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Cho SB. Comorbidity Genes of Alzheimer's Disease and Type 2 Diabetes Associated with Memory and Cognitive Function. Int J Mol Sci 2024; 25:2211. [PMID: 38396891 PMCID: PMC10889845 DOI: 10.3390/ijms25042211] [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: 01/02/2024] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) are comorbidities that result from the sharing of common genes. The molecular background of comorbidities can provide clues for the development of treatment and management strategies. Here, the common genes involved in the development of the two diseases and in memory and cognitive function are reviewed. Network clustering based on protein-protein interaction network identified tightly connected gene clusters that have an impact on memory and cognition among the comorbidity genes of AD and T2DM. Genes with functional implications were intensively reviewed and relevant evidence summarized. Gene information will be useful in the discovery of biomarkers and the identification of tentative therapeutic targets for AD and T2DM.
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Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, 38-13, Dokgeom-ro 3 Street, Namdon-gu, Incheon 21565, Republic of Korea
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2
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Kano Y, Yamaguchi S, Mise K, Kawakita C, Onishi Y, Kurooka N, Sugawara R, Albuayjan HHH, Nakatsuka A, Eguchi J, Wada J. Inhibition of Amino Acids Influx into Proximal Tubular Cells Improves Lysosome Function in Diabetes. KIDNEY360 2024; 5:182-194. [PMID: 38062578 PMCID: PMC10914197 DOI: 10.34067/kid.0000000000000333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/29/2023] [Indexed: 03/01/2024]
Abstract
Key Points Collectrin serves as a chaperone for the trafficking of neutral amino acid (AA) transporters in the apical membranes of proximal tubular cells (PTCs). Cltrn knockout reduced AAs influx into PTCs, inactivated mTOR, activated transcription factor EB, improved lysosome function, and ameliorated vacuolar formation of PTCs in diabetic mice treated with streptozotocin and high-fat diet. The inhibition of neutral AA transporter, such as B0AT1 (SLC6A19), and transcription factor EB activator is a new therapeutic strategy against diabetic kidney disease. Background Inhibition of glucose influx into proximal tubular cells (PTCs) by sodium–glucose cotransporter 2 inhibitors revealed prominent therapeutic effects on diabetic kidney disease. Collectrin (CLTRN) serves as a chaperone for the trafficking of neutral amino acid (AA) transporters in the apical membranes of PTCs. We investigated the beneficial effects of reduced influx of AAs into PTCs in diabetes and obesity model of Cltrn−/y mice. Methods Cltrn+/y and Cltrn−/y mice at age 5 weeks were assigned to standard diet and streptozotocin and high-fat diet (STZ-HFD)–treated groups. Results At age 22–23 weeks, body weight and HbA1c levels significantly increased in STZ-HFD-Cltrn+/y compared with standard diet-Cltrn+/y; however, they were not altered in STZ-HFD-Cltrn−/y compared with STZ-HFD-Cltrn+/y. At age 20 weeks, urinary albumin creatinine ratio was significantly reduced in STZ-HFD-Cltrn−/y compared with STZ-HFD-Cltrn+/y. Under the treatments with STZ and HFD, the Cltrn gene deficiency caused significant increase in urinary concentration of AAs such as Gln, His, Gly, Thr, Tyr, Val, Trp, Phe, Ile, Leu, and Pro. In PTCs in STZ-HFD-Cltrn+/y, the enlarged lysosomes with diameter of 10 μ m or more were associated with reduced autolysosomes, and the formation of giant lysosomes was prominently suppressed in STZ-HFD-Cltrn−/y. Phospho-mTOR and inactive form of phospho-transcription factor EB were reduced in STZ-HFD-Cltrn−/y compared with STZ-HFD-Cltrn+/y. Conclusions The reduction of AAs influx into PTCs inactivated mTOR, activated transcription factor EB, improved lysosome function, and ameliorated vacuolar formation of PTCs in STZ-HFD-Cltrn−/y mice.
