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Nurhan AD, Gani MA, Budiatin AS, Siswodihardjo S, Khotib J. Molecular docking studies of Nigella sativa L and Curcuma xanthorrhiza Roxb secondary metabolites against histamine N-methyltransferase with their ADMET prediction. J Basic Clin Physiol Pharmacol 2021; 32:795-802. [PMID: 34214299 DOI: 10.1515/jbcpp-2020-0425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/29/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Histamine N-methyltransferase (HNMT) is an enzyme that plays a crucial role in the inactivation of histamine in central nervous system, kidneys and bronchi. Inhibition of HNMT is known to have a potential role in treating attention-deficit hyperactivity disorder, memory impairment, mental illness and neurodegenerative illnesses. Therefore, to find potential compounds that could be developed as novel HNMT inhibitors, this study conducted an in silico study of the secondary metabolites of Nigella sativa L and Curcuma xanthorrhiza Roxb. METHODS In this study, we conducted a molecular docking study of 36 secondary metabolites of N. sativa L and 26 secondary metabolites of C. xanthorrhiza Roxb using an in silico approach targeting HNMT protein (PDB ID: 2AOT) using AutoDockVina software. The prediction of ADMET characteristics was done using the pkCSM Online Tool. RESULTS This study obtained one metabolite from N. sativa L (longifolene) and seven metabolites from C. xanthorrhiza Roxb {(+)-beta-atlantone, humulene epoxide, (-)-beta-curcumene, (E)-caryophyllene, germacrone, (R)-(-)-xanthorrhizol, and (-)-beta-caryophyllene epoxide} which were predicted to have potential to be developed as HNMT inhibitors. CONCLUSIONS This study found several secondary metabolites of N. sativa L and C. xanthorrhiza Roxb which had activity as HNMT inhibitors. This research can likewise be utilized as a basis for further research, both in vitro, in vivo, and clinical trials related to the development of secondary metabolites from N. sativa L and C. xanthorrhiza Roxb as novel HNMT inhibitor compounds.
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Affiliation(s)
- Ahmad Dzulfikri Nurhan
- Department of Clinical Pharmacy, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
| | - Maria Apriliani Gani
- Department of Clinical Pharmacy, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
| | - Aniek Setiya Budiatin
- Department of Clinical Pharmacy, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
| | - Siswandono Siswodihardjo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
| | - Junaidi Khotib
- Department of Clinical Pharmacy, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
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2
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Bengel LL, Aberle B, Egler-Kemmerer AN, Kienzle S, Hauer B, Hammer SC. Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles With Simple Haloalkanes. Angew Chem Int Ed Engl 2021; 60:5554-5560. [PMID: 33300646 PMCID: PMC7986378 DOI: 10.1002/anie.202014239] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Indexed: 01/06/2023]
Abstract
Selective alkylation of pyrazoles could solve a challenge in chemistry and streamline synthesis of important molecules. Here we report catalyst‐controlled pyrazole alkylation by a cyclic two‐enzyme cascade. In this enzymatic system, a promiscuous enzyme uses haloalkanes as precursors to generate non‐natural analogs of the common cosubstrate S‐adenosyl‐l‐methionine. A second engineered enzyme transfers the alkyl group in highly selective C−N bond formations to the pyrazole substrate. The cosubstrate is recycled and only used in catalytic amounts. Key is a computational enzyme‐library design tool that converted a promiscuous methyltransferase into a small enzyme family of pyrazole‐alkylating enzymes in one round of mutagenesis and screening. With this enzymatic system, pyrazole alkylation (methylation, ethylation, propylation) was achieved with unprecedented regioselectivity (>99 %), regiodivergence, and in a first example on preparative scale.
