms25053059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Type 2 diabetes is a chronic metabolic disorder characterized by high blood glucose levels due to either insufficient insulin production or ineffective utilization of insulin by the body. The enzyme dipeptidyl peptidase IV (DPP IV) plays a crucial role in degrading incretins that stimulate insulin secretion. Therefore, the inhibition of DPP IV is an established approach for the treatment of diabetes. Hemorphins are a class of short endogenous bioactive peptides produced by the enzymatic degradation of hemoglobin chains. Numerous in vitro and in vivo physiological effects of hemorphins, including DPP IV inhibiting activity, have been documented in different systems and tissues. However, the underlying molecular binding behavior of these peptides with DPP IV remains unknown. Here, computational approaches such as protein-peptide molecular docking and extensive molecular dynamics (MD) simulations were employed to identify the binding pose and stability of peptides in the active site of DPP IV. Findings indicate that hemorphins lacking the hydrophobic residues LVV and VV at the N terminal region strongly bind to the conserved residues in the active site of DPP IV. Furthermore, interactions with these critical residues were sustained throughout the duration of multiple 500 ns MD simulations. Notably, hemorphin 7 showed higher binding affinity and sustained interactions by binding to S1 and S2 pockets of DPP IV.
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Affiliation(s)
- Priya Antony
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Bincy Baby
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Amie Jobe
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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7
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Chandravanshi K, Singh R, Bhange GN, Kumar A, Yadav P, Kumar A, Makde RD. Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Lett 2024; 598:684-701. [PMID: 38426217 DOI: 10.1002/1873-3468.14834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Acylaminoacyl peptidases (AAPs) play a pivotal role in various pathological conditions and are recognized as potential therapeutic targets. AAPs exhibit a wide range of activities, such as acylated amino acid-dependent aminopeptidase, endopeptidase, and less studied carboxypeptidase activity. We have determined the crystal structure of an AAP from Geobacillus stearothermophilus (S9gs) at 2.0 Å resolution. Despite being annotated as an aminopeptidase in the NCBI database, our enzymatic characterization proved S9gs to be a carboxypeptidase. Solution-scattering studies showed that S9gs exists as a tetramer in solution, and crystal structure analysis revealed adaptations responsible for the carboxypeptidase activity of S9gs. The findings present a hypothesis for substrate selection, substrate entry, and product exit from the active site, enriching our understanding of this rare carboxypeptidase.
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Affiliation(s)
| | - Rahul Singh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Gauri N Bhange
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Amit Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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8
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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9
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Tantapakul C, Krobthong S, Jakkaew P, Sittisaree W, Aonbangkhen C, Yingchutrakul Y. Potential of Arabica Coffee Beans from Northern Thailand: Exploring Antidiabetic Metabolites through Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS) Metabolomic Profiling across Diverse Postharvest Processing Techniques. Foods 2023; 12:3893. [PMID: 37959013 PMCID: PMC10648821 DOI: 10.3390/foods12213893] [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: 09/25/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Coffee, a widely consumed beverage worldwide, undergoes postharvest methods that influence its physicochemical characteristics, while roasting modulates its composition, affecting sensory attributes. This study investigates the impact of distinct postharvest methods (washed and natural) on the antidiabetic activities, including α-amylase and DPP4, as well as the phytochemical profiling of geological indicator (GI) coffee beans (Coffea arabica L.). The results indicate notable differences in antidiabetic activity and phytochemical profiles between washed and natural processing methods. Coffee beans processed naturally exhibit significant suppression of DPP4 and α-amylase activities (p-value < 0.01) compared to beans processed using the washed technique. TLC profiling using the ratios of the solvent systems of ethyl acetate/dichloromethane (DCM) and acetone/DCM as separation solvents reveals dominant spots for the washed technique. LC-MS/MS-based untargeted metabolomics analysis using principle component analysis (PCA) clearly segregates samples processed by the natural and washed techniques without any overlap region. A total of 1114 phytochemicals, including amino acids and short peptides, are annotated. The natural processing of coffee beans has been shown to yield a slightly higher content of chlorogenic acid (CGA) compared to the washed processing method. Our findings highlight the distinct bioactivities and phytochemical compositions of GI coffee beans processed using different techniques. This information can guide consumers in choosing coffee processing methods that offer potential benefits in terms of alternative treatment for diabetes.
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Affiliation(s)
- Cholpisut Tantapakul
- The Research Unit of Natural Product Utilization, School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Prasara Jakkaew
- School of Information Technology, Mae Fah Luang University, Thasud, Muang, Chiang Rai 57100, Thailand
| | | | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
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10
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Li Q, Deng X, Xu YJ, Dong L. Development of Long-Acting Dipeptidyl Peptidase-4 Inhibitors: Structural Evolution and Long-Acting Determinants. J Med Chem 2023; 66:11593-11631. [PMID: 37647598 DOI: 10.1021/acs.jmedchem.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Considerable effort has been made to achieve less frequent dosing in the development of DPP-4 inhibitors. Enthusiasm for long-acting DPP-4 inhibitors is based on the promise that such agents with less frequent dosing regimens are associated with improved patient adherence, but the rational design of long-acting DPP-4 inhibitors remains a major challenge. In this Perspective, the development of long-acting DPP-4 inhibitors is comprehensively summarized to highlight the evolution of initial lead compounds on the path toward developing long-acting DPP-4 inhibitors over nearly three decades. The determinants for long duration of action are then examined, including the nature of the target, potency, binding kinetics, crystal structures, selectivity, and preclinical and clinical pharmacokinetic and pharmacodynamic profiles. More importantly, several possible approaches for the rational design of long-acting drugs are discussed. We hope that this information will facilitate the design and development of safer and more effective long-acting DPP-4 inhibitors and other oral drugs.
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Affiliation(s)
- Qing Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Xiaoyan Deng
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Yan-Jun Xu
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China
| | - Lin Dong
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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11
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deKay JT, May TL, Riker RR, Rud J, Gagnon DJ, Sawyer DB, Seder DB, Ryzhov S. The number of circulating CD26 expressing cells is decreased in critical COVID-19 illness. Cytometry A 2023; 103:153-161. [PMID: 35246910 PMCID: PMC9087143 DOI: 10.1002/cyto.a.24547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/11/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022]
Abstract
We evaluated the number of CD26 expressing cells in peripheral blood of patients with COVID-19 within 72 h of admission and on day 4 and day 7 after enrollment. The majority of CD26 expressing cells were presented by CD3+ CD4+ lymphocytes. A low number of CD26 expressing cells were found to be associated with critical-severity COVID-19 disease. Conversely, increasing numbers of CD26 expressing T cells over the first week of standard treatment was associated with good outcomes. Clinically, the number of circulating CD26 cells might be a marker of recovery or the therapeutic efficacy of anti-COVID-19 treatment. New therapies aimed at preserving and increasing the level of CD26 expressing T cells may prove useful in the treatment of COVID-19 disease.
