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Shao Y, Molestak E, Su W, Stankevič M, Tchórzewski M. Sordarin - the antifungal antibiotic with a unique modus operandi. Br J Pharmacol 2021; 179:1125-1145. [PMID: 34767248 DOI: 10.1111/bph.15724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 12/01/2022] Open
Abstract
Fungal infections cause serious problems in many aspects of human life, in particular infections in immunocompromised patients represent serious problems. Current antifungal antibiotics target various metabolic pathways, predominantly the cell wall or cellular membrane. Numerous compounds are available to combat fungal infections, but their efficacy is far from being satisfactory and some of them display high toxicity. The emerging resistance represents a serious issue as well; hence, there is a considerable need for new anti-fungal compounds with lower toxicity and higher effectiveness. One of the unique antifungal antibiotics is sordarin, the only known compound that acts on the fungal translational machinery per se. Sordarin inhibits protein synthesis at the elongation step of the translational cycle, acting on eukaryotic translation elongation factor 2. In this review, we intend to deliver a robust scientific platform promoting the development of antifungal compounds, in particular focusing on the molecular action of sordarin.
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Affiliation(s)
- Yutian Shao
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, PR China.,Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Eliza Molestak
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, PR China.,National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, PR China.,Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, PR China
| | - Marek Stankevič
- Department of Organic Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie Sklodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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Tang W, Dong X, Meng J, Feng Y, Xie M, Xu H, Song P. Biochemical characterization and redesign of the coenzyme specificity of a novel monofunctional NAD +-dependent homoserine dehydrogenase from the human pathogen Neisseria gonorrhoeae. Protein Expr Purif 2021; 186:105909. [PMID: 34022392 DOI: 10.1016/j.pep.2021.105909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/17/2022]
Abstract
Gonorrhoea, caused by Neisseria gonorrhoeae, is a major global public health concern. Homoserine dehydrogenase (HSD), a key enzyme in the aspartate pathway, is a promising metabolic target against pathogenic infections. In this study, a monofunctional HSD from N. gonorrhoeae (NgHSD) was overexpressed in Escherichia coli and purified to >95% homogeneity for biochemical characterization. Unlike the classic dimeric structure, the purified recombinant NgHSD exists as a tetramer in solution. We determined the enzymatic activity of recombinant NgHSD for l-homoserine oxidation, which revealed that this enzyme was NAD+ dependent, with an approximate 479-fold (kcat/Km) preference for NAD+ over NADP+, and that optimal activity for l-homoserine oxidation occurred at pH 10.5 and 40 °C. At 800 mM, neither NaCl nor KCl increased the activity of NgHSD, in contrast to the behavior of several reported NAD+-independent homologs. Moreover, threonine did not markedly inhibit the oxidation activity of NgHSD. To gain insight into the cofactor specificity, site-directed mutagenesis was used to alter coenzyme specificity. The double mutant L45R/S46R, showing the highest affinity for NADP+, caused a shift in coenzyme preference from NAD+ to NADP+ by a factor of ~974, with a catalytic efficiency comparable with naturally occurring NAD+-independent homologs. Collectively, our results should allow the exploration of drugs targeting NgHSD to treat gonococcal infections and contribute to the prediction of the coenzyme specificity of novel HSDs.
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Affiliation(s)
- Wanggang Tang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China.
| | - Xue Dong
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Jiang Meng
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Yanan Feng
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Manman Xie
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Haonan Xu
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Ping Song
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, China.