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Affiliation(s)
- Yuzuki Kano
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Yeap YJ, Kandiah N, Nizetic D, Lim KL. BACE2: A Promising Neuroprotective Candidate for Alzheimer's Disease. J Alzheimers Dis 2023; 94:S159-S171. [PMID: 36463454 PMCID: PMC10473127 DOI: 10.3233/jad-220867] [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] [Accepted: 10/28/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia that affects millions of predominantly elderly individuals worldwide. Despite intensive research over several decades, controversies still surround the etiology of AD and the disease remains incurable. Meanwhile, new molecular players of the central amyloid cascade hypothesis have emerged and among these is a protease known as β-site APP cleavage enzyme 2 (BACE2). Unlike BACE1, BACE2 cleaves the amyloid-β protein precursor within the Aβ domain that accordingly prevents the generation of Aβ42 peptides, the aggregation of which is commonly regarded as the toxic entity that drives neurodegeneration in AD. Given this non-amyloidogenic role of BACE2, it is attractive to position BACE2 as a therapeutic target for AD. Indeed, several groups including ours have demonstrated a neuroprotective role for BACE2 in AD. In this review, we discuss emerging evidence supporting the ability of BACE2 in mitigating AD-associated pathology in various experimental systems including human pluripotent stem cell-derived cerebral organoid disease models. Alongside this, we also provide an update on the identification of single nucleotide polymorphisms occurring in the BACE2 gene that are linked to increased risk and earlier disease onset in the general population. In particular, we highlight a recently identified point mutation on BACE2 that apparently leads to sporadic early-onset AD. We believe that a better understanding of the role of BACE2 in AD would provide new insights for the development of viable therapeutic strategies for individuals with dementia.
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Affiliation(s)
- Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Nagaendran Kandiah
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Dean Nizetic
- Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kah-Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Brain Sciences, Imperial College London, London, UK
- Shanxi Medical University, Taiyuan, People’s Republic of China
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Guanidine-based β amyloid precursor protein cleavage enzyme 1 (BACE-1) inhibitors for the Alzheimer's disease (AD): A review. Bioorg Med Chem 2022; 74:117047. [DOI: 10.1016/j.bmc.2022.117047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/02/2022]
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Abstract
Epigenetic modifications have been implicated to mediate several complications of diabetes mellitus (DM), especially nephropathy and retinopathy. Our aim was to ascertain whether epigenetic alterations in whole blood discriminate among patients with DM with normal, delayed, and rapid gastric emptying (GE).
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Ghosh AK, Brindisi M, Yen YC, Lendy EK, Kovela S, Cárdenas EL, Reddy BS, Rao KV, Downs D, Huang X, Tang J, Mesecar AD. Highly Selective and Potent Human β-Secretase 2 (BACE2) Inhibitors against Type 2 Diabetes: Design, Synthesis, X-ray Structure and Structure-Activity Relationship Studies. ChemMedChem 2019; 14:545-560. [PMID: 30637955 DOI: 10.1002/cmdc.201800725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/04/2019] [Indexed: 11/09/2022]
Abstract
Herein we present the design, synthesis, and biological evaluation of potent and highly selective β-secretase 2 (memapsin 1, beta-site amyloid precursor protein cleaving enzyme 2, or BACE 2) inhibitors. BACE2 has been recognized as an exciting new target for type 2 diabetes. The X-ray structure of BACE1 bound to inhibitor 2 a {N3 -[(1S,2R)-1-benzyl-2-hydroxy-3-[[(1S,2S)-2-hydroxy-1-(isobutylcarbamoyl)propyl]amino]propyl]-5-[methyl(methylsulfonyl)amino]-N1 -[(1R)-1-phenylpropyl]benzene-1,3-dicarboxamide} containing a hydroxyethylamine isostere was determined. Based on this structure, a computational docking study was performed which led to inhibitor 2 a-bound BACE2 models. These were used to optimize the potency and selectivity of inhibitors. A systematic structure-activity relationship study led to the identification of determinants of the inhibitors' potency and selectivity toward the BACE2 enzyme. Inhibitors 2 d [N3 -[(1S,2R)-1-benzyl-2-hydroxy-3-[[(1S,2S)-2-hydroxy-1-(isobutylcarbamoyl)pentyl]amino]propyl]-N1 -methyl-N1 -[(1R)-1-phenylpropyl]benzene-1,3-dicarboxamide; Ki =0.031 nm, selectivity over BACE1: ≈174 000-fold] and 3 l [N1 -((2S,3R)-3-hydroxy-1-phenyl-4-((3-(trifluoromethyl)benzyl)amino)butan-2-yl)-N3 ,5-dimethyl-N3 -((R)-1-phenylethyl)isophthalamide; Ki =1.6 nm, selectivity over BACE1: >500-fold] displayed outstanding potency and selectivity. Inhibitor 3 l is nonpeptide in nature and may pave the way to the development of a new class of potent and selective BACE2 inhibitors with clinical potential.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Yu-Chen Yen
