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Kamble SA, Barale SS, Mohammed AA, Paymal SB, Naik NM, Sonawane KD. Structural insights into the potential binding sites of Cathepsin D using molecular modelling techniques. Amino Acids 2024; 56:33. [PMID: 38649596 PMCID: PMC11035400 DOI: 10.1007/s00726-023-03367-1] [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: 06/15/2023] [Accepted: 12/11/2023] [Indexed: 04/25/2024]
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia caused by the accumulation of amyloid beta (Aβ) peptides. The extracellular deposition of Aβ peptides in human AD brain causes neuronal death. Therefore, it has been found that Aβ peptide degradation is a possible therapeutic target for AD. CathD has been known to breakdown amyloid beta peptides. However, the structural role of CathD is not yet clear. Hence, for the purpose of gaining a deeper comprehension of the structure of CathD, the present computational investigation was performed using virtual screening technique to predict CathD's active site residues and substrate binding mode. Ligand-based virtual screening was implemented on small molecules from ZINC database against crystal structure of CathD. Further, molecular docking was utilised to investigate the binding mechanism of CathD with substrates and virtually screened inhibitors. Localised compounds obtained through screening performed by PyRx and AutoDock 4.2 with CathD receptor and the compounds having highest binding affinities were picked as; ZINC00601317, ZINC04214975 and ZINCC12500925 as our top choices. The hydrophobic residues Viz. Gly35, Val31, Thr34, Gly128, Ile124 and Ala13 help stabilising the CathD-ligand complexes, which in turn emphasises substrate and inhibitor selectivity. Further, MM-GBSA approach has been used to calculate binding free energy between CathD and selected compounds. Therefore, it would be beneficial to understand the active site pocket of CathD with the assistance of these discoveries. Thus, the present study would be helpful to identify active site pocket of CathD, which could be beneficial to develop novel therapeutic strategies for the AD.
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Affiliation(s)
- Subodh A Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, M.S., 416004, India
| | - Sagar S Barale
- Department of Microbiology, Shivaji University, 416004, M.S., Kolhapur, India
| | - Ali Abdulmawjood Mohammed
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, M.S., 416004, India
| | - Sneha B Paymal
- Department of Microbiology, Shivaji University, 416004, M.S., Kolhapur, India
| | - Nitin M Naik
- Department of Microbiology, Shivaji University, 416004, M.S., Kolhapur, India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, M.S., 416004, India.
- Department of Chemistry, Shivaji University, Kolhapur, M.S., 416004, India.
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Marunaka Y. The Role of Ion-Transporting Proteins in Human Disease. Int J Mol Sci 2024; 25:1726. [PMID: 38339004 PMCID: PMC10855098 DOI: 10.3390/ijms25031726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
This Special Issue focuses on the significance of ion-transporting proteins, such as ion channels and transporters, providing evidence for their significant contribution to bodily and cellular functions via the regulation of signal transduction and ionic environments [...].
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Affiliation(s)
- Yoshinori Marunaka
- Medical Research Institute, Kyoto Industrial Health Association, 67 Kitatsuboi-cho, Nishinokyo, Nakagyo-ku, Kyoto 604-8472, Japan;
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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Li Y, Wu M, Kong M, Sui S, Wang Q, He Y, Gu J. Impact of Donepezil Supplementation on Alzheimer's Disease-like Pathology and Gut Microbiome in APP/PS1 Mice. Microorganisms 2023; 11:2306. [PMID: 37764150 PMCID: PMC10537997 DOI: 10.3390/microorganisms11092306] [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: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Based on published information, the occurrence and development of Alzheimer's disease (AD) are potentially related to gut microbiota changes. Donepezil hydrochloride (DH), which enhances cholinergic activity by blocking acetylcholinesterase (AChE), is one of the first-line drugs for AD treatment approved by the Food and Drug Administration (FDA) of the USA. However, the potential link between the effects of DH on the pathophysiological processes of AD and the gut microbiota remains unclear. In this study, pathological changes in the brain and colon, the activities of superoxide dismutase (SOD) and AChE, and changes in intestinal flora were observed. The results showed that Aβ deposition in the prefrontal cortex and hippocampus of AD mice was significantly decreased, while colonic inflammation was significantly alleviated by DH treatment. Concomitantly, SOD activity was significantly improved, while AChE was significantly reduced after DH administration. In addition, the gut microbiota community composition of AD mice was significantly altered after DH treatment. The relative abundance of Akkermansia in the AD group was 54.8% higher than that in the N group. The relative abundance of Akkermansia was increased by 18.3% and 53.8% in the AD_G group and the N_G group, respectively. Interestingly, Akkermansia showed a potential predictive value and might be a biomarker for AD. Molecular docking revealed the binding mode and major forces between DH and membrane proteins of Akkermansia. The overall results suggest a novel therapeutic mechanism for treating AD and highlight the critical role of gut microbiota in AD pathology.