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Affiliation(s)
- Joanne T. deKay
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
| | - Teresa L. May
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
- Department of Critical Care ServicesMaine Medical CenterPortlandMaineUSA
| | - Richard R. Riker
- Department of Critical Care ServicesMaine Medical CenterPortlandMaineUSA
| | - Jonathan Rud
- Department of Critical Care ServicesMaine Medical CenterPortlandMaineUSA
| | - David J. Gagnon
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
- Department of PharmacyMaine Medical CenterPortlandMaineUSA
- Tufts University School of MedicineBostonMassachusettsUSA
| | - Douglas B. Sawyer
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
- Department of Critical Care ServicesMaine Medical CenterPortlandMaineUSA
| | - David B. Seder
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
- Department of Critical Care ServicesMaine Medical CenterPortlandMaineUSA
| | - Sergey Ryzhov
- Center for Molecular MedicineMaine Medical Center Research InstituteScarboroughMaineUSA
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12
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Bozorgmehr N, Hnatiuk M, Peters AC, Elahi S. Depletion of polyfunctional CD26 highCD8 + T cells repertoire in chronic lymphocytic leukemia. Exp Hematol Oncol 2023; 12:13. [PMID: 36707896 PMCID: PMC9881277 DOI: 10.1186/s40164-023-00375-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND CD8+ T cells play an essential role against tumors but the role of human CD8+CD26+ T cell subset against tumors, in particular, haematological cancers such as chronic lymphocytic leukemia (CLL) remains unknown. Although CD4+CD26high T cells are considered for adoptive cancer immunotherapy, the role of CD8+CD26+ T cells is ill-defined. Therefore, further studies are required to better determine the role of CD8+CD26+ T cells in solid tumors and haematological cancers. METHODS We studied 55 CLL and 44 age-sex-matched healthy controls (HCs). The expression of CD26 on different T cell subsets (e.g. naïve, memory, effector, and etc.) was analyzed. Also, functional properties of CD8+CD26+ and CD8+CD26- T cells were evaluated. Finally, the plasma cytokine/chemokine and Galectin-9 (Gal-9) levels were examined. RESULTS CD26 expression identifies three CD8+ T cell subsets with distinct immunological properties. While CD26negCD8+ T cells are mainly transitional, effector memory and effectors, CD26lowCD8+ T cells are mainly naïve, stem cell, and central memory but CD26high T cells are differentiated to transitional and effector memory. CD26+CD8+ T cells are significantly reduced in CLL patients versus HCs. CD26high cells are enriched with Mucosal Associated Invariant T (MAIT) cells co-expressing CD161TVα7.2 and IL-18Rα. Also, CD26high cells have a rich chemokine receptor profile (e.g. CCR5 and CCR6), profound cytokine (TNF-α, IFN-γ, and IL-2), and cytolytic molecules (Granzyme B, K, and perforin) expression upon stimulation. CD26high and CD26low T cells exhibit significantly lower frequencies of CD160, 2B4, TIGIT, ICOS, CD39, and PD-1 but higher levels of CD27, CD28, and CD73 versus CD26neg cells. To understand the mechanism linked to CD26high depletion, we found that malignant B cells by shedding Galectin-9 (Gal-9) contribute to the elevation of plasma Gal-9 in CLL patients. In turn, Gal-9 and the inflammatory milieu (IL-18, IL-12, and IL-15) in CLL patients contribute to increased apoptosis of CD26high T cells. CONCLUSIONS Our results demonstrate that CD26+ T cells possess a natural polyfunctionality to traffic and exhibit effector functions and resist exhaustion. Therefore, they can be proposed for adoptive cancer immunotherapy. Finally, neutralizing and/or inhibiting Gal-9 may preserve CD26highCD8+ T cells in CLL.
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Affiliation(s)
- Najmeh Bozorgmehr
- grid.17089.370000 0001 2190 316XSchool of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Mark Hnatiuk
- grid.17089.370000 0001 2190 316XDepatment of Medicine Division of Hematology, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Anthea C. Peters
- grid.17089.370000 0001 2190 316XDepartment of Oncology, Division of Medical Oncology, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Shokrollah Elahi
- grid.17089.370000 0001 2190 316XSchool of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada ,grid.17089.370000 0001 2190 316XDepartment of Oncology, Division of Medical Oncology, University of Alberta, Edmonton, AB T6G 2E1 Canada ,grid.17089.370000 0001 2190 316XLi Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1 Canada
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13
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Human Coronavirus Cell Receptors Provide Challenging Therapeutic Targets. Vaccines (Basel) 2023; 11:vaccines11010174. [PMID: 36680018 PMCID: PMC9862439 DOI: 10.3390/vaccines11010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Coronaviruses interact with protein or carbohydrate receptors through their spike proteins to infect cells. Even if the known protein receptors for these viruses have no evolutionary relationships, they do share ontological commonalities that the virus might leverage to exacerbate the pathophysiology. ANPEP/CD13, DPP IV/CD26, and ACE2 are the three protein receptors that are known to be exploited by several human coronaviruses. These receptors are moonlighting enzymes involved in several physiological processes such as digestion, metabolism, and blood pressure regulation; moreover, the three proteins are expressed in kidney, intestine, endothelium, and other tissues/cell types. Here, we spot the commonalities between the three enzymes, the physiological functions of the enzymes are outlined, and how blocking either enzyme results in systemic deregulations and multi-organ failures via viral infection or therapeutic interventions is addressed. It can be difficult to pinpoint any coronavirus as the target when creating a medication to fight them, due to the multiple processes that receptors are linked to and their extensive expression.
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14
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Cieślińska A, Fiedorowicz E, Rozmus D, Sienkiewicz-Szłapka E, Jarmołowska B, Kamiński S. Does a Little Difference Make a Big Difference? Bovine β-Casein A1 and A2 Variants and Human Health-An Update. Int J Mol Sci 2022; 23:15637. [PMID: 36555278 PMCID: PMC9779325 DOI: 10.3390/ijms232415637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
For over 20 years, bovine beta-casein has been a subject of increasing scientific interest because its genetic A1 variant during gastrointestinal digestion releases opioid-like peptide β-casomorphin-7 (β-CM-7). Since β-CM-7 is involved in the dysregulation of many physiological processes, there is a growing discussion of whether the consumption of the β-casein A1 variant has an influence on human health. In the last decade, the number of papers dealing with this problem has substantially increased. The newest clinical studies on humans showed a negative effect of variant A1 on serum glutathione level, digestive well-being, cognitive performance score in children, and mood score in women. Scientific reports in this field can affect the policies of dairy cattle breeders and the milk industry, leading to the elimination of allele A1 in dairy cattle populations and promoting milk products based on milk from cows with the A2A2 genotype. More scientific proof, especially in well-designed clinical studies, is necessary to determine whether a little difference in the β-casein amino acid sequence negatively affects the health of milk consumers.
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Affiliation(s)
- Anna Cieślińska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Ewa Fiedorowicz
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Dominika Rozmus
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Edyta Sienkiewicz-Szłapka
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Beata Jarmołowska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Stanisław Kamiński
- Department of Animal Genetics, University of Warmia and Mazury, 10-719 Olsztyn, Poland
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15
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Barchetta I, Cimini FA, Dule S, Cavallo MG. Dipeptidyl Peptidase 4 (DPP4) as A Novel Adipokine: Role in Metabolism and Fat Homeostasis. Biomedicines 2022; 10:biomedicines10092306. [PMID: 36140405 PMCID: PMC9496088 DOI: 10.3390/biomedicines10092306] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Dipeptidyl peptidase 4 (DPP4) is a molecule implicated in the regulation of metabolic homeostasis and inflammatory processes, and it exerts its main action through its enzymatic activity. DPP4 represents the enzyme most involved in the catabolism of incretin hormones; thus, its activity impacts appetite, energy balance, and the fine regulation of glucose homeostasis. Indeed, DPP4 inhibitors represent a class of antidiabetic agents widely used for the treatment of Type 2 diabetes mellitus (T2DM). DPP4 also acts as an adipokine and is mainly secreted by the adipose tissue, mostly from mature adipocytes of the visceral compartment, where it exerts autocrine and paracrine activities. DPP4 can disrupt insulin signaling within the adipocyte and in other target cells and tissues, where it also favors the development of a proinflammatory environment. This is likely at the basis of the presence of elevated circulating DPP4 levels in several metabolic diseases. In this review, we summarize the most recent evidence of the role of the DPP4 as an adipokine-regulating glucose/insulin metabolism and fat homeostasis, with a particular focus on clinical outcomes associated with its increased secretion in the presence of adipose tissue accumulation and dysfunction.
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16
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Zhang M, Zhu L, Wu G, Liu T, Qi X, Zhang H. Rapid Screening of Novel Dipeptidyl Peptidase-4 Inhibitory Peptides from Pea ( Pisum sativum L.) Protein Using Peptidomics and Molecular Docking. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10221-10228. [PMID: 35951551 DOI: 10.1021/acs.jafc.2c03949] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pea protein hydrolysates (PPHs) possess good hypoglycemic effects; however, their dipeptidyl peptidase-4 (DPP-4) inhibitory activity is poorly understood, and none of the DPP-4 inhibitory peptides have been identified from PPHs. This paper aims to rapidly screen these peptides from PPHs by combining peptidomics and molecular docking. In this study, 543 peptides were identified by peptidomics, and four peptides (IPYWTY, IPYWT, LPNYN, and LAFPGSS) with DPP-4 half-maximal inhibitory concentration (IC50) values <100 μM were screened for the first time. Significantly, peptide IPYWTY exhibited the most potent DPP-4 inhibitory activity (IC50 = 11.04 μM) mainly because it formed hydrophobic interactions with the S1 pocket in DPP-4. These results indicated that combining peptidomics and molecular docking is an effective strategy for rapidly screening DPP-4 inhibitory peptides.