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Affiliation(s)
- Ludwig L Bengel
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Benjamin Aberle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alexander-N Egler-Kemmerer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Samuel Kienzle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Bengel LL, Aberle B, Egler‐Kemmerer A, Kienzle S, Hauer B, Hammer SC. Modifizierte Enzyme ermöglichen die selektive
N
‐Alkylierung von Pyrazolen unter Verwendung einfacher Halogenalkane. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ludwig L. Bengel
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Benjamin Aberle
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Alexander‐N. Egler‐Kemmerer
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Samuel Kienzle
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Bernhard Hauer
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Stephan C. Hammer
- Fakultät Chemie Organische Chemie und Biokatalyse Universität Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
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Histamine N-Methyltransferase in the Brain. Int J Mol Sci 2019; 20:ijms20030737. [PMID: 30744146 PMCID: PMC6386932 DOI: 10.3390/ijms20030737] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
Brain histamine is a neurotransmitter and regulates diverse physiological functions. Previous studies have shown the involvement of histamine depletion in several neurological disorders, indicating the importance of drug development targeting the brain histamine system. Histamine N-methyltransferase (HNMT) is a histamine-metabolising enzyme expressed in the brain. Although pharmacological studies using HNMT inhibitors have been conducted to reveal the direct involvement of HNMT in brain functions, HNMT inhibitors with high specificity and sufficient blood–brain barrier permeability have not been available until now. Recently, we have phenotyped Hnmt-deficient mice to elucidate the importance of HNMT in the central nervous system. Hnmt disruption resulted in a robust increase in brain histamine concentration, demonstrating the essential role of HNMT in the brain histamine system. Clinical studies have suggested that single nucleotide polymorphisms of the human HNMT gene are associated with several brain disorders such as Parkinson’s disease and attention deficit hyperactivity disorder. Postmortem studies also have indicated that HNMT expression is altered in human brain diseases. These findings emphasise that an increase in brain histamine levels by novel HNMT inhibitors could contribute to the improvement of brain disorders.
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Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
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Wennerstrand P, Blissing A, Mårtensson LG. In Vitro Protein Stability of Two Naturally Occurring Thiopurine S-Methyltransferase Variants: Biophysical Characterization of TPMT*6 and TPMT*8. ACS OMEGA 2017; 2:4991-4999. [PMID: 30023734 PMCID: PMC6044926 DOI: 10.1021/acsomega.7b00801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/18/2017] [Indexed: 06/02/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is a polymorphic enzyme involved in the metabolism and inactivation of thiopurine substances administered as immunosuppressants in the treatment of malignancies and autoimmune diseases. In this study, the naturally occurring variants, TPMT*6 (Y180F) and TPMT*8 (R215H), have been biophysically characterized. Despite being classified as low and intermediate in vivo enzyme activity variants, respectively, our results demonstrate a discrepancy because both TPMT*6 and TPMT*8 were found to exhibit normal functionality in vitro. While TPMT*8 exhibited biophysical properties almost indistinguishable from those of TPMTwt, the TPMT*6 variant was found to be destabilized. Furthermore, the contributions of the cofactor S-adenosylmethionine (SAM) to the thermodynamic stability of TPMT were investigated, but only a modest stabilizing effect was observed. Also presented herein is a new method for studies of the biophysical characteristics of TPMT and its variants using the extrinsic fluorescent probe 8-anilinonaphthalene-1-sulfonic acid (ANS). ANS was found to bind strongly to all investigated TPMT variants with a Kd of approximately 0.2 μM and a 1:1 binding ratio as determined by isothermal titration calorimetry (ITC). Circular dichroism and fluorescence measurements showed that ANS binds exclusively to the native state of TPMT, and binding to the active site was confirmed by molecular modeling and simulated docking as well as ITC measurements. The strong binding of the probe to native TPMT and the conformity of the obtained results demonstrate the advantages of using ANS binding characteristics in studies of this protein and its variants.
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Shan L, Bao AM, Swaab DF. Changes in Histidine Decarboxylase, Histamine N-Methyltransferase and Histamine Receptors in Neuropsychiatric Disorders. Handb Exp Pharmacol 2017; 241:259-276. [PMID: 28233178 DOI: 10.1007/164_2016_125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Compared to other monoamine neurotransmitters, information on the association between the histaminergic system and neuropsychiatric disorders is scarce, resulting in a lack of histamine-related treatment for these disorders. The current chapter tries to combine information obtained from genetic studies, neuroimaging, post-mortem human brain studies and cerebrospinal fluid measurements with data from recent clinical trials on histamine receptor agonists and antagonists, with a view to determining the possible role of the histaminergic system in neuropsychiatric disorders and to pave the way for novel histamine-related therapeutic strategies.
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Affiliation(s)
- Ling Shan
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
- Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, University of Amsterdam, Meibergdreef 47, Amsterdam, 1105 BA, The Netherlands
| | - Ai-Min Bao
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, China.
| | - Dick F Swaab
- Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, University of Amsterdam, Meibergdreef 47, Amsterdam, 1105 BA, The Netherlands.
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