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Emilio Leal Cárdenas
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Bhavanam Sekhara Reddy
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Kalapala Venketeswara Rao
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Deborah Downs
- Protein Studies Program, Oklahoma Medical Research Foundation, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Xiangping Huang
- Protein Studies Program, Oklahoma Medical Research Foundation, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Jordan Tang
- Protein Studies Program, Oklahoma Medical Research Foundation, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Andrew D Mesecar
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
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Um J, Lee JH, Jung DW, Williams DR. Re-education begins at home: an overview of the discovery of in vivo-active small molecule modulators of endogenous stem cells. Expert Opin Drug Discov 2018; 13:307-326. [PMID: 29421943 DOI: 10.1080/17460441.2018.1437140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Degenerative diseases, such as Alzheimer's disease, heart disease and arthritis cause great suffering and are major socioeconomic burdens. An attractive treatment approach is stem cell transplantation to regenerate damaged or destroyed tissues. However, this can be problematic. For example, donor cells may not functionally integrate into the host tissue. An alternative methodology is to deliver bioactive agents, such as small molecules, directly into the diseased tissue to enhance the regenerative potential of endogenous stem cells. Areas covered: In this review, the authors discuss the necessity of developing these small molecules to treat degenerative diseases and survey progress in their application as therapeutics. They describe both the successes and caveats of developing small molecules that target endogenous stem cells to induce tissue regeneration. This article is based on literature searches which encompass databases for biomedical research and clinical trials. These small molecules are also categorized per their target disease and mechanism of action. Expert opinion: The development of small molecules targeting endogenous stem cells is a high-profile research area. Some compounds have made the successful transition to the clinic. Novel approaches, such as modulating the stem cell niche or targeted delivery to disease sites, should increase the likelihood of future successes in this field.
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Affiliation(s)
- JungIn Um
- a New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology , Buk-Gu , Gwangju , Republic of Korea
| | - Ji-Hyung Lee
- a New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology , Buk-Gu , Gwangju , Republic of Korea
| | - Da-Woon Jung
- a New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology , Buk-Gu , Gwangju , Republic of Korea
| | - Darren R Williams
- a New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology , Buk-Gu , Gwangju , Republic of Korea
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Kulas JA, Puig KL, Combs CK. Amyloid precursor protein in pancreatic islets. J Endocrinol 2017; 235:49-67. [PMID: 28710249 PMCID: PMC6267436 DOI: 10.1530/joe-17-0122] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 01/04/2023]
Abstract
The amyloid precursor protein (APP) has been extensively investigated for its role in the production of amyloid beta (Aβ), a plaque-forming peptide in Alzheimer's disease (AD). Epidemiological evidence suggests type 2 diabetes is a risk factor for AD. The pancreas is an essential regulator of blood glucose levels through the secretion of the hormones insulin and glucagon. Pancreatic dysfunction is a well-characterized consequence of type 1 and type 2 diabetes. In this study, we have examined the expression and processing of pancreatic APP to test the hypothesis that APP may play a role in pancreatic function and the pathophysiology of diabetes. Our data demonstrate the presence of APP within the pancreas, including pancreatic islets in both mouse and human samples. Additionally, we report that the APP/PS1 mouse model of AD overexpresses APP within pancreatic islets, although this did not result in detectable levels of Aβ. We compared whole pancreas and islet culture lysates by Western blot from C57BL/6 (WT), APP-/- and APP/PS1 mice and observed APP-dependent differences in the total protein levels of GLUT4, IDE and BACE2. Immunohistochemistry for BACE2 detected high levels in pancreatic α cells. Additionally, both mouse and human islets processed APP to release sAPP into cell culture media. Moreover, sAPP stimulated insulin but not glucagon secretion from islet cultures. We conclude that APP and its metabolites are capable of influencing the basic physiology of the pancreas, possibly through the release of sAPP acting in an autocrine or paracrine manner.
