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Chrobak E, Marciniec K, Dąbrowska A, Pęcak P, Bębenek E, Kadela-Tomanek M, Bak A, Jastrzębska M, Boryczka S. New Phosphorus Analogs of Bevirimat: Synthesis, Evaluation of Anti-HIV-1 Activity and Molecular Docking Study. Int J Mol Sci 2019; 20:ijms20205209. [PMID: 31640137 PMCID: PMC6829466 DOI: 10.3390/ijms20205209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of the human immunodeficiency virus (HIV) epidemic, many groups of drugs characterized by diverse mechanisms of action have been developed, which can suppress HIV viremia. 3-O-(3′,3′-Dimethylsuccinyl) betulinic acid, known as bevirimat (BVM), was the first compound in the class of HIV maturation inhibitors. In the present work, phosphate and phosphonate derivatives of 3-carboxyacylbetulinic acid were synthesized and evaluated for anti-HIV-1 activity. In vitro studies showed that 30-diethylphosphonate analog of BVM (compound 14a) has comparable effects to BVM (half maximal inhibitory concentrations (IC50) equal to 0.02 μM and 0.03 μM, respectively) and is also more selective (selectivity indices: 3450 and 967, respectively). To investigate the possible mechanism of antiviral effect of 14a, molecular docking was carried out on the C-terminal domain (CTD) of HIV-1 capsid (CA)–spacer peptide 1 (SP1) fragment of Gag protein, designated as CTD-SP1, which was described as a molecular target for maturation inhibitors. Compared with interactions between BVM and the protein, an increased number of strong interactions between ligand 14a and protein, generated by the phosphonate group, was observed.
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Affiliation(s)
- Elwira Chrobak
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
| | - Krzysztof Marciniec
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
| | | | - Paweł Pęcak
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
| | - Ewa Bębenek
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
| | - Monika Kadela-Tomanek
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, 9 Szkolna Str., 40-007 Katowice, Poland.
| | - Maria Jastrzębska
- Department of Solid State Physics, Institute of Physics, Silesian Center for Education and Interdisciplinary Research, University of Silesia, 75 Pułku Piechoty 1a, 41-500 Chorzów, Poland.
| | - Stanisław Boryczka
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 4 Jagiellońska Str., 41-200 Sosnowiec, Poland.
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Petronikolou N, Ortega MA, Borisova SA, Nair SK, Metcalf WW. Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin. ACS Chem Biol 2019; 14:742-750. [PMID: 30830751 DOI: 10.1021/acschembio.9b00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Rhizocticins are phosphono-oligopeptide antibiotics that contain a toxic C-terminal ( Z) -l -2-amino-5-phosphono-3-pentenoic acid (APPA) moiety. APPA is an irreversible inhibitor of threonine synthase (ThrC), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of O-phospho-l-homoserine to l-threonine. ThrCs are essential for the viability of bacteria, plants, and fungi and are a target for antibiotic development, as de novo threonine biosynthetic pathway is not found in humans. Given the ability of APPA to interfere in threonine metabolism, it is unclear how the producing strain B. subtilis ATCC 6633 circumvents APPA toxicity. Notably, in addition to the housekeeping APPA-sensitive ThrC ( BsThrC), B. subtilis encodes a second threonine synthase (RhiB) encoded within the rhizocticin biosynthetic gene cluster. Kinetic and spectroscopic analyses show that PLP-dependent RhiB is an authentic threonine synthase, converting O-phospho-l-homoserine to threonine with a catalytic efficiency comparable to BsThrC. To understand the structural basis of inhibition, we determined the crystal structure of APPA bound to the housekeeping BsThrC, revealing a covalent complex between the inhibitor and PLP. Structure-based sequence analyses reveal structural determinants within the RhiB active site that contribute to rendering this ThrC homologue resistant to APPA. Together, this work establishes the self-resistance mechanism utilized by B. subtilis ATCC 6633 against APPA exemplifying one of many ways by which bacteria can overcome phosphonate toxicity.
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Affiliation(s)
- Nektaria Petronikolou
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Manuel A. Ortega
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
| | - Svetlana A. Borisova
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
- Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana Illinois 61801, United States
| | - William W. Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave., Urbana, Illinois 61801, United States
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Liu N, Tu J, Dong G, Wang Y, Sheng C. Emerging New Targets for the Treatment of Resistant Fungal Infections. J Med Chem 2018; 61:5484-5511. [DOI: 10.1021/acs.jmedchem.7b01413] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Na Liu
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Jie Tu
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Yan Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People’s Republic of China
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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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: 54] [Impact Index Per Article: 5.4] [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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Ju KS, Doroghazi JR, Metcalf WW. Genomics-enabled discovery of phosphonate natural products and their biosynthetic pathways. J Ind Microbiol Biotechnol 2014; 41:345-56. [PMID: 24271089 PMCID: PMC3946943 DOI: 10.1007/s10295-013-1375-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/22/2013] [Indexed: 01/01/2023]
Abstract
Phosphonate natural products have proven to be a rich source of useful pharmaceutical, agricultural, and biotechnology products, whereas study of their biosynthetic pathways has revealed numerous intriguing enzymes that catalyze unprecedented biochemistry. Here we review the history of phosphonate natural product discovery, highlighting technological advances that have played a key role in the recent advances in their discovery. Central to these developments has been the application of genomics, which allowed discovery and development of a global phosphonate metabolic framework to guide research efforts. This framework suggests that the future of phosphonate natural products remains bright, with many new compounds and pathways yet to be discovered.
