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Friday SN, Cheng DW, Zagler SG, Zanella BS, Dietz JD, Calbat CN, Roach LT, Bagnal C, Faile IS, Halkides CJ, Viola RE. Design and testing of selective inactivators against an antifungal enzyme target. Drug Dev Res 2021; 83:447-460. [PMID: 34469014 DOI: 10.1002/ddr.21875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022]
Abstract
Systemic infections from fungal organisms are becoming increasingly difficult to treat as drug resistance continues to emerge. To substantially expand the antifungal drug landscape new compounds must be identified and developed with novel modes of action against previously untested drug targets. Most drugs block the activity of their targets through reversible, noncovalent interactions. However, a significant number of drugs form irreversible, covalent bonds with their selected targets. While more challenging to develop, these irreversible inactivators offer some significant advantages as novel antifungal agents. Vinyl sulfones contain a potentially reactive functional group that could function as a selective enzyme inactivator, and members of this class of compounds are now being developed as inactivators against an antifungal drug target. The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a key step in an essential microbial pathway and is essential for the survival of every microorganism examined. A series of vinyl sulfones have been designed, guided by molecular modeling and docking studies to enhance their affinity for fungal ASADHs. These newly synthesized compounds have been examined against this target enzyme from the pathogenic fungal organism Candida albicans. Vinyl sulfones containing complementary structural elements inhibit this enzyme with inhibition constants in the low-micromolar range. These inhibitors have also led to the rapid and irreversible inactivation of this enzyme, and show some initial selectivity when compared to the inactivation of a bacterial ASADH. The best inactivators will serve as lead compounds for the development of potent and selective antifungal agents.
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Affiliation(s)
- Samantha N Friday
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Daniel W Cheng
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Sebastian G Zagler
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Brady S Zanella
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Jordan D Dietz
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher N Calbat
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Logan T Roach
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Cindy Bagnal
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ian S Faile
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
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Dahal GP, Launder D, McKeone KMM, Hunter JP, Conti HR, Viola RE. Aspartate semialdehyde dehydrogenase inhibition suppresses the growth of the pathogenic fungus Candida albicans. Drug Dev Res 2020; 81:736-744. [PMID: 32383780 DOI: 10.1002/ddr.21682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 12/27/2022]
Abstract
Potent inhibitors of an essential microbial enzyme have been shown to be effective growth inhibitors of Candida albicans, a pathogenic fungus. C. albicans is the main cause of oropharyngeal candidiasis, and also causes invasive fungal infections, including systemic sepsis, leading to serious complications in immunocompromised patients. As the rates of drug-resistant fungal infections continue to rise novel antifungal treatments are desperately needed. The enzyme aspartate semialdehyde dehydrogenase (ASADH) is critical for the functioning of the aspartate biosynthetic pathway in microbes and plants. Because the aspartate pathway is absent in humans, ASADH has the potential to be a promising new target for antifungal research. Deleting the asd gene encoding for ASADH significantly decreases the survival of C. albicans, establishing this enzyme as essential for this organism. Previously developed ASADH inhibitors were tested against several strains of C. albicans to measure their possible therapeutic impact. The more potent inhibitors show a good correlation between enzyme inhibitor potency and fungal growth inhibition. Growth curves generated by incubating different C. albicans strains with varying enzyme inhibitor levels show significant slowing of fungal growth by these inhibitors against each of these strains, similar to the effect observed with a clinical antifungal drug. The most effective inhibitors also demonstrated relatively low cytotoxicity against a human epithelial cell line. Taken together, these results establish that the ASADH enzyme is a promising new target for further development as a novel antifungal treatment against C. albicans and related fungal species.