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Affiliation(s)
- Yuan Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; (Y.L.); (M.W.); (M.K.)
| | - Mengyao Wu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; (Y.L.); (M.W.); (M.K.)
| | - Mengmeng Kong
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; (Y.L.); (M.W.); (M.K.)
| | - Shaomei Sui
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China; (S.S.); (Q.W.)
| | - Qi Wang
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China; (S.S.); (Q.W.)
| | - Yan He
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China; (S.S.); (Q.W.)
| | - Jinsong Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; (Y.L.); (M.W.); (M.K.)
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Patil PJ, Kamble SA, Dhanavade MJ, Liang X, Zhang C, Li X. Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study. BIOLOGY 2023; 12:1051. [PMID: 37626937 PMCID: PMC10451383 DOI: 10.3390/biology12081051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst's functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.
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Affiliation(s)
- Prasanna J. Patil
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (P.J.P.); (X.L.)
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Subodh A. Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, MH, India;
| | - Maruti J. Dhanavade
- Department of Microbiology, Bharati Vidyapeeth’s Dr. Patangrao Kadam Mahavidyalaya College, Sangli 416416, MH, India;
| | - Xin Liang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (P.J.P.); (X.L.)
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (P.J.P.); (X.L.)
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
| | - Xiuting Li
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (P.J.P.); (X.L.)
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
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Marunaka Y. Molecular Mechanisms of Obesity-Induced Development of Insulin Resistance and Promotion of Amyloid-β Accumulation: Dietary Therapy Using Weak Organic Acids via Improvement of Lowered Interstitial Fluid pH. Biomolecules 2023; 13:biom13050779. [PMID: 37238649 DOI: 10.3390/biom13050779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/31/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Insulin resistance is one of the etiologies of type 2 diabetes mellitus (T2DM) and has been suggested to contribute to the development of Alzheimer's disease by promoting amyloid-β accumulation. Various causes of insulin resistance have been suggested; however, mechanisms of insulin resistance development remain to be elucidated in many respects. Elucidating the mechanisms underlying the development of insulin resistance is one of the key factors in developing methods to prevent the onset of T2DM and Alzheimer's disease. It has been suggested that the body pH environment plays an important role in the control of cellular functions by regulating the action of hormones including insulin and the activity of enzymes and neurons, thereby maintaining homeostatic conditions of the body. This review introduces: (1) Mitochondrial dysfunction through oxidative stress caused by obesity-induced inflammation. (2) Decreased pH of interstitial fluid due to mitochondrial dysfunction. (3) Development of insulin resistance due to diminution of insulin affinity to its receptor caused by the lowered interstitial fluid pH. (4) Accelerated accumulation of amyloid-β due to elevated activities of β- and γ-secretases caused by the lowered interstitial fluid pH. (5) Diet therapies for improving insulin resistance with weak organic acids that act as bases in the body to raise the pH of lowered interstitial fluid and food factors that promote absorption of weak organic acids in the gut.