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Affiliation(s)
- Mingkai Zhang
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Ling Zhu
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Gangcheng Wu
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Tongtong Liu
- Binzhou Zhongyu Food Company Limited, Key Laboratory of Wheat Processing, Ministry of Agriculture and Rural Affairs, National Industry Technical Innovation Center for Wheat Processing, Bohai Advanced Technology Institute, Binzhou, 256600, China
| | - Xiguang Qi
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Hui Zhang
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
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17
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Role of Dipeptidyl Peptidase-4 (DPP4) on COVID-19 Physiopathology. Biomedicines 2022; 10:biomedicines10082026. [PMID: 36009573 PMCID: PMC9406088 DOI: 10.3390/biomedicines10082026] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
DPP4/CD26 is a single-pass transmembrane protein with multiple functions on glycemic control, cell migration and proliferation, and the immune system, among others. It has recently acquired an especial relevance due to the possibility to act as a receptor or co-receptor for SARS-CoV-2, as it has been already demonstrated for other coronaviruses. In this review, we analyze the evidence for the role of DPP4 on COVID-19 risk and clinical outcome, and its contribution to COVID-19 physiopathology. Due to the pathogenetic links between COVID-19 and diabetes mellitus and the hyperinflammatory response, with the hallmark cytokine storm developed very often during the disease, we dive deep into the functions of DPP4 on carbohydrate metabolism and immune system regulation. We show that the broad spectrum of functions regulated by DPP4 is performed both as a protease enzyme, as well as an interacting partner of other molecules on the cell surface. In addition, we provide an update of the DPP4 inhibitors approved by the EMA and/or the FDA, together with the newfangled approval of generic drugs (in 2021 and 2022). This review will also cover the effects of DPP4 inhibitors (i.e., gliptins) on the progression of SARS-CoV-2 infection, showing the role of DPP4 in this disturbing disease.
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18
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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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19
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Pan J, Zhang Q, Zhang C, Yang W, Liu H, Lv Z, Liu J, Jiao Z. Inhibition of Dipeptidyl Peptidase-4 by Flavonoids: Structure–Activity Relationship, Kinetics and Interaction Mechanism. Front Nutr 2022; 9:892426. [PMID: 35634373 PMCID: PMC9134086 DOI: 10.3389/fnut.2022.892426] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022] Open
Abstract
With the aim to establish a structure-inhibitory activity relationship of flavonoids against dipeptidyl peptidase-4 (DPP-4) and elucidate the interaction mechanisms between them, a pannel of 70 structurally diverse flavonoids was used to evaluate their inhibitory activities against DPP-4, among which myricetin, hyperoside, narcissoside, cyanidin 3-O-glucoside, and isoliquiritigenin showed higher inhibitory activities in a concentration-dependent manner. Structure-activity relationship analysis revealed that introducing hydroxyl groups to C3', C4', and C6 of the flavonoid structure was beneficial to improving the inhibitory efficacy against DPP-4, whereas the hydroxylation at position 3 of ring C in the flavonoid structure was unfavorable for the inhibition. Besides, the methylation of the hydroxyl groups at C3', C4', and C7 of the flavonoid structure tended to lower the inhibitory activity against DPP-4, and the 2,3-double bond and 4-carbonyl group on ring C of the flavonoid structure was essential for the inhibition. Glycosylation affected the inhibitory activity diversely, depending on the structure of flavonoid aglycone, type of glycoside, as well as the position of substitution. Inhibition kinetic analysis suggested that myricetin reversibly inhibited DPP-4 in a non-competitive mode, whereas hyperoside, narcissoside, cyanidin 3-O-glucoside, and isoliquiritigenin all reversibly inhibited DPP-4 in a mixed type. Moreover, the fluorescence quenching analysis indicated that all the five flavonoid compounds could effectively quench the intrinsic fluorescence of DPP-4 by spontaneously binding with it to form an unstable complex. Hydrogen bonds and van der Waals were the predominant forces to maintain the complex of myricetin with DPP-4, and electrostatic forces might play an important role in stabilizing the complexes of the remaining four flavonoids with DPP-4. The binding of the tested flavonoids to DPP-4 could also induce the conformation change of DPP-4 and thus led to inhibition on the enzyme. Molecular docking simulation further ascertained the binding interactions between DPP-4 and the selected five flavonoids, among which hyperoside, narcissoside, cyaniding 3-O-glucoside, and isoliquiritigenin inserted into the active site cavity of DPP-4 and interacted with the key amino acid residues of the active site, whereas the binding site of myricetin was located in a minor cavity close to the active pockets of DPP-4.
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20
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Liao HJ, Tzen JTC. The Potential Role of Cyclopeptides from Pseudostellaria heterophylla, Linum usitatissimum and Drymaria diandra, and Peptides Derived from Heterophyllin B as Dipeptidyl Peptidase IV Inhibitors for the Treatment of Type 2 Diabetes: An In Silico Study. Metabolites 2022; 12:metabo12050387. [PMID: 35629891 PMCID: PMC9146144 DOI: 10.3390/metabo12050387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Dipeptidyl peptidase 4 (DPP4) inhibitors can treat type 2 diabetes by slowing GLP-1 degradation to increase insulin secretion. Studies have reported that Pseudostellaria heterophylla, Linum usita-tissimum (flaxseed), and Drymaria diandra, plants rich in Caryophyllaceae-type cyclopeptides and commonly used as herbal or dietary supplements, are effective in controlling blood sugar. The active site of DPP4 is in a cavity large enough to accommodate their cyclopeptides. Molecular modeling by AutoDock Vina reveals that certain cyclopeptides in these plants have the potential for DPP4 inhibition. In particular, “Heterophyllin B” from P. heterophylla, “Cyclolinopeptide C” from flaxseed, and “Diandrine C” from D. diandra, with binding affinities of −10.4, −10.0, and −10.7 kcal/mol, are promising. Docking suggests that DPP4 inhibition may be one of the reasons why these three plants are beneficial for lowering blood sugar. Because many protein hydrolysates have shown the effect of DPP4 inhibition, a series of peptides derived from Heterophyllin B precursor “IFGGLPPP” were included in the study. It was observed that IFWPPP (−10.5 kcal/mol), IFGGWPPP (−11.4 kcal/mol), and IFGWPPP (−12.0 kcal/mol) showed good binding affinity and interaction for DPP4. Various IFGGLPPP derivatives have the potential to serve as scaffolds for the design of novel DPP4 inhibitors.
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21
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Faucher M, Geoffroy TR, Thibodeau J, Gaaloul S, Bazinet L. Semi-Industrial Production of a DPP-IV and ACE Inhibitory Peptide Fraction from Whey Protein Concentrate Hydrolysate by Electrodialysis with Ultrafiltration Membrane. MEMBRANES 2022; 12:membranes12040409. [PMID: 35448379 PMCID: PMC9025977 DOI: 10.3390/membranes12040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/05/2023]
Abstract
The separation by electrodialysis with ultrafiltration membranes (EDUF), at a semi-industrial scale, of a new whey protein hydrolysate obtained from a whey protein concentrate was assessed. After 6 h of treatment, more than 9 g of peptides were recovered in the peptide recovery fraction, for a recovery yield of 5.46 ± 0.56% and containing 18 major components. Among these components, positively charged peptides, such as ALPMHIR + PHMIR, LIVTQTMK and TKIPAVF, were present, and their relative abundances increased by nearly 1.25 X and up to 7.55 X. The presence of these peptides may be promising, as ALPMHIR has a strong activity against angiotensin-converting enzyme (ACE), and LIVTQTMK has structural properties that could interfere with dipeptidyl peptidase-IV (DPP-IV). Many neutral peptides were also recovered alongside those. Nevertheless, the inhibitory activity against DPP-IV and ACE increased from 2 X and 4 X, respectively, in the peptide recovery fraction compared to the initial hydrolysate, due to the improved content in bioactive peptides. Thus, this new hydrolysate is well-suited for the large-scale production of a peptide fraction with high bioactivities. Furthermore, what was achieved in this work came close to what could be achieved for the industrial production of a bioactive peptide fraction from whey proteins.
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Affiliation(s)
- Mélanie Faucher
- Institute of Nutrition and Functional Food (INAF) and Food Science Department, Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada; (M.F.); (T.R.G.); (J.T.)
- Laboratoire de Transformation Alimentaire et Procédés Électro-membranaires (LTAPEM, Laboratory of Food Processing and Electro-Membrane Processes), Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Thibaud R. Geoffroy
- Institute of Nutrition and Functional Food (INAF) and Food Science Department, Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada; (M.F.); (T.R.G.); (J.T.)
- Laboratoire de Transformation Alimentaire et Procédés Électro-membranaires (LTAPEM, Laboratory of Food Processing and Electro-Membrane Processes), Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Jacinthe Thibodeau
- Institute of Nutrition and Functional Food (INAF) and Food Science Department, Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada; (M.F.); (T.R.G.); (J.T.)
- Laboratoire de Transformation Alimentaire et Procédés Électro-membranaires (LTAPEM, Laboratory of Food Processing and Electro-Membrane Processes), Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sami Gaaloul
- Lactalis Canada, Victoriaville, QC G6P 9V7, Canada;
| | - Laurent Bazinet
- Institute of Nutrition and Functional Food (INAF) and Food Science Department, Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada; (M.F.); (T.R.G.); (J.T.)