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Affiliation(s)
- Joshua A Kulas
- Department of Biomedical SciencesUniversity of North Dakota School of Medicine and Health Sciences, Grand Forks, USA
| | - Kendra L Puig
- Department of Biomedical SciencesUniversity of North Dakota School of Medicine and Health Sciences, Grand Forks, USA
| | - Colin K Combs
- Department of Biomedical SciencesUniversity of North Dakota School of Medicine and Health Sciences, Grand Forks, USA
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Alcarraz-Vizán G, Castaño C, Visa M, Montane J, Servitja JM, Novials A. BACE2 suppression promotes β-cell survival and function in a model of type 2 diabetes induced by human islet amyloid polypeptide overexpression. Cell Mol Life Sci 2017; 74:2827-2838. [PMID: 28337562 PMCID: PMC11107557 DOI: 10.1007/s00018-017-2505-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 02/07/2023]
Abstract
BACE2 (β-site APP-cleaving enzyme 2) is a protease expressed in the brain, but also in the pancreas, where it seems to play a physiological role. Amyloidogenic diseases, including Alzheimer's disease and type 2 diabetes (T2D), share the accumulation of abnormally folded and insoluble proteins that interfere with cell function. In T2D, islet amyloid polypeptide (IAPP) deposits have been shown to be a pathogenic key feature of the disease. The aim of the present study was to investigate the effect of BACE2 modulation on β-cell alterations in a mouse model of T2D induced by IAPP overexpression. Heterozygous mice carrying the human transcript of IAPP (hIAPP-Tg) were used as a model to study the deleterious effects of IAPP upon β-cell function. These animals showed glucose intolerance and impaired insulin secretion. When crossed with BACE2-deficient mice, the animals presented a significant improvement in glucose tolerance accompanied with an enhanced insulin secretion, as compared to hIAPP-Tg mice. BACE2 deficiency also partially reverted gene expression changes observed in islets from hIAPP-Tg mice, including a set of genes related to inflammation. Moreover, homozygous hIAPP mice presented a severe hyperglycemia and a high lethality rate from 8 weeks onwards due to a massive destruction of β-cell mass. This process was significantly reduced when crossed with the BACE2-KO model, improving the survival rate of the animals. Altogether, the absence of BACE2 ameliorates glucose tolerance defects induced by IAPP overexpression in the β-cell and promotes β-cell survival. Thus, targeting BACE2 may represent a promising therapeutic strategy to improve β-cell function in T2D.
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Affiliation(s)
- Gema Alcarraz-Vizán
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain
| | - Carlos Castaño
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain
| | - Montse Visa
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain
| | - Joel Montane
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain
| | - Joan-Marc Servitja
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain.
| | - Anna Novials
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), C/Rosselló 149-153, 5th floor, 08036, Barcelona, Spain.
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10
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Ghosh AK, Reddy BS, Yen YC, Cardenas E, Rao KV, Downs D, Huang X, Tang J, Mesecar AD. Design of Potent and Highly Selective Inhibitors for Human β-Secretase 2 (Memapsin 1), a Target for Type 2 Diabetes. Chem Sci 2016; 7:3117-3122. [PMID: 27347366 PMCID: PMC4916918 DOI: 10.1039/c5sc03718b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structure-based design and syntheses of potent and highly selective BACE2 inhibitors are described.
