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1.
J Biomol Struct Dyn ; : 1-12, 2024 Mar 18.
Article in English | MEDLINE | ID: mdl-38498364

ABSTRACT

Plasmodium falciparum parasites export more than 400 proteins to remodel the host cell environment and increase its chances of surviving and reproducing. The endoplasmic reticulum (ER) plays a central role in protein export by facilitating protein sorting and folding. The ER resident member of the Hsp90 family, glucose-regulated protein 94 (Grp94), is a molecular chaperone that facilitates the proper folding of client proteins in the ER lumen. In P. falciparum, Grp94 (PfGrp94) is essential for parasite survival, rendering it a promising anti-malarial drug target. Despite this, its druggability has not been fully explored. Consequently, this study sought to identify small molecule inhibitors targeting the PfGrp94. Potential small molecule inhibitors of PfGrp94 were designed and screened using in silico studies. Molecular docking studies indicate that two novel compounds, Compound S