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Affiliation(s)
- Kou-San Ju
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - James R. Doroghazi
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - William W. Metcalf
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL 61801
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The antibiotic dehydrophos is converted to a toxic pyruvate analog by peptide bond cleavage in Salmonella enterica. Antimicrob Agents Chemother 2011; 55:3357-62. [PMID: 21537024 DOI: 10.1128/aac.01483-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The metabolic processing of dehydrophos, a broad-spectrum peptide antibiotic containing an unusual vinyl-phosphonate moiety, was examined by using a panel of Salmonella enterica mutants deficient in peptide uptake and catabolism. Dehydrophos bioactivity is lost in opp tpp double mutants, demonstrating a requirement for uptake via nonspecific oligopeptide permeases. Dehydrophos bioactivity is also abolished in a quadruple Salmonella mutant lacking the genes encoding peptidases A, B, D, and N, showing that hydrolysis of the peptide bond is required for activity. (31)P nuclear magnetic resonance spectroscopy was used to assess the fate of dehydrophos following in vitro digestion of the antibiotic with purified PepA. The results suggest that the initial product of peptidase processing is 1-aminovinyl-phosphonate O-methyl ester. This phosphonate analogue of dehydroalanine undergoes rearrangement to the more stable imine, followed by spontaneous hydrolysis to yield O-methyl-acetylphosphonate, a structural analogue of pyruvate. This compound is a known inhibitor of pyruvate dehydrogenase and pyruvate oxidase and is probably the active species responsible for dehydrophos bioactivity.
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Borisova SA, Circello BT, Zhang JK, van der Donk WA, Metcalf WW. Biosynthesis of rhizocticins, antifungal phosphonate oligopeptides produced by Bacillus subtilis ATCC6633. ACTA ACUST UNITED AC 2010; 17:28-37. [PMID: 20142038 DOI: 10.1016/j.chembiol.2009.11.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/23/2009] [Accepted: 11/30/2009] [Indexed: 11/16/2022]
Abstract
Rhizocticins are phosphonate oligopeptide antibiotics containing the C-terminal nonproteinogenic amino acid (Z)-l-2-amino-5-phosphono-3-pentenoic acid (APPA). Here we report the identification and characterization of the rhizocticin biosynthetic gene cluster (rhi) in Bacillus subtilis ATCC6633. Rhizocticin B was heterologously produced in the nonproducer strain Bacillus subtilis 168. A biosynthetic pathway is proposed on the basis of bioinformatics analysis of the rhi genes. One of the steps during the biosynthesis of APPA is an unusual aldol reaction between phosphonoacetaldehyde and oxaloacetate catalyzed by an aldolase homolog RhiG. Recombinant RhiG was prepared, and the product of an in vitro enzymatic conversion was characterized. Access to this intermediate allows for biochemical characterization of subsequent steps in the pathway.
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Affiliation(s)
- Svetlana A Borisova
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Berkowitz DB, Charette BD, Karukurichi KR, McFadden JM. α-Vinylic Amino Acids: Occurrence, Asymmetric Synthesis and Biochemical Mechanisms. TETRAHEDRON, ASYMMETRY 2006; 17:869-882. [PMID: 29977107 PMCID: PMC6029878 DOI: 10.1016/j.tetasy.2006.02.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This report presents an overview of the family of naturally occurring 'vinylic' amino acids, namely those that feature a C-C double bond directly attached to the α-carbon, along the side chain. Strategies that have been brought to bear on the stereocontrolled synthesis of these olefinic amino acids are surveyed. The mechanistic diversity by which such 'vinylic triggers' can be actuated in a PLP (pyridoxal phosphate) enzyme active site is then highlighted by discussions of vinylglycine (VG), its substituted congeners, particularly AVG [4E-(2'-aminoethoxy)vinylglycine], and a naturally occurring VG-progenitor, SMM (S-methylmethionine).
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
| | | | | | - Jill M McFadden
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
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Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J 2001; 356:415-23. [PMID: 11368768 PMCID: PMC1221852 DOI: 10.1042/0264-6021:3560415] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have determined the kinetic parameters of the individual steps of the threonine pathway from aspartate in Escherichia coli under a single set of experimental conditions chosen to be physiologically relevant. Our aim was to summarize the kinetic behaviour of each enzyme in a single tractable equation that takes into account the effect of the products as competitive inhibitors of the substrates in the forward reaction and also, when appropriate (e.g. near-equilibrium reactions), as substrates of the reverse reactions. Co-operative feedback inhibition by threonine and lysine was also included as necessary. We derived the simplest rate equations that describe the salient features of the enzymes in the physiological range of metabolite concentrations in order to incorporate them ultimately into a complete model of the threonine pathway, able to predict quantitatively the behaviour of the pathway under natural or engineered conditions.
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Affiliation(s)
- C Chassagnole
- INSERM EMI 9929, University Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France
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