- Laboratoire de Transformation Alimentaire et Procédés Électro-membranaires (LTAPEM, Laboratory of Food Processing and Electro-Membrane Processes), Pavillon Paul Comtois, Université Laval, Quebec City, QC G1V 0A6, Canada
- Correspondence:
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22
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Nasr NE, Sadek KM. Role and mechanism(s) of incretin-dependent therapies for treating diabetes mellitus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:18408-18422. [PMID: 35031999 DOI: 10.1007/s11356-022-18534-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Diabetes mellitus (DM) is a worldwide ailment which leads to chronic complications like cardiac disorders, renal perturbations, limb amputation and blindness. Type one diabetes (T1DM), Type two diabetes (T2DM), Another types of diabetes, such as genetic errors in function of β-cell and action of insulin, cystic fibrosis, chemical-instigated diabetes or following tissue transplantation), and pregnancy DM (GDM). In response to nutritional ingestion, the gut may release a pancreatic stimulant that affects carbohydrate metabolism. The duodenum produces a 'chemical excitant' that stimulates pancreatic output, and researchers have sought to cure diabetes using gut extract injections, coining the word 'incretin' to describe the phenomena. Incretins include GIP and GLP-1. The 'enteroinsular axis' is the link between pancreas and intestine. Nutrient, neuronal and hormonal impulses from intestine to cells secreting insulin were thought to be part of this axis. In addition, the hormonal component, incretin, must meet two requirements: (1) it secreted by foods, mainly carbohydrates, and (2) it must induce an insulinotropic effect which is glucose-dependent. In this review, we clarify the ability of using incretin-dependent treatments for treating DM.
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Affiliation(s)
- Nasr E Nasr
- Department of Biochemistry, Faculty of Veterinary Medicine, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt
| | - Kadry M Sadek
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt.
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23
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Kęska P, Stadnik J. Dipeptidyl Peptidase IV Inhibitory Peptides Generated in Dry-Cured Pork Loin during Aging and Gastrointestinal Digestion. Nutrients 2022; 14:nu14040770. [PMID: 35215420 PMCID: PMC8878428 DOI: 10.3390/nu14040770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
The ability of peptides from an aqueous and salt-soluble protein extract of dry-cured pork loins to inhibit the action of dipeptidyl peptidase IV was determined. This activity was assessed at different times of the production process, i.e., 28, 90, 180, 270 and 360 days. The resistance of the biological property during the simulated digestive process was also assessed. For this, the extracts were hydrolyzed with pepsin and pancreatin as a simulated digestion step of the gastrointestinal tract and fractionated (>7 kDa) as an intestinal absorption step. The results indicate that dried-pork-loin peptides may have potential as functional food ingredients in the prevention and treatment of type 2 diabetes mellitus. In particular, the APPPPAEV, APPPPAEVH, KLPPLPL, RLPLLP, VATPPPPPPK, VPIPVPLPM and VPLPVPVPI sequences show promise as natural food compounds helpful in maintaining good health.
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Pascual Alonso I, Valiente PA, Valdés-Tresanco ME, Arrebola Y, Almeida García F, Díaz L, García G, Guirola O, Pastor D, Bergado G, Sánchez B, Charli JL. Discovery of tight-binding competitive inhibitors of dipeptidyl peptidase IV. Int J Biol Macromol 2022; 196:120-130. [PMID: 34920066 DOI: 10.1016/j.ijbiomac.2021.12.056] [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: 06/01/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022]
Abstract
Dipeptidyl peptidase IV (DPP-IV, EC 3.4.14.5) is an abundant serine aminopeptidase that preferentially cleaves N-terminal Xaa-Pro or Xaa-Ala dipeptides from oligopeptides. Inhibitors of DPP-IV activity are used for treating type 2 diabetes mellitus and other diseases. DPP-IV is also involved in tumor progression. We identified four new non-peptide tight-binding competitive inhibitors of porcine DPP-IV by virtual screening and enzymatic assays. Molecular docking simulations supported the competitive behavior, and the selectivity of one of the compounds in the DPP-IV family. Since three of these inhibitors are also aminopeptidase N (APN) inhibitors, we tested their impact on APN+/DPP-IV+ and DPP-IV+ human tumor cells' viability. Using kinetic assays, we determined that HL-60 tumor cells express both APN and DPP-IV activities and that MDA-MB-231 tumor cells express DPP-IV activity. The inhibitors had a slight inhibitory effect on human HEK-293 cell viability but reduced the viability of APN+/DPP-IV+ and DPP-IV+ human tumor cells more potently. Remarkably, the intraperitoneal injection of these compounds inhibited DPP-IV activity in rat brain, liver, and pancreas. In silico studies suggested inhibitors binding to serum albumin contribute to blood-brain barrier crossing. The spectrum of action of some of these compounds may be useful for niche applications.
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Affiliation(s)
| | - Pedro A Valiente
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Canada.
| | - Mario E Valdés-Tresanco
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Yarini Arrebola
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba
| | | | - Lisset Díaz
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba
| | - Gabriela García
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba
| | - Osmany Guirola
- Centro de Ingeniería Genética y Biotecnología, BioCubafarma, Cuba
| | - Daniel Pastor
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba
| | | | | | - Jean-Louis Charli
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
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Sharma A, Virmani T, Sharma A, Chhabra V, Kumar G, Pathak K, Alhalmi A. Potential Effect of DPP-4 Inhibitors Towards Hepatic Diseases and Associated Glucose Intolerance. Diabetes Metab Syndr Obes 2022; 15:1845-1864. [PMID: 35733643 PMCID: PMC9208633 DOI: 10.2147/dmso.s369712] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/10/2022] [Indexed: 11/23/2022] Open
Abstract
Dipeptidyl-peptidase-4 (DPP-4) is an enzyme having various properties and physiological roles in lipid accumulation, resistance to anticancer agents, and immune stimulation. DPP-4 includes membrane-bound peptidases and is a kind of enzyme that cleaves alanine or proline-containing peptides such as incretins, chemokines, and appetite-suppressing hormones (neuropeptide) at their N-terminal dipeptides. DPP-4 plays a role in the final breakdown of peptides produced by other endo and exo-peptidases from nutritious proteins and their absorption in these tissues. DPP-4 enzyme activity has different modes of action on glucose metabolism, hunger regulation, gastrointestinal motility, immune system function, inflammation, and pain regulation. According to the literature survey, as DPP-4 levels increase in individuals with liver conditions, up-regulation of hepatic DPP-4 expression is likely to be the cause of glucose intolerance or insulin resistance. This review majorly focuses on the cleavage of alanine or proline-containing peptides such as incretins by the DPP-4 and its resulting conditions like glucose intolerance and cause of DPP-4 level elevation due to some liver conditions. Thus, we have discussed the various effects of DPP-4 on the liver diseases like hepatitis C, non-alcoholic fatty liver, hepatic regeneration and stem cell, hepatocellular carcinoma, and the impact of elevated DPP-4 levels in association with liver diseases as a cause of glucose intolerance and their treatment drug of choices. In addition, the effect of DPP-4 inhibitors on obesity and their negative aspects are also discussed in brief.
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Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana, 121105, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana, 121105, India
| | - Anjali Sharma
- Freelancer, Pharmacovigilance Expert, Uttar Pradesh, India
| | - Vaishnavi Chhabra
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana, 121105, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana, 121105, India
| | - Kamla Pathak
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences, Uttar Pradesh, 206130, India
| | - Abdulsalam Alhalmi
- Department of Pharmaceutical Science, College of Pharmacy, Aden University, Aden, Yemen
- Correspondence: Abdulsalam Alhalmi, Department of Pharmaceutical Science, College of Pharmacy, Aden University, Aden, Yemen, Email
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Santos-Hernández M, Cermeño M, Recio I, FitzGerald RJ. In vitro dipeptidyl peptidase IV inhibitory activity and in situ insulinotropic activity of milk and egg white protein digests. Food Funct 2021; 12:12372-12380. [PMID: 34854453 DOI: 10.1039/d1fo00641j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Dietary proteins are involved in the regulation of glucose homeostasis by different mechanisms. Food protein digestion products are reported to inhibit dipeptidyl peptidase IV (DPP-IV), induce incretin secretion or directly exert an insulinotropic effect in pancreatic β-cells. This study illustrates the DPP-IV inhibitory activity of gastric and intestinal digests of casein, whey and egg white proteins determined in vitro, using Gly-Pro-AMC, and in situ using non-differentiated Caco-2 cells. Comparable trends in the DPP-IV inhibitory profiles were obtained by these two methods although the extent of inhibition in situ was consistently lower than the inhibition observed in vitro. Casein intestinal digests and whey protein gastric and intestinal digests showed potent DPP-IV inhibitory activities in Caco-2 cells with IC50 values ranging from 0.8 to 1.2 mg mL-1. The absorbed fraction of the intestinal digests from whey and egg white protein induced insulin secretion in BRIN-BD11 cells when determined using a two-tiered cellular model (Caco-2 and BRIN-BD11). However, the gastric digests from the same substrates showed no insulin secretion. This may be related to limited trans-epithelial transport through the Caco-2 monolayer of the gastric digestion products. However, both, gastric and intestinal digests were able to induce insulin secretion in BRIN-BD11 cells when the monolayer was composed of a co-culture of STC-1 and Caco-2 cells. This result may be attributed to the activation of STC-1 cells and subsequent incretin secretion, induced by the gastric digest, as shown by an enhanced intracellular calcium uptake.