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3
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l-amino acid ligase: A promising alternative for the biosynthesis of l-dipeptides. Enzyme Microb Technol 2020; 136:109537. [DOI: 10.1016/j.enzmictec.2020.109537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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4
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Potential targets for the development of new antifungal drugs. J Antibiot (Tokyo) 2018; 71:978-991. [DOI: 10.1038/s41429-018-0100-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 12/19/2022]
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5
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Targeting the Homoserine Dehydrogenase of Paracoccidioides Species for Treatment of Systemic Fungal Infections. Antimicrob Agents Chemother 2017; 61:AAC.00165-17. [PMID: 28652239 DOI: 10.1128/aac.00165-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/09/2017] [Indexed: 11/20/2022] Open
Abstract
This work evaluated new potential inhibitors of the enzyme homoserine dehydrogenase (HSD) of Paracoccidioides brasiliensis, one of the etiological agents of paracoccidioidomycosis. The tertiary structure of the protein bonded to the analogue NAD, and l-homoserine was modeled by homology. The model with the best output was subjected to gradient minimization, redocking, and molecular dynamics simulation. Virtual screening simulations with 187,841 molecules purchasable from the Zinc database were performed. After the screenings, 14 molecules were selected and analyzed by the use of absorption, distribution, metabolism, excretion, and toxicity criteria, resulting in four compounds for in vitro assays. The molecules HS1 and HS2 were promising, exhibiting MICs of 64 and 32 μg · ml-1, respectively, for the Pb18 isolate of P. brasilensis, 64 μg · ml-1 for two isolates of P. lutzii, and also synergy with itraconazole. The application of these molecules to human-pathogenic fungi confirmed that the HSD enzyme may be used as a target for the development of drugs with specific action against paracoccidioidomycosis; moreover, these compounds may serve as leads in the design of new antifungals.
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Abstract
In December 2001, the McMaster HTS Lab officially opened its doors. Since that time, we have made significant strides in demonstrating that university-based, high-throughput screening (HTS) is a viable proposition for academic scientists seeking to discover novel small molecule probes of biological function. Although the lab has been running screens for just over two years, the process of designing, building and maintaining the lab has been on-going for more than four years. As high-throughput screening technology moves from the industrial sector to the academic and small biotech sectors, strategies for setting up a successful, highly flexible HTS lab on a limited budget becomes very important. In the current communication, we outline some of the considerations in setting up the lab and some of our experiences to date with screening and automation in academe.
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Inhibitors of amino acids biosynthesis as antifungal agents. Amino Acids 2014; 47:227-49. [PMID: 25408465 PMCID: PMC4302243 DOI: 10.1007/s00726-014-1873-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
Fungal microorganisms, including the human pathogenic yeast and filamentous fungi, are able to synthesize all proteinogenic amino acids, including nine that are essential for humans. A number of enzymes catalyzing particular steps of human-essential amino acid biosynthesis are fungi specific. Numerous studies have shown that auxotrophic mutants of human pathogenic fungi impaired in biosynthesis of particular amino acids exhibit growth defect or at least reduced virulence under in vivo conditions. Several chemical compounds inhibiting activity of one of these enzymes exhibit good antifungal in vitro activity in minimal growth media, which is not always confirmed under in vivo conditions. This article provides a comprehensive overview of the present knowledge on pathways of amino acids biosynthesis in fungi, with a special emphasis put on enzymes catalyzing particular steps of these pathways as potential targets for antifungal chemotherapy.
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Exploring the molecular basis for selective binding of homoserine dehydrogenase from Mycobacterium leprae TN toward inhibitors: a virtual screening study. Int J Mol Sci 2014; 15:1826-41. [PMID: 24469317 PMCID: PMC3958823 DOI: 10.3390/ijms15021826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 12/12/2022] Open
Abstract
Homoserine dehydrogenase (HSD) from Mycobacterium leprae TN is an antifungal target for antifungal properties including efficacy against the human pathogen. The 3D structure of HSD has been firmly established by homology modeling methods. Using the template, homoserine dehydrogenase from Thiobacillus denitrificans (PDB Id 3MTJ), a sequence identity of 40% was found and molecular dynamics simulation was used to optimize a reliable structure. The substrate and co-factor-binding regions in HSD were identified. In order to determine the important residues of the substrate (l-aspartate semialdehyde (l-ASA)) binding, the ASA was docked to the protein; Thr163, Asp198, and Glu192 may be important because they form a hydrogen bond with HSD through AutoDock 4.2 software. After use of a virtual screening technique of HSD, the four top-scoring docking hits all seemed to cation–π ion pair with the key recognition residue Lys107, and Lys207. These ligands therefore seemed to be new chemotypes for HSD. Our results may be helpful for further experimental investigations.