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Affiliation(s)
- Gopal P Dahal
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Dylan Launder
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, USA
| | | | - Joseph P Hunter
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, USA
| | - Heather R Conti
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
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Abstract
Pathogenic fungi represent a growing threat to human health, with an increase in the frequency of drug-resistant fungal infections. Identifying targets from among the selected metabolic pathways that are unique to microbial species presents an opportunity to develop new antifungal agents against new and untested targets to combat this growth threat. Aspartate semialdehyde dehydrogenase (ASADH) catalyzes a key step in a uniquely microbial amino acid biosynthetic pathway and is essential for microbial viability. This enzyme, purified from four pathogenic fungal organisms ( Candida albicans, Aspergillus fumigatus, Cryptococcus neoformans, and Blastomyces dermatitidis), has been screened against fragment libraries to identify initial enzyme inhibitors. The binding of structural analogs of the most promising lead compounds was measured against these fungal ASADHs to establish important structure-activity relationships among these different inhibitor classes. The most potent of these inhibitors have been docked into structures of this fungal enzyme target to identify important structural elements that serve as critical binding determinants. Several inhibitors with low micromolar inhibition constants have been identified that showed selectivity against these related enzymes from different fungal species. Subsequent screening against a library of drugs and drug candidates identified some additional inhibitors containing a consistent set of functional groups required for fungal ASADH inhibition. Additional elaboration of these core structures will likely lead to more potent and selective inhibitors.
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Affiliation(s)
- Gopal P Dahal
- 1 Department of Chemistry and Biochemistry, University of Toledo, OH, USA
| | - Ronald E Viola
- 1 Department of Chemistry and Biochemistry, University of Toledo, OH, USA
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Amala M, Rajamanikandan S, Prabhu D, Surekha K, Jeyakanthan J. Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: combined molecular docking and molecular dynamics approaches. J Biomol Struct Dyn 2018; 37:394-410. [PMID: 29334340 DOI: 10.1080/07391102.2018.1427633] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Lymphatic filariasis is a debilitating vector borne parasitic disease that infects human lymphatic system by nematode Brugia malayi. Currently available anti-filarial drugs are effective only on the larval stages of parasite. So far, no effective drugs are available for humans to treat filarial infections. In this regard, aspartate semialdehyde dehydrogenase (ASDase) in lysine biosynthetic pathway from Wolbachia endosymbiont Brugia malayi represents an attractive therapeutic target for the development of novel anti-filarial agents. In this present study, molecular modeling combined with molecular dynamics simulations and structure-based virtual screening were performed to identify potent lead molecules against ASDase. Based on Glide score, toxicity profile, binding affinity and mode of interactions with the ASDase, five potent lead molecules were selected. The molecular docking and dynamics results revealed that the amino acid residues Arg103, Asn133, Cys134, Gln161, Ser164, Lys218, Arg239, His246, and Asn321 plays a crucial role in effective binding of Top leads into the active site of ASDase. The stability of the ASDase-lead complexes was confirmed by running the 30 ns molecular dynamics simulations. The pharmacokinetic properties of the identified lead molecules are in the acceptable range. Furthermore, density functional theory and binding free energy calculations were performed to rank the lead molecules. Thus, the identified lead molecules can be used for the development of anti-filarial agents to combat the pathogenecity of Brugia malayi.