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Affiliation(s)
- Marta Santos-Hernández
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolás Cabrera, 9, 28049 Madrid, Spain.,Department of Biological Sciences, University of Limerick, Castletroy, Limerick, Ireland.
| | - Maria Cermeño
- Department of Biological Sciences, University of Limerick, Castletroy, Limerick, Ireland.
| | - Isidra Recio
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - Richard J FitzGerald
- Department of Biological Sciences, University of Limerick, Castletroy, Limerick, Ireland.
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López-Cortés GI, Díaz-Alvarez L, Ortega E. Leukocyte Membrane Enzymes Play the Cell Adhesion Game. Front Immunol 2021; 12:742292. [PMID: 34887854 PMCID: PMC8650063 DOI: 10.3389/fimmu.2021.742292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
For a long time, proteins with enzymatic activity have not been usually considered to carry out other functions different from catalyzing chemical reactions within or outside the cell. Nevertheless, in the last few years several reports have uncovered the participation of numerous enzymes in other processes, placing them in the category of moonlighting proteins. Some moonlighting enzymes have been shown to participate in complex processes such as cell adhesion. Cell adhesion plays a physiological role in multiple processes: it enables cells to establish close contact with one another, allowing communication; it is a key step during cell migration; it is also involved in tightly binding neighboring cells in tissues, etc. Importantly, cell adhesion is also of great importance in pathophysiological scenarios like migration and metastasis establishment of cancer cells. Cell adhesion is strictly regulated through numerous switches: proteins, glycoproteins and other components of the cell membrane. Recently, several cell membrane enzymes have been reported to participate in distinct steps of the cell adhesion process. Here, we review a variety of examples of membrane bound enzymes participating in adhesion of immune cells.
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Affiliation(s)
- Georgina I López-Cortés
- Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Díaz-Alvarez
- Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Ortega
- Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Setayesh-Mehr Z, Poorsargol M. HL-7 and HL-10 Peptides Stimulate Insulin Secretion in the INS-1 Insulinoma Cell Line through Incretin-Dependent Pathway and Increasing the Glucose Uptake in L6 Myoblast. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kumar S, Mittal A, Mittal A. A review upon medicinal perspective and designing rationale of DPP-4 inhibitors. Bioorg Med Chem 2021; 46:116354. [PMID: 34428715 DOI: 10.1016/j.bmc.2021.116354] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022]
Abstract
Type 2 Diabetes Mellitus (T2DM) is one of the highly prevalence disorder and increasing day by day worldwidely. T2DM is a metabolic disorder, which is characterized by deficiency in insulin or resistance to insulin and thus increases the glucose levels in the blood. Various approaches are there to treat diabetes but still there is no cure for this disease. DPP-4 inhibitor is a privileged target in the field of drug discovery and provides various opportunities in exploring this target for development of molecules as antidiabetic agents. DPP-4 acts by inhibiting the incretin action and thus decreases the level of blood glucose by imparting minimal side effects. Sitagliptin, vildagliptin, linagliptin etc. are the different DPP-4 based drugs approved throughout the world for the treatment of diabetes mellitus. Cyanopyrrolidines, triazolopiperazine amide, pyrrolidines are basic core nucleus present in various DPP-4 inhibitors and has potential effects. In the past few years, researchers had applied various approaches to synthesize potent DPP-4 inhibitors as antidiabetic agent without side effects like weight gain, cardiovascular risks, retinopathy etc. This review will also emphasize the recent strategies and rationale utilized by researchers for the development of DPP-4 inhibitors. This review also reveals about the various other approaches like molecular modelling, ligand based drug designing, high throughput screening etc. are used by the various research group for the development of potential DPP-4 inhibitors.
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Affiliation(s)
- Shubham Kumar
- Faculty of Pharmaceutical Sciences, PCTE Group of Institutes, Campus-2, Near Baddowal Cantt. Ferozepur Road, Ludhiana 142021, India; Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road (NH-1), Phagwara, Punjab 144411, India
| | - Anu Mittal
- Department of Chemistry, Guru Nanak Dev University College, Patti, Distt. Tarn Taran, India
| | - Amit Mittal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road (NH-1), Phagwara, Punjab 144411, India.
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Zhao L, Zhang M, Pan F, Li J, Dou R, Wang X, Wang Y, He Y, Wang S, Cai S. In silico analysis of novel dipeptidyl peptidase-IV inhibitory peptides released from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and the possible pathways involved in diabetes protection. Curr Res Food Sci 2021; 4:603-611. [PMID: 34522898 PMCID: PMC8424447 DOI: 10.1016/j.crfs.2021.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/14/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
The aim of the present study was to screen novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and evaluate the potential antidiabetic targets and involved signaling pathways using in silico approaches. In silico digestion of MiAMP2 with pepsin, trypsin and chymotrypsin was performed with ExPASy PeptideCutter and the generated peptides were subjected to BIOPEP-UWM, iDrug, INNOVAGEN and Autodock Vina for further analyses. Six novel peptides EQVR, EQVK, AESE, EEDNK, EECK, and EVEE were predicted to possess good DPP-IV inhibitory potentials, water solubility, and absorption, distribution, metabolism, excretion, and toxicity properties. Molecular dynamic simulation and molecular docking displayed that AESE was the most potent DPP-IV inhibitory peptide and can bind with the active sites of DPP-IV through hydrogen bonding and van der Waals forces. The potential antidiabetic targets of AESE were retrieved from SwissTargetPrediction and GeneCards databases. Protein-protein interaction analysis identified BIRC2, CASP3, MMP7 and BIRC3 to be the hub targets. Moreover, the KEGG pathway enrichment analysis showed that AESE prevented diabetes through the apoptosis and TNF signaling pathways. These results will provide new insights into utilization of MiAMP2 as functional food ingredients for the prevention and treatment of diabetes.
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Affiliation(s)
- Lei Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Mingxin Zhang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Fei Pan
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ran Dou
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Xinyi Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Yangyang Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Yumeng He
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Shaoxuan Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, China
| | - Shengbao Cai
- Faculty of Agriculture and Food, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
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Textile Dye Biodecolorization by Manganese Peroxidase: A Review. Molecules 2021; 26:molecules26154403. [PMID: 34361556 PMCID: PMC8348190 DOI: 10.3390/molecules26154403] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/25/2022] Open
Abstract
Wastewater emissions from textile factories cause serious environmental problems. Manganese peroxidase (MnP) is an oxidoreductase with ligninolytic activity and is a promising biocatalyst for the biodegradation of hazardous environmental contaminants, and especially for dye wastewater decolorization. This article first summarizes the origin, crystal structure, and catalytic cycle of MnP, and then reviews the recent literature on its application to dye wastewater decolorization. In addition, the application of new technologies such as enzyme immobilization and genetic engineering that could improve the stability, durability, adaptability, and operating costs of the enzyme are highlighted. Finally, we discuss and propose future strategies to improve the performance of MnP-assisted dye decolorization in industrial applications.
