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Šmak P, Tvaroška I, Koča J. The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1. Phys Chem Chem Phys 2021; 23:23850-23860. [PMID: 34647946 DOI: 10.1039/d1cp03718h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tyrosine sulfation alters the biological activity of many proteins involved in different physiological and pathophysiological conditions, such as non-specific immune reaction, response to inflammation and ischemia, targeting of leukocytes and stem cells, or the formation of cancer metastases. Tyrosine sulfation is catalyzed by the enzymes tyrosylprotein sulfotransferases (TPST). In this study, we used QM/MM Car-Parrinello metadynamics simulations together with QM/MM potential energy calculations to investigate the catalytic mechanism of isoform TPST-1. The structural changes along the reaction coordinate are analyzed and discussed. Furthermore, both the methods supported the SN2 type of catalytic mechanism. The reaction barrier obtained from CPMD metadynamics was 12.8 kcal mol-1, and the potential energy scan led to reaction barriers of 11.6 kcal mol-1 and 13.7 kcal mol-1 with the B3LYP and OPBE functional, respectively. The comparison of the two methods (metadynamics and potential energy scan) may be helpful for future mechanistic studies. The insight into the reaction mechanism of TPST-1 might help with the rational design of transition-state TPST inhibitors.
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Affiliation(s)
- Pavel Šmak
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Igor Tvaroška
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Jaroslav Koča
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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2
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Mendoza F, Masgrau L. Computational modeling of carbohydrate processing enzymes reactions. Curr Opin Chem Biol 2021; 61:203-213. [PMID: 33812143 DOI: 10.1016/j.cbpa.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022]
Abstract
Carbohydrate processing enzymes are of biocatalytic interest. Glycoside hydrolases and the recently discovered lytic polysaccharide monooxygenase for their use in biomass degradation to obtain biofuels or valued chemical entities. Glycosyltransferases or engineered glycosidases and phosphorylases for the synthesis of carbohydrates and glycosylated products. Quantum mechanics-molecular mechanics (QM/MM) methods are highly contributing to establish their different chemical reaction mechanisms. Other computational methods are also used to study enzyme conformational changes, ligand pathways, and processivity, e.g. for processive glycosidases like cellobiohydrolases. There is still a long road to travel to fully understand the role of conformational dynamics in enzyme activity and also to disclose the variety of reaction mechanisms these enzymes employ. Additionally, computational tools for enzyme engineering are beginning to be applied to evaluate substrate specificity or aid in the design of new biocatalysts with increased thermostability or tailored activity, a growing field where molecular modeling is finding its way.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Talcahuano, 4260000, Chile
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Institut de Biotecnología i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018, Barcelona, Spain.
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3
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Janoš P, Tvaroška I, Dellago C, Koča J. Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation. ACS OMEGA 2020; 5:21374-21384. [PMID: 32905330 PMCID: PMC7469130 DOI: 10.1021/acsomega.0c01434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
We applied the transition path sampling (TPS) method to study the translocation step of the catalytic mechanism of galactofuranosyl transferase 2 (GlfT2). Using TPS in the field of enzymatic reactions is still relatively rare, and we show its effectiveness on this enzymatic system. We decipher an unknown mechanism of the translocation step and, thus, provide a complete understanding of the catalytic mechanism of GlfT2 at the atomistic level. The GlfT2 enzyme is involved in the formation of the mycobacterial cell wall and transfers galactofuranose (Galf) from UDP-Galf onto a growing acceptor Galf chain. The biosynthesis of the galactan chain is accomplished in a processive manner, with the growing acceptor substrate remaining bound to GlfT2. The glycosidic bond formed by GlfT2 between the two Galf residues alternates between β-(1-6) and β-(1-5) linkages. The translocation of the growing galactan between individual additions of Galf residues is crucial for the function of GlfT2. Analysis of unbiased trajectory ensembles revealed that the translocation proceeds differently depending on the glycosidic linkage between the last two Galf residues. We also showed that the protonation state of the catalytic residue Asp372 significantly influences the translocation. Approximate transition state structures and potential energy reaction barriers of the translocation process were determined. The calculated potential reaction barriers in the range of 6-14 kcal/mol show that the translocation process is not the rate-limiting step in galactan biosynthesis.