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Affiliation(s)
- Yoshinori Marunaka
- Medical Research Institute, Kyoto Industrial Health Association, Kyoto 604-8472, Japan
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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Qian XH, Liu XL, Chen G, Chen SD, Tang HD. Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease. J Neuroinflammation 2022; 19:236. [PMID: 36171620 PMCID: PMC9520842 DOI: 10.1186/s12974-022-02599-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disease and its pathogenesis is still unclear. There is dysbiosis of gut microbiota in AD patients. More importantly, dysbiosis of the gut microbiota has been observed not only in AD patients, but also in patients with mild cognitive impairment (MCI). However, the mechanism of gut microbiota dysbiosis in AD is poorly understood. Cholinergic anti-inflammatory pathway is an important pathway for the central nervous system (CNS) regulation of peripheral immune homeostasis, especially in the gut. Therefore, we speculated that dysfunction of cholinergic anti-inflammatory pathway is a potential pathway for dysbiosis of the gut microbiota in AD. METHODS In this study, we constructed AD model mice by injecting Aβ1-42 into the lateral ventricle, and detected the cognitive level of mice by the Morris water maze test. In addition, 16S rDNA high-throughput analysis was used to detect the gut microbiota abundance of each group at baseline, 2 weeks and 4 weeks after surgery. Furthermore, immunofluorescence and western blot were used to detect alteration of intestinal structure of mice, cholinergic anti-inflammatory pathway, and APP process of brain and colon in each group. RESULTS Aβ1-42 i.c.v induced cognitive impairment and neuron damage in the brain of mice. At the same time, Aβ1-42 i.c.v induced alteration of gut microbiota at 4 weeks after surgery, while there was no difference at the baseline and 2 weeks after surgery. In addition, changes in colon structure and increased levels of pro-inflammatory factors were detected in Aβ1-42 treatment group, accompanied by inhibition of cholinergic anti-inflammatory pathways. Amyloidogenic pathways in both the brain and colon were accelerated in Aβ1-42 treatment group. CONCLUSIONS The present findings suggested that Aβ in the CNS can induce gut microbiota dysbiosis, alter intestinal structure and accelerate the amyloidogenic pathways, which were related to inhibiting cholinergic anti-inflammatory pathways.
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Affiliation(s)
- Xiao-Hang Qian
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiao-Li Liu
- Department of Neurology, Shanghai Fengxian District Central Hospital, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai, 201406, China
| | - Guang Chen
- The Second Hospital of Anhui Medical University, Anhui, 230601, China
| | - Sheng-di Chen
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hui-Dong Tang
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Medical Center on Aging of Ruijin Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Schreiner TG, Popescu BO. Amyloid Beta Dynamics in Biological Fluids-Therapeutic Impact. J Clin Med 2021; 10:5986. [PMID: 34945282 PMCID: PMC8706225 DOI: 10.3390/jcm10245986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Despite the significant impact of Alzheimer's disease (AD) at individual and socioeconomic levels and the numerous research studies carried out on this topic over the last decades, the treatments available in daily clinical practice remain less than satisfactory. Among the accepted etiopathogenic hypotheses, the amyloidogenic pathway theory, although intensively studied and even sometimes controversial, is still providing relevant theoretical elements for understanding the etiology of AD and for the further development of possible therapeutic tools. In this sense, this review aims to offer new insights related to beta amyloid (Aβ), an essential biomarker in AD. First the structure and function of Aβ in normal and pathological conditions are presented in detail, followed by a discussion on the dynamics of Aβ at the level of different biological compartments. There is focus on Aβ elimination modalities at central nervous system (CNS) level, and clearance via the blood-brain barrier seems to play a crucial/dominant role. Finally, different theoretical and already-applied therapeutic approaches for CNS Aβ elimination are presented, including the recent "peripheral sink therapeutic strategy" and "cerebrospinal fluid sinks therapeutic strategy". These data outline the need for a multidisciplinary approach designed to deliver a solution to stimulate Aβ clearance in more direct ways, including from the cerebrospinal fluid level.
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Affiliation(s)
- Thomas Gabriel Schreiner
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
- Neurology Department, University of Medicine and Pharmacy “Grigore T. Popa”, 700115 Iași, Romania
- Department of Electrical Measurements and Materials, Faculty of Electrical Engineering and Information Technology, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania
| | - Bogdan Ovidiu Popescu
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
- Neurology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
- Laboratory of Cell Biology, Neurosciences and Experimental Myology, ‘Victor Babes’ National Institute of Pathology, 050096 Bucharest, Romania
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