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Synthesis and biological evaluation of potential threonine synthase inhibitors: Rhizocticin A and Plumbemycin A. Bioorg Med Chem 2013; 21:4958-67. [DOI: 10.1016/j.bmc.2013.06.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/17/2013] [Accepted: 06/26/2013] [Indexed: 11/23/2022]
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10
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Styger G, Jacobson D, Bauer FF. Identifying genes that impact on aroma profiles produced by Saccharomyces cerevisiae and the production of higher alcohols. Appl Microbiol Biotechnol 2011; 91:713-30. [DOI: 10.1007/s00253-011-3237-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
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11
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De Pascale G, Griffiths EJ, Shakya T, Nazi I, Wright GD. Identification and Characterization of New Inhibitors of Fungal Homoserine Kinase. Chembiochem 2011; 12:1179-82. [DOI: 10.1002/cbic.201100121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Indexed: 11/09/2022]
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12
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De Pascale G, Nazi I, Harrison PHM, Wright GD. β-Lactone natural products and derivatives inactivate homoserine transacetylase, a target for antimicrobial agents. J Antibiot (Tokyo) 2011; 64:483-7. [DOI: 10.1038/ja.2011.37] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Schroeder AC, Zhu C, Yanamadala SR, Cahoon RE, Arkus KAJ, Wachsstock L, Bleeke J, Krishnan HB, Jez JM. Threonine-insensitive homoserine dehydrogenase from soybean: genomic organization, kinetic mechanism, and in vivo activity. J Biol Chem 2010; 285:827-34. [PMID: 19897476 PMCID: PMC2801284 DOI: 10.1074/jbc.m109.068882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 11/05/2009] [Indexed: 11/06/2022] Open
Abstract
Aspartate kinase (AK) and homoserine dehydrogenase (HSD) function as key regulatory enzymes at branch points in the aspartate amino acid pathway and are feedback-inhibited by threonine. In plants the biochemical features of AK and bifunctional AK-HSD enzymes have been characterized, but the molecular properties of the monofunctional HSD remain unexamined. To investigate the role of HSD, we have cloned the cDNA and gene encoding the monofunctional HSD (GmHSD) from soybean. Using heterologously expressed and purified GmHSD, initial velocity and product inhibition studies support an ordered bi bi kinetic mechanism in which nicotinamide cofactor binds first and leaves last in the reaction sequence. Threonine inhibition of GmHSD occurs at concentrations (K(i) = 160-240 mM) more than 1000-fold above physiological levels. This is in contrast to the two AK-HSD isoforms in soybean that are sensitive to threonine inhibition (K(i) approximately 150 microM). In addition, GmHSD is not inhibited by other aspartate-derived amino acids. The ratio of threonine-resistant to threonine-sensitive HSD activity in soybean tissues varies and likely reflects different demands for amino acid biosynthesis. This is the first cloning and detailed biochemical characterization of a monofunctional feedback-insensitive HSD from any plant. Threonine-resistant HSD offers a useful biotechnology tool for manipulating the aspartate amino acid pathway to increase threonine and methionine production in plants for improved nutritional content.
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Affiliation(s)
- Amy C. Schroeder
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Chuanmei Zhu
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Srinivasa Rao Yanamadala
- the Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
| | - Rebecca E. Cahoon
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Kiani A. J. Arkus
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Leia Wachsstock
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Jeremy Bleeke
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Hari B. Krishnan
- the Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
| | - Joseph M. Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
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High-throughput screening identifies novel inhibitors of the acetyltransferase activity of Escherichia coli GlmU. Antimicrob Agents Chemother 2009; 53:2306-11. [PMID: 19349513 DOI: 10.1128/aac.01572-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bifunctional GlmU protein catalyzes the formation of UDP-N-acetylglucosamine in a two-step reaction using the substrates glucosamine-1-phosphate, acetyl coenzyme A, and UTP. This metabolite is a common precursor to the synthesis of bacterial cell surface carbohydrate polymers, such as peptidoglycan, lipopolysaccharide, and wall teichoic acid that are involved in the maintenance of cell shape, permeability, and virulence. The C-terminal acetyltransferase domain of GlmU exhibits structural and mechanistic features unique to bacterial UDP-N-acetylglucosamine synthases, making it an excellent target for antibacterial design. In the work described here, we have developed an absorbance-based assay to screen diverse chemical libraries in high throughput for inhibitors to the acetyltransferase reaction of Escherichia coli GlmU. The primary screen of 50,000 drug-like small molecules identified 63 hits, 37 of which were specific to acetyltransferase activity of GlmU. Secondary screening and mode-of-inhibition studies identified potent inhibitors where compound binding within the acetyltransferase active site was requisite on the presence of glucosamine-1-phosphate and were competitive with the substrate acetyl coenzyme A. These molecules may represent novel chemical scaffolds for future antimicrobial drug discovery. In addition, this work outlines the utility of catalytic variants in targeting specific activities of bifunctional enzymes in high-throughput screens.