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Ayoub BM, Michel HE, Mowaka S, Hendy MS, Tadros MM. Repurposing of Omarigliptin as a Neuroprotective Agent Based on Docking with A 2A Adenosine and AChE Receptors, Brain GLP-1 Response and Its Brain/Plasma Concentration Ratio after 28 Days Multiple Doses in Rats Using LC-MS/MS. Molecules 2021; 26:molecules26040889. [PMID: 33567615 PMCID: PMC7915074 DOI: 10.3390/molecules26040889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
Abstract
The authors in the current work suggested the potential repurposing of omarigliptin (OMR) for neurodegenerative diseases based on three new findings that support the preliminary finding of crossing BBB after a single dose study in the literature. The first finding is the positive results of the docking study with the crystal structures of A2A adenosine (A2AAR) and acetylcholine esterase (AChE) receptors. A2AAR is a member of non-dopaminergic GPCR superfamily receptor proteins and has essential role in regulation of glutamate and dopamine release in Parkinson’s disease while AChE plays a major role in Alzheimer’s disease as the primary enzyme responsible for the hydrolytic metabolism of the neurotransmitter acetylcholine into choline and acetate. Docking showed that OMR perfectly fits into A2AAR binding pocket forming a distinctive hydrogen bond with Threonine 256. Besides other non-polar interactions inside the pocket suggesting the future of the marketed anti-diabetic drug (that cross BBB) as a potential antiparkinsonian agent while OMR showed perfect fit inside AChE receptor binding site smoothly because of its optimum length and the two fluorine atoms that enables quite lean fitting. Moreover, a computational comparative study of OMR docking, other 12 DPP-4 inhibitors and 11 SGLT-2 inhibitors was carried out. Secondly, glucagon-like peptide-1 (GLP-1) concentration in rats’ brain tissue was determined by the authors using sandwich GLP-1 ELISA kit bio-analysis to ensure the effect of OMR after the multiple doses’ study. Brain GLP-1 concentration was elevated by 1.9-fold following oral multiple doses of OMR (5 mg/kg/day, p.o. for 28 days) as compared to the control group. The third finding is the enhanced BBB crossing of OMR after 28 days of multiple doses that had been studied using LC-MS/MS method with enhanced liquid–liquid extraction. A modified LC-MS/MS method was established for bioassay of OMR in rats’ plasma (10–3100 ng/mL) and rats’ brain tissue (15–2900 ng/mL) using liquid–liquid extraction. Alogliptin (ALP) was chosen as an internal standard (IS) due to its LogP value of 1.1, which is very close to the LogP of OMR. Extraction of OMR from samples of both rats’ plasma and rats’ brain tissue was effectively achieved with ethyl acetate as the extracting solvent after adding 1N sodium carbonate to enhance the drug migration, while choosing acetonitrile to be the diluent solvent for the IS to effectively decrease any emulsion between the layers in the stated method of extraction. Validation results were all pleasing including good stability studies with bias of value below 20%. Concentration of OMR in rats’ plasma were determined after 2 h of the latest dose from 28 days multiple doses, p.o, 5 mg/kg/day. It was found to be 1295.66 ± 684.63 ng/mL estimated from the bio-analysis regression equation. OMR passed through the BBB following oral administration and exhibited concentration of 543.56 ± 344.15 ng/g in brain tissue, taking in consideration the dilution factor of 10. The brain/plasma concentration ratio of 0.42 (543.56/1295.66) was used to illustrate the penetration power through the BBB after the multiple doses for 28 days. Results showed that OMR passed through the BBB more effectively in the multiple dose study as compared to the previously published single dose study by the authors. Thus, the present study suggests potential repositioning of OMR as antiparkinsonian agent that will be of interest for researchers interested in neurodegenerative diseases.
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Affiliation(s)
- Bassam M. Ayoub
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; (S.M.); (M.S.H.)
- The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
- Correspondence: ; Tel.: +20-226-890-000; Fax: +20-226-300-010
| | - Haidy E. Michel
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo 11566, Egypt;
| | - Shereen Mowaka
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; (S.M.); (M.S.H.)
- The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
- Analytical Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo 11795, Egypt
| | - Moataz S. Hendy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; (S.M.); (M.S.H.)
- The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Mariam M. Tadros
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo 11566, Egypt;
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Bestatin and bacitracin inhibit porcine kidney cortex dipeptidyl peptidase IV activity and reduce human melanoma MeWo cell viability. Int J Biol Macromol 2020; 164:2944-2952. [DOI: 10.1016/j.ijbiomac.2020.08.157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023]
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Strollo R, Pozzilli P. DPP4 inhibition: Preventing SARS-CoV-2 infection and/or progression of COVID-19? Diabetes Metab Res Rev 2020; 36:e3330. [PMID: 32336007 PMCID: PMC7267128 DOI: 10.1002/dmrr.3330] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/15/2022]
Abstract
Dipeptidyl peptidase 4 (DPP4), also known as cluster of differentiation 26 (CD26), is a serine exopeptidase expressed ubiquitously in several tissues, including but not limited to lung, kidney, liver, gut, and immune cells. The question has been raised on whether DPP4 modulation or inhibition may prevent infection and/or progression of the COVID-19. A docked complex model of the SARS-CoV-2 spike glycoprotein and DPP4 has been proposed, showing a large interface between the proteins and proposing close similarity with other coronaviruses using DPP4 as functional receptor. In absence of experimental validation, these data should be interpreted with caution. Nevertheless, this observation may rise the question on whether DPP4 is directly involved in SARS-CoV-2 cell adhesion/virulence, and whether DPP4 inhibition might be a therapeutic strategy for preventing infection. Although a direct involvement of DPP4 in SARS-CoV-2 infection needs to be clarified, there is also evidence suggesting that DPP4 inhibitors modulate inflammation and exert anti-fibrotic activity. These properties may be of potential use for halting progression to the hyperinflammatory state associated with severe COVID-19. Taken together these findings may suggest a potential role for DPP4 inhibition or modulation in one or more steps of COVID-19 immunopathogenesis.
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Affiliation(s)
- Rocky Strollo
- Unit of Endocrinology and Diabetes, Department of MedicineCampus Bio‐Medico, University of RomeRomeItaly
| | - Paolo Pozzilli
- Unit of Endocrinology and Diabetes, Department of MedicineCampus Bio‐Medico, University of RomeRomeItaly
- Centre for Immunobiology, Barts and The London School of Medicine and DentistryQueen Mary, University of LondonLondonUK
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Craig PA. Developing and applying computational resources for biochemistry education. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:579-584. [PMID: 32203640 PMCID: PMC7508772 DOI: 10.1002/bmb.21347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process.
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Affiliation(s)
- Paul A Craig
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA
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Levy E, Delvin E, Marcil V, Spahis S. Can phytotherapy with polyphenols serve as a powerful approach for the prevention and therapy tool of novel coronavirus disease 2019 (COVID-19)? Am J Physiol Endocrinol Metab 2020; 319:E689-E708. [PMID: 32755302 PMCID: PMC7518070 DOI: 10.1152/ajpendo.00298.2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 02/08/2023]
Abstract
Much more serious than the previous severe acute respiratory syndrome (SARS) coronavirus (CoV) outbreaks, the novel SARS-CoV-2 infection has spread speedily, affecting 213 countries and causing ∼17,300,000 cases and ∼672,000 (∼+1,500/day) deaths globally (as of July 31, 2020). The potentially fatal coronavirus disease (COVID-19), caused by air droplets and airborne as the main transmission modes, clearly induces a spectrum of respiratory clinical manifestations, but it also affects the immune, gastrointestinal, hematological, nervous, and renal systems. The dramatic scale of disorders and complications arises from the inadequacy of current treatments and absence of a vaccine and specific anti-COVID-19 drugs to suppress viral replication, inflammation, and additional pathogenic conditions. This highlights the importance of understanding the SARS-CoV-2 mechanisms of actions and the urgent need of prospecting for new or alternative treatment options. The main objective of the present review is to discuss the challenging issue relative to the clinical utility of plants-derived polyphenols in fighting viral infections. Not only is the strong capacity of polyphenols highlighted in magnifying health benefits, but the underlying mechanisms are also stressed. Finally, emphasis is placed on the potential ability of polyphenols to combat SARS-CoV-2 infection via the regulation of its molecular targets of human cellular binding and replication, as well as through the resulting host inflammation, oxidative stress, and signaling pathways.