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Key Words
- ADLA, Acute Dermato-Lymphangio-Adenitis
- ADMET, Absorption, Distribution, Metabolism, Excretion and Toxicity
- ASDase, aspartate semialdehyde dehydrogenase
- BlastP, Basic Local Alignment Search Tool
- DFT, Density Functional Theory
- GRAVY, Grand Average of Hydropathicity
- GROMACS, Groingen Machine for Chemical Simulations
- Glide, Grid-based ligand docking with energetic
- HOMO, Highest Occupied Molecular Orbital
- HTVS, High Throughput Virtual Screening
- LUMO, Lowest Unoccupied Molecular Orbital
- MD, Molecular Dynamics
- MM-GBSA, Molecular Mechanics, The Generalized Born Model and Solvent Accessibility
- NPT, Number of particles, Pressure and Temperature
- NVT, Number of particles, Volume and Temperature
- OPLS-AA, Optimised Potential for Liquid Simulation All Atom
- PDB, Brookhaven Protein Databank
- PME, Particle-Mesh Ewald
- RMSD, Root Mean Square Deviation
- RMSF, Root Mean Square Fluctuation
- Rg, Radius of gyration
- SP, Standard Precision
- SPC, Simple Point Charge
- WHO, World Health Organization
- XP, Extra Precision
- aspartate semialdehyde dehydrogenase
- density functional theory
- lymphatic filariasis
- molecular dynamics simulations
- pI, iso-electric point
- structure-based virtual screening
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Affiliation(s)
- Mathimaran Amala
- a Department of Bioinformatics , Alagappa University , Karaikudi , India
| | | | - Dhamodharan Prabhu
- a Department of Bioinformatics , Alagappa University , Karaikudi , India
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Dahal G, Viola RE. Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans. Acta Crystallogr F Struct Biol Commun 2015; 71:1365-71. [PMID: 26527262 PMCID: PMC4631584 DOI: 10.1107/s2053230x15017495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/18/2015] [Indexed: 11/10/2022] Open
Abstract
Aspartate semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate-biosynthetic pathway and represents a valid target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. Production of this intermediate represents the first committed step in the biosynthesis of the essential amino acids methionine, isoleucine and threonine in fungi, and also the amino acid lysine in bacteria. The structure of a new fungal form of ASADH from Cryptococcus neoformans has been determined to 2.6 Å resolution. The overall structure of CnASADH is similar to those of its bacterial orthologs, but with some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs.
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Affiliation(s)
- Gopal Dahal
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Ronald E. Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
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Eilert E, Kranz A, Hollenberg CP, Piontek M, Suckow M. Synthesis and release of the bacterial compatible solute 5-hydroxyectoine in Hansenula polymorpha. J Biotechnol 2013; 167:85-93. [PMID: 23467000 DOI: 10.1016/j.jbiotec.2013.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
Ectoine and 5-hydroxyectoine belong to the family of compatible solutes which are known to mainly contribute to the adaptation of the cell to osmotic stress by mediation of a constant turgor. In addition the cell's essential functions are maintained under stress conditions like high salinity, heat or aridity stress. Hansenula polymorpha was engineered to catalyze the transformation of monomeric substrates to 5-hydroxyectoine. For this purpose four genes encoding the enzymes of the 5-hydroxyectoine biosynthesis pathway of Halomonas elongata, EctA, EctB, EctC, and EctD, were inserted into the genome of H. polymorpha. Subsequently the syntheses of ectoine and 5-hydroxyectoine were analyzed and optimized. We showed that H. polymorpha is a suitable system for recombinant 5-hydroxyectoine synthesis in gram per liter scale (2.8 g L⁻¹ culture supernatant, 365 μmol/g dcw) in which almost 100% conversion of ectoine to 5-hydroxyectoine without necessity of high salinity were achieved.
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Affiliation(s)
- Eva Eilert
- ARTES Biotechnology GmbH, Elisabeth-Selbert-Str. 9, 40764 Langenfeld-Rheinland, Germany.
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Vyas R, Kumar V, Panjikar S, Karthikeyan S, Kishan KVR, Tewari R, Weiss MS. Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:167-70. [PMID: 18323599 PMCID: PMC2374159 DOI: 10.1107/s1744309108002753] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/24/2008] [Indexed: 11/10/2022]
Abstract
Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B.
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Affiliation(s)
- Rajan Vyas
- Department of Biotechnology, Panjab University, Chandigarh 160 014, India
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Vijay Kumar
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
| | - Santosh Panjikar
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | - K. V. Radha Kishan
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
- GVK Biosciences Pvt. Ltd, Hyderabad 500 037, India
| | - Rupinder Tewari
- Department of Biotechnology, Panjab University, Chandigarh 160 014, India
| | - Manfred S. Weiss
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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