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Zubieta C, Arkus KAJ, Cahoon RE, Jez JM. A single amino acid change is responsible for evolution of acyltransferase specificity in bacterial methionine biosynthesis. J Biol Chem 2008; 283:7561-7. [PMID: 18216013 DOI: 10.1074/jbc.m709283200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria and yeast rely on either homoserine transsuccinylase (HTS, metA) or homoserine transacetylase (HTA; met2) for the biosynthesis of methionine. Although HTS and HTA catalyze similar chemical reactions, these proteins are typically unrelated in both sequence and three-dimensional structure. Here we present the 2.0 A resolution x-ray crystal structure of the Bacillus cereus metA protein in complex with homoserine, which provides the first view of a ligand bound to either HTA or HTS. Surprisingly, functional analysis of the B. cereus metA protein shows that it does not use succinyl-CoA as a substrate. Instead, the protein catalyzes the transacetylation of homoserine using acetyl-CoA. Therefore, the B. cereus metA protein functions as an HTA despite greater than 50% sequence identity with bona fide HTS proteins. This result emphasizes the need for functional confirmation of annotations of enzyme function based on either sequence or structural comparisons. Kinetic analysis of site-directed mutants reveals that the B. cereus metA protein and the E. coli HTS share a common catalytic mechanism. Structural and functional examination of the B. cereus metA protein reveals that a single amino acid in the active site determines acetyl-CoA (Glu-111) versus succinyl-CoA (Gly-111) specificity in the metA-like of acyltransferases. Switching of this residue provides a mechanism for evolving substrate specificity in bacterial methionine biosynthesis. Within this enzyme family, HTS and HTA activity likely arises from divergent evolution in a common structural scaffold with conserved catalytic machinery and homoserine binding sites.
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Affiliation(s)
- Chloe Zubieta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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Nazi I, Scott A, Sham A, Rossi L, Williamson PR, Kronstad JW, Wright GD. Role of homoserine transacetylase as a new target for antifungal agents. Antimicrob Agents Chemother 2007; 51:1731-6. [PMID: 17353245 PMCID: PMC1855549 DOI: 10.1128/aac.01400-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial amino acid biosynthesis is a proven yet underexploited target of antibiotics. The biosynthesis of methionine in particular has been shown to be susceptible to small-molecule inhibition in fungi. The first committed step in Met biosynthesis is the acylation of homoserine (Hse) by the enzyme homoserine transacetylase (HTA). We have identified the MET2 gene of Cryptococcus neoformans H99 that encodes HTA (CnHTA) by complementation of an Escherichia coli metA mutant that lacks the gene encoding homoserine transsuccinylase (HTS). We cloned, expressed, and purified CnHTA and determined its steady-state kinetic parameters for the acetylation of L-Hse by acetyl coenzyme A. We next constructed a MET2 mutant in C. neoformans H99 and tested its growth behavior in Met-deficient media, confirming the expected Met auxotrophy. Furthermore, we used this mutant in a mouse inhalation model of infection and determined that MET2 is required for virulence. This makes fungal HTA a viable target for new antibiotic discovery. We screened a 1,000-compound library of small molecules for HTA inhibitors and report the identification of the first inhibitor of fungal HTA. This work validates HTA as an attractive drug-susceptible target for new antifungal agent design.
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Affiliation(s)
- Ishac Nazi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Brown ED, Wright GD. New Targets and Screening Approaches in Antimicrobial Drug Discovery. Chem Rev 2005; 105:759-74. [PMID: 15700964 DOI: 10.1021/cr030116o] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric D Brown
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5
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