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Affiliation(s)
- Emile Levy
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Edgard Delvin
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Valérie Marcil
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Schohraya Spahis
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
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37
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Charoenkwan P, Kanthawong S, Nantasenamat C, Hasan MM, Shoombuatong W. iDPPIV-SCM: A Sequence-Based Predictor for Identifying and Analyzing Dipeptidyl Peptidase IV (DPP-IV) Inhibitory Peptides Using a Scoring Card Method. J Proteome Res 2020; 19:4125-4136. [PMID: 32897718 DOI: 10.1021/acs.jproteome.0c00590] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The inhibition of dipeptidyl peptidase IV (DPP-IV, E.C.3.4.14.5) is well recognized as a new avenue for the treatment of Type 2 diabetes (T2D). Until now, peptide-like DDP-IV inhibitors have been shown to normalize the blood glucose concentration in T2D subjects. To the best of our knowledge, there is yet no computational model for predicting and analyzing DPP-IV inhibitory peptides using sequence information. In this study, we present for the first time a simple and easily interpretable sequence-based predictor using the scoring card method (SCM) for modeling the bioactivity of DPP-IV inhibitory peptides (iDPPIV-SCM). Particularly, the iDPPIV-SCM was developed by employing the SCM method together with the propensity scores of amino acids. Rigorous independent test results demonstrated that the proposed iDPPIV-SCM was found to be superior to those of well-known machine learning (ML) classifiers (e.g., k-nearest neighbor, logistic regression, and decision tree) with demonstrated improvements of 2-11, 4-22, and 7-10% for accuracy, MCC, and AUC, respectively, while also achieving comparable results to that of the support vector machine. Furthermore, the analysis of estimated propensity scores of amino acids as derived from the iDPPIV-SCM was performed so as to provide a more in-depth understanding on the molecular basis for enhancing the DPP-IV inhibitory potency. Taken together, these results revealed that iDPPIV-SCM was superior to those of other well-known ML classifiers owing to its simplicity, interpretability, and validity. For the convenience of biologists, the predictive model is deployed as a publicly accessible web server at http://camt.pythonanywhere.com/iDPPIV-SCM. It is anticipated that iDPPIV-SCM can serve as an important tool for the rapid screening of promising DPP-IV inhibitory peptides prior to their synthesis.
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Affiliation(s)
- Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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38
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Alaofi AL. Exploring structural dynamics of the MERS-CoV receptor DPP4 and mutant DPP4 receptors. J Biomol Struct Dyn 2020; 40:752-763. [PMID: 32909925 DOI: 10.1080/07391102.2020.1818626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mouse DPP4 (mDPP4) receptor is not a functional receptor for MERS-CoV while human DPP4 (hDPP4) is, despite the high similarities between hDPP4 and mDPP4 receptors. The variability of DPP4 receptors against MERS-CoV is not fully investigated, especially conformational and structural differences. Therefore, investigating the conformational differences of the DPP4 receptors can aid in developing new small animal models for MERS-CoV vaccines and antiviral agents evaluation. Here we used MD simulations and docking techniques to investigate these structural differences in DPP4 receptors. The results showed chimeric mouse mDPP4 (cmDPP4) has a similar compact conformation as wild-type hDPP4 based on the structural analysis. Interestingly, a single Thr288Ala mutation induced a relaxed conformation in chimeric 2 hDPP4 (c2hDPP4) and chimeric 2 mDPP4 (c2mDPP4); in addition to its significant effect on the DPP4 flexibility. The Thr288 residue is known for its critical function in MERS-CoV RBD interaction. Moreover, MERS-CoV RBD adopts a "standing" conformation when docked to hDPP4 and cmDPP4 in blade IV and V regions. In conclusion, the results could explain the functionality differences between mouse and human DPP4 receptors against MERS-CoV. However, further structural studies are needed to evaluate how DPP4 conformations affects MERS-CoV RBD binding and affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed L Alaofi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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39
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Dunaevsky YE, Tereshchenkova VF, Oppert B, Belozersky MA, Filippova IY, Elpidina EN. Human proline specific peptidases: A comprehensive analysis. Biochim Biophys Acta Gen Subj 2020; 1864:129636. [DOI: 10.1016/j.bbagen.2020.129636] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
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40
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Upadhyay J, Gajjar A, Suhagia BN. Combined Ligand-Based and Structure-Based Virtual Screening Approach for Identification of New Dipeptidyl Peptidase 4 Inhibitors. Curr Drug Discov Technol 2020; 16:426-436. [PMID: 30255759 DOI: 10.2174/1570163815666180926111558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dipeptidyl Peptidase 4 (DPP 4) enzyme cleaves an incretin-based glucoregulatory hormone Glucagon Like Peptide -1 from N-terminal where penultimate amino acid is either alanine or proline. Several DPP 4 inhibitors, "gliptins", are approved for the management of Type 2 Diabetes or are under clinical trial. In the present study, combined pharmacophore and docking-based virtual screening protocol were used for the identification of new hits from the Specs Database, which would inhibit DPP 4. METHODS The entire computational studies were performed using the Discovery Studio v. 4.1 software package, Pipeline Pilot v. 9.2 (Accelrys Inc.) and FRED v. 2.2.5 (OpenEye Scientific Software). Common feature pharmacophore model was generated from known DPP 4 inhibitors and validated by Receiver Operating curve analysis and GH-scoring method. Database search of Specs commercial database was performed using validated pharmacophore. Hits obtained from pharmacophore search were further docked into the binding site of DPP 4. Based on the analysis of docked poses of hits, 10 compounds were selected for in- vitro DPP 4 enzyme inhibition assay. RESULTS Based on docking studies, virtual hits were predicted to form interaction with essential amino acid residues of DPP 4 and have an almost similar binding orientation as that of the reference molecule. Three compounds having Specs database ID- AN-465/42837213, AP-064/42049348 and AN- 465/43369427 were found to inhibit DPP 4 enzyme moderately. CONCLUSION The present study demonstrates a successful utilization of in-silico tools in the identification of new DPP 4 inhibitor, which can serve as a starting point for the development of novel DPP 4 inhibitors.
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Affiliation(s)
- Jagatkumar Upadhyay
- Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, India.,Faculty of Pharmacy, Dharmsinh Desai University, Nadiad, Gujarat, India
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41
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Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
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Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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42
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Yoshii K, Ogasawara M, Wada J, Yamamoto Y, Inouye K. Exploration of dipeptidyl-peptidase IV (DPP IV) inhibitors in a low-molecular mass extract of the earthworm Eisenia fetida and identification of the inhibitors as amino acids like methionine, leucine, histidine, and isoleucine. Enzyme Microb Technol 2020; 137:109534. [PMID: 32423671 DOI: 10.1016/j.enzmictec.2020.109534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022]
Abstract
We have reported previously that the water extract of the earthworm Eisenia fetida has inhibitory effect on human dipeptidyl-peptidase IV (DPP IV) in vitro. Here we studied to identify DPP IV inhibitors in a low-molecular mass extract (designated U3EE) under 3 kDa prepared from the water extract. U3EE showed 50 % inhibition (IC50) at the concentration of 5.3 ± 0.3 mg/mL. An inhibitory active fraction obtained by solid-phase extraction of U3EE was separated into three parts by reversed-phase HPLC. These parts were shown by GC/MS to be composed of ten (Ala, Gly, Thr, Ser, Asn, Asp, Lys, His, Orn, and cystine), two (Leu and Ile), and one (Met) amino acids, respectively. Among them, Met, Leu, and His showed strong inhibition with IC50 values of 3.4 ± 0.3, 6.1 ± 0.3 and 14.7 ± 1.2 mM, respectively; Ala, Lys, Orn, and Ile showed rather weaker inhibition than those, while the others showed no inhibition. Met, Leu, and Ile were competitive inhibitors and His was a mixed-type one. DPP IV inhibition by U3EE might be due to additive and/or synergistic effects of the inhibitory amino acids, suggesting that it could be useful as pharmaceutical and supplement for diabetes prevention.
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Affiliation(s)
- Katsuhiro Yoshii
- Research and Development Division, Waki Pharmaceutical Co., Ltd., Room 307, Advanced Chemical Technology Center in Kyoto (ACT Kyoto), 105 Jibu-cho, Fushimi-ku, Kyoto, 612-8374, Japan
| | - Masako Ogasawara
- Research and Development Division, Waki Pharmaceutical Co., Ltd., Room 307, Advanced Chemical Technology Center in Kyoto (ACT Kyoto), 105 Jibu-cho, Fushimi-ku, Kyoto, 612-8374, Japan
| | - Jun Wada
- Kyoto Municipal Institute of Industrial Technology and Culture, 91 Chudoji Awata-cho, Shimogyo-ku, Kyoto, 600-8815, Japan
| | - Yoshihiro Yamamoto
- Kyoto Municipal Institute of Industrial Technology and Culture, 91 Chudoji Awata-cho, Shimogyo-ku, Kyoto, 600-8815, Japan
| | - Kuniyo Inouye
- Research and Development Division, Waki Pharmaceutical Co., Ltd., Room 307, Advanced Chemical Technology Center in Kyoto (ACT Kyoto), 105 Jibu-cho, Fushimi-ku, Kyoto, 612-8374, Japan.