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Affiliation(s)
- Pavel Janoš
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno 601 77, Czech Republic
- Faculty
of Science, National Centre for Biomolecular Research, Masaryk University, Brno 601 77, Czech Republic
| | - Igor Tvaroška
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno 601 77, Czech Republic
- Institute
of Chemistry, Slovak Academy of Sciences, Bratislava 84536, Slovak Republic
| | | | - Jaroslav Koča
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno 601 77, Czech Republic
- Faculty
of Science, National Centre for Biomolecular Research, Masaryk University, Brno 601 77, Czech Republic
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Baráth M, Jakubčinová J, Konyariková Z, Kozmon S, Mikušová K, Bella M. Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2. Beilstein J Org Chem 2020; 16:1853-1862. [PMID: 32802202 PMCID: PMC7404141 DOI: 10.3762/bjoc.16.152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/09/2020] [Indexed: 12/02/2022] Open
Abstract
A series of ten novel ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones bearing a 1-O-phosphono moiety and three different substituents at C-2 has been prepared. Due to the structural similarities of these scaffolds to the native substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active site of GlfT2, none of these compounds serve as efficient inhibitors of the enzymes involved in the mycobacterial galactan biosynthesis.
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Affiliation(s)
- Marek Baráth
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Jana Jakubčinová
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Zuzana Konyariková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Stanislav Kozmon
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Maroš Bella
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
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Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target? Antibiotics (Basel) 2020; 9:antibiotics9010020. [PMID: 31935842 PMCID: PMC7168186 DOI: 10.3390/antibiotics9010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
While target-based drug design has proved successful in several therapeutic areas, this approach has not yet provided compelling outcomes in the field of antibacterial agents. This statement remains especially true for the development of novel therapeutic interventions against tuberculosis, an infectious disease that is among the top ten leading causes of death globally. Mycobacterial galactan is an important component of the protective cell wall core of the tuberculosis pathogen and it could provide a promising target for the design of new drugs. In this review, we summarize the current knowledge on galactan biosynthesis in Mycobacterium tuberculosis, including landmark findings that led to the discovery and understanding of three key enzymes in this pathway: UDP-galactose mutase, and galactofuranosyl transferases GlfT1 and GlfT2. Moreover, we recapitulate the efforts aimed at their inhibition. The predicted common transition states of the three enzymes provide the lucrative possibility of multitargeting in pharmaceutical development, a favourable property in the mitigation of drug resistance. We believe that a tight interplay between target-based computational approaches and experimental methods will result in the development of original inhibitors that could serve as the basis of a new generation of drugs against tuberculosis.
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Hu JP, Wu ZX, Xie T, Liu XY, Yan X, Sun X, Liu W, Liang L, He G, Gan Y, Gou XJ, Shi Z, Zou Q, Wan H, Shi HB, Chang S. Applications of Molecular Simulation in the Discovery of Antituberculosis Drugs: A Review. Protein Pept Lett 2019; 26:648-663. [PMID: 31218945 DOI: 10.2174/0929866526666190620145919] [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: 12/29/2018] [Revised: 04/10/2019] [Accepted: 05/03/2019] [Indexed: 02/05/2023]
Abstract
After decades of efforts, tuberculosis has been well controlled in most places. The existing drugs are no longer sufficient for the treatment of drug-resistant Mycobacterium tuberculosis due to significant toxicity and selective pressure, especially for XDR-TB. In order to accelerate the development of high-efficiency, low-toxic antituberculosis drugs, it is particularly important to use Computer Aided Drug Design (CADD) for rational drug design. Here, we systematically reviewed the specific role of molecular simulation in the discovery of new antituberculosis drugs. The purpose of this review is to overview current applications of molecular simulation methods in the discovery of antituberculosis drugs. Furthermore, the unique advantages of molecular simulation was discussed in revealing the mechanism of drug resistance. The comprehensive use of different molecular simulation methods will help reveal the mechanism of drug resistance and improve the efficiency of rational drug design. With the help of molecular simulation methods such as QM/MM method, the mechanisms of biochemical reactions catalyzed by enzymes at atomic level in Mycobacterium tuberculosis has been deeply analyzed. QSAR and virtual screening both accelerate the development of highefficiency, low-toxic potential antituberculosis drugs. Improving the accuracy of existing algorithms and developing more efficient new methods for CADD will always be a hot topic in the future. It is of great value to utilize molecular dynamics simulation to investigate complex systems that cannot be studied in experiments, especially for drug resistance of Mycobacterium tuberculosis.
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Affiliation(s)
- Jian-Ping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Zhi-Xiang Wu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Tao Xie
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xin-Yu Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiao Yan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Wei Liu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Li Liang
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Gang He
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Ya Gan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xiao-Jun Gou
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Zheng Shi
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Qiang Zou
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
| | - Hu-Bing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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