Design, synthesis and evaluation of very potent and selective β-secretase 2 (memapsin 1, BACE 2) inhibitors are described. The inhibitors were designed specifically to interact with the S2′-site of β-secretase 2 to provide >170 000-fold selectivity over β-secretase (BACE 1) and >15 000-fold selectivity over cathepsin D. BACE 2 is implicated in type 2 diabetes. The studies serve as an important guide to selective BACE 2 inhibitors.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Bhavanam Sekhara Reddy
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (USA)
| | - Emilio Cardenas
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Kalapala Venketeswara Rao
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Deborah Downs
- Protein Studies Program, Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City, OK 73104 (USA)
| | - Xiangping Huang
- Protein Studies Program, Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City, OK 73104 (USA)
| | - Jordan Tang
- Protein Studies Program, Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City, OK 73104 (USA)
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (USA); Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA); Department of Biochemistry, Purdue University, West Lafayette, IN 47907 (USA)
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Kumalo HM, Soliman ME. A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility. J Recept Signal Transduct Res 2016; 36:505-14. [PMID: 26804314 DOI: 10.3109/10799893.2015.1130058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Beta-amyloid precursor protein cleavage enzyme1 (BACE1) and beta-amyloid precursor protein cleavage enzyme2 (BACE2), members of aspartyl protease family, are close homologs and have high similarity in their protein crystal structures. However, their enzymatic properties are different, which leads to different clinical outcomes. In this study, we performed sequence analysis and all-atom molecular dynamic (MD) simulations for both enzymes in their ligand-free states in order to compare their dynamical flap behaviors. This is to enhance our understanding of the relationship between sequence, structure and the dynamics of this protein family. Sequence analysis shows that in BACE1 and BACE2, most of the ligand-binding sites are conserved, indicative of their enzymatic property as aspartyl protease members. The other conserved residues are more or less unsystematically localized throughout the structure. Herein, we proposed and applied different combined parameters to define the asymmetric flap motion; the distance, d1, between the flap tip and the flexible region; the dihedral angle, φ, to account for the twisting motion and the TriCα angle, θ2 and θ1. All four combined parameters were found to appropriately define the observed "twisting" motion during the flaps different conformational states. Additional analysis of the parameters indicated that the flaps can exist in an ensemble of conformations, i.e. closed, semi-open and open conformations for both systems. However, the behavior of the flap tips during simulations is different between BACE1 and BACE2. The BACE1 active site cavity is more spacious as compared to that of BACE2. The analysis of 10S loop and 113S loop showed a similar trend to that of flaps, with the BACE1 loops being more flexible and less stable than those of BACE2. We believe that the results, methods and perspectives highlighted in this report would assist researchers in the discovery of BACE inhibitors as potential Alzheimer's disease therapies.
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Affiliation(s)
- H M Kumalo
- a Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
| | - Mahmoud E Soliman
- a Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
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Southan C, Sharman JL, Benson HE, Faccenda E, Pawson AJ, Alexander SPH, Buneman OP, Davenport AP, McGrath JC, Peters JA, Spedding M, Catterall WA, Fabbro D, Davies JA. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. Nucleic Acids Res 2016; 44:D1054-68. [PMID: 26464438 PMCID: PMC4702778 DOI: 10.1093/nar/gkv1037] [Citation(s) in RCA: 987] [Impact Index Per Article: 123.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 01/05/2023] Open
Abstract
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.
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Affiliation(s)
- Christopher Southan
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Joanna L Sharman
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Helen E Benson
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Elena Faccenda
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Adam J Pawson
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Stephen P H Alexander
- School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK
| | - O Peter Buneman
- Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, EH8 9LE, UK
| | | | - John C McGrath
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | | | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195-7280, USA
| | | | - Jamie A Davies
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
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Expanding opportunities for mining bioactive chemistry from patents. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 14:3-9. [PMID: 26194581 PMCID: PMC4548146 DOI: 10.1016/j.ddtec.2014.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/12/2014] [Accepted: 12/05/2014] [Indexed: 11/24/2022]
Abstract
Bioactive structures published in medicinal chemistry patents typically exceed those in papers by at least twofold and may precede them by several years. The Big-Bang of open automated extraction since 2012 has contributed to over 15 million patent-derived compounds in PubChem. While mapping between chemical structures, assay results and protein targets from patent documents is challenging, these relationships can be harvested using open tools and are beginning to be curated into databases.