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43
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Abstract
Today, excluding insulin, there are eight classes of anti-diabetic medicines that have been added to the pharmacy since the introduction of metformin in the mid-1950s; the sulfonylureas, biguanides, thiazolidinediones, α-glucosidase inhibitors, meglitinides, incretins, and sodium glucose transport 2 inhibitors. Does the fact that metformin is still first-line treatment suggest that our drug discovery efforts over the past 60 years have not been good enough? Or does it suggest that diabetes is such a complex disorder that no single treatment, other than gastric bypass surgery, can affect true normalization of not only blood sugar but also the underlying pathologies? Our understanding of the disease has most definitely improved which may bring hope for the future in terms of science, but for it to be beneficial, this science has to be translated into better drug treatments for the disease. In this review, I have examined the eight classes of anti-diabetes drugs from a drug discovery perspective.
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Affiliation(s)
- John C Clapham
- Medical School, University of Buckingham, Buckingham, UK.
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44
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Mohd Salim MAS, Gan CY. Dual-function peptides derived from egg white ovalbumin: Bioinformatics identification with validation using in vitro assay. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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45
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Evaluating in vitro dipeptidyl peptidase IV inhibition by peptides from common carp (Cyprinus carpio) roe in cell culture models. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03399-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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46
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Smith NK, Hackett TA, Galli A, Flynn CR. GLP-1: Molecular mechanisms and outcomes of a complex signaling system. Neurochem Int 2019; 128:94-105. [PMID: 31002893 PMCID: PMC7081944 DOI: 10.1016/j.neuint.2019.04.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/26/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022]
Abstract
Meal ingestion provokes the release of hormones and transmitters, which in turn regulate energy homeostasis and feeding behavior. One such hormone, glucagon-like peptide-1 (GLP-1), has received significant attention in the treatment of obesity and diabetes due to its potent incretin effect. In addition to the peripheral actions of GLP-1, this hormone is able to alter behavior through the modulation of multiple neural circuits. Recent work that focused on elucidating the mechanisms and outcomes of GLP-1 neuromodulation led to the discovery of an impressive array of GLP-1 actions. Here, we summarize the many levels at which the GLP-1 signal adapts to different systems, with the goal being to provide a background against which to guide future research.
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Affiliation(s)
- Nicholas K Smith
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Troy A Hackett
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aurelio Galli
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Charles R Flynn
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
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47
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Lima RDCL, Berg RS, Rønning SB, Afseth NK, Knutsen SH, Staerk D, Wubshet SG. Peptides from chicken processing by-product inhibit DPP-IV and promote cellular glucose uptake: potential ingredients for T2D management. Food Funct 2019; 10:1619-1628. [PMID: 30821796 DOI: 10.1039/c8fo02450b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV) and stimulation of muscle glucose uptake are two of the key strategies for management of type-2-diabetes (T2D). In the present study, four protein hydrolysates generated by enzymatic hydrolysis of chicken by-product, i.e., mechanical chicken deboning residue, were evaluated for their DPP-IV inhibitory activity as well as their effect on glucose uptake by skeletal muscle cells. The DPP-IV inhibitory assay was performed at two concentrations (1000 μg mL-1 and 10 μg mL-1) for the crude chicken protein hydrolysates. The hydrolysate with the highest DPP-IV inhibition was selected for preparative-scale fractionation using size-exclusion chromatography (SEC). The SEC fractions were tested for DPP-IV inhibitory activity as well as their effect on glucose uptake and metabolic activity of skeletal muscle cells. The muscle cells were treated with the SEC fractions and glucose uptake was measured based on luminescence detection of 2-deoxyglucose-6-phosphate (2DG6P). A fraction with peptides in the lower molecular weight range was shown to promote glucose uptake and to inhibit DPP-IV. Further chromatographic fractionation followed by inhibition assaying of the most potent SEC fraction led to isolation of five refined peptide fractions with more than 80% DPP-IV inhibition, which were subsequently analyzed with LC-HRMS/MS. This led to identification of 14 peptides as potential DPP-IV inhibitors from protein hydrolysates of mechanical chicken deboning residue.
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48
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Han R, Maycock J, Murray BS, Boesch C. Identification of angiotensin converting enzyme and dipeptidyl peptidase-IV inhibitory peptides derived from oilseed proteins using two integrated bioinformatic approaches. Food Res Int 2019; 115:283-291. [PMID: 30599943 DOI: 10.1016/j.foodres.2018.12.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/25/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022]
Abstract
Angiotensin-converting enzyme (ACE) and dipeptidyl peptidase-IV (DPP-IV) play critical roles in the development of hypertension and type 2 diabetes, respectively. Inhibiting ACE and DPP-IV activity using peptides has become part of new therapeutic strategies for supporting medicinal treatment of both diseases. In this study, oilseed proteins, including soybean, flaxseed, rapeseed, sunflower and sesame are evaluated for the possibility of generating ACE and DPP-IV inhibitory peptides using different integrated bioinformatic approaches (UniProt knowledgebase, ProtParam, BLAST, BIOPEP, PeptideRanker, Pepsite2 and ToxinPred), and three bovine proteins (β-lactoglobulin, β-casein and κ-casein) as comparisons. Compared with bovine proteins, the potency indices of ACE and DPP-IV inhibitory peptides, calculated using the BIOPEP database, suggest that oilseed proteins may be considered as good precursors of ACE inhibitory peptides but generate a relative lower yield of DPP-IV inhibitory peptides following subtilisin, pepsin (pH = 1.3) or pepsin (pH > 2) hydrolysis. Average scores aligned using PeptideRanker confirmed oilseed proteins as significant potential sources of bioactive peptides: over 105 peptides scored over 0.8. Pepsite2 predicted that these peptides would largely bind via Gln281, His353, Lys511, His513, Tyr520 and Tyr523 of ACE to inhibit the enzyme, while Trp629 would be the predominant binding site of peptides in reducing DPP-IV activity. All peptides were capable of inhibiting ACE and DPP-IV whilst 65 of these 105 peptides are not currently recorded in BIOPEP database. In conclusion, our in silico study demonstrates that oilseed proteins could be considered as good precursors of ACE and DPP-IV inhibitory peptides as well as so far unexplored peptides that potentially have roles in ACE and DPP-IV inhibition and beyond.
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Affiliation(s)
- Ruixian Han
- School of Food Science and Nutrition, University of Leeds, LS2 9JT Leeds, UK
| | - Joanne Maycock
- School of Food Science and Nutrition, University of Leeds, LS2 9JT Leeds, UK
| | - Brent S Murray
- School of Food Science and Nutrition, University of Leeds, LS2 9JT Leeds, UK
| | - Christine Boesch
- School of Food Science and Nutrition, University of Leeds, LS2 9JT Leeds, UK.
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49
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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50
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Nongonierma AB, Dellafiora L, Paolella S, Galaverna G, Cozzini P, FitzGerald RJ. In Silico Approaches Applied to the Study of Peptide Analogs of Ile-Pro-Ile in Relation to Their Dipeptidyl Peptidase IV Inhibitory Properties. Front Endocrinol (Lausanne) 2018; 9:329. [PMID: 29963014 PMCID: PMC6010526 DOI: 10.3389/fendo.2018.00329] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 12/17/2022] Open
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV) may be exploited to maintain the incretin effect during the postprandial phase. As a result, glycemic regulation and energy homeostasis may be improved. Food protein-derived peptides have been identified as natural agents capable of inhibiting DPP-IV. Ile-Pro-Ile is the most potent DPP-IV inhibitory peptide identified to date. A minimum analog peptide set approach was used to study peptide analogs of Ile-Pro-Ile. The DPP-IV half maximal inhibitory concentration (IC50) values of the 25 peptides evaluated ranged from 3.9 ± 1.0 µM (Ile-Pro-Ile) to 247.0 ± 32.7 µM (Phe-Pro-Phe). The presence of Pro at position 2 of tripeptides was required to achieve high DPP-IV inhibition. Most peptides behaved as competitive inhibitors of DPP-IV with the exception of peptides with a N-terminal Trp, which were mixed-type inhibitors. While possessing the structure of preferred DPP-IV substrates, most peptides studied were particularly stable during 30 min incubation with DPP-IV. Molecular docking revealed that Ile-Pro-Ile and its peptide analogs interacted in a very similar manner with the active site of DPP-IV. In addition, no correlation was found between the Hydropathic INTeraction score and the DPP-IV IC50 values of the peptides studied. This outcome suggests that free energy may not be directly responsible for enzyme inhibition by the peptides. Finally, novel DPP-IV inhibitory peptides were identified using the strategy employed herein. These results may be relevant for the development of food protein-derived peptides with serum glucose lowering and food intake regulatory properties in humans.
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Affiliation(s)
- Alice B. Nongonierma
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Sara Paolella
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Pietro Cozzini
- Food and Drug Department, University of Parma, Parma, Italy
| | - Richard J. FitzGerald
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
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