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Alcarraz‐Vizán G, Casini P, Cadavez L, Visa M, Montane J, Servitja J, Novials A. Inhibition of BACE2 counteracts hIAPP‐induced insulin secretory defects in pancreatic β‐cells. FASEB J 2014; 29:95-104. [DOI: 10.1096/fj.14-255489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Gema Alcarraz‐Vizán
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Paola Casini
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Lisa Cadavez
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Montse Visa
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Joel Montane
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Joan‐Marc Servitja
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
| | - Anna Novials
- Diabetes and Obesity Research LaboratoryInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM)BarcelonaSpain
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Längle D, Halver J, Rathmer B, Willems E, Schade D. Small molecules targeting in vivo tissue regeneration. ACS Chem Biol 2014; 9:57-71. [PMID: 24372447 DOI: 10.1021/cb4008277] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of regenerative medicine has boomed in recent years thanks to milestone discoveries in stem cell biology and tissue engineering, which has been driving paradigm shifts in the pharmacotherapy of degenerative and ischemic diseases. Small molecule-mediated replenishment of lost and/or dysfunctional tissue in vivo, however, is still in its infancy due to a limited understanding of mechanisms that control such endogenous processes of tissue homeostasis or regeneration. Here, we discuss current progress using small molecules targeting in vivo aspects of regeneration, including adult stem cells, stem cell niches, and mechanisms of homing, mobilization, and engraftment as well as somatic cell proliferation. Many of these compounds derived from both knowledge-based design and screening campaigns, illustrating the feasibility of translating in vitro discovery to in vivo regeneration. These early examples of drug-mediated in vivo regeneration provide a glimpse of the future directions of in vivo regenerative medicine approaches.
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Affiliation(s)
- Daniel Längle
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jonas Halver
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Bernd Rathmer
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Erik Willems
- Muscle
Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis Schade
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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Southan C, Hancock JM. A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet 2013; 4:293. [PMID: 24381583 PMCID: PMC3865767 DOI: 10.3389/fgene.2013.00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 11/29/2013] [Indexed: 11/22/2022] Open
Abstract
The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35-45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.
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Affiliation(s)
- Christopher Southan
- IUPHAR Database and Guide to Pharmacology Web Portal Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of EdinburghEdinburgh, UK
| | - John M. Hancock
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridge, UK
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Tracking 20 years of compound-to-target output from literature and patents. PLoS One 2013; 8:e77142. [PMID: 24204758 PMCID: PMC3812171 DOI: 10.1371/journal.pone.0077142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/28/2013] [Indexed: 12/19/2022] Open
Abstract
The statistics of drug development output and declining yield of approved medicines has been the subject of many recent reviews. However, assessing research productivity that feeds development is more difficult. Here we utilise an extensive database of structure-activity relationships extracted from papers and patents. We have used this database to analyse published compounds cumulatively linked to nearly 4000 protein target identifiers from multiple species over the last 20 years. The compound output increases up to 2005 followed by a decline that parallels a fall in pharmaceutical patenting. Counts of protein targets have plateaued but not fallen. We extended these results by exploring compounds and targets for one large pharmaceutical company. In addition, we examined collective time course data for six individual protease targets, including average molecular weight of the compounds. We also tracked the PubMed profile of these targets to detect signals related to changes in compound output. Our results show that research compound output had decreased 35% by 2012. The major causative factor is likely to be a contraction in the global research base due to mergers and acquisitions across the pharmaceutical industry. However, this does not rule out an increasing stringency of compound quality filtration and/or patenting cost control. The number of proteins mapped to compounds on a yearly basis shows less decline, indicating the cumulative published target capacity of global research is being sustained in the region of 300 proteins for large companies. The tracking of six individual targets shows uniquely detailed patterns not discernible from cumulative snapshots. These are interpretable in terms of events related to validation and de-risking of targets that produce detectable follow-on surges in patenting. Further analysis of the type we present here can provide unique insights into the process of drug discovery based on the data it actually generates.
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Gilbert EJ. 1,3-Oxazines as BACE1 and/or BACE2 inhibitors: a patent evaluation (WO2012156284). Expert Opin Ther Pat 2013; 23:1069-73. [DOI: 10.1517/13543776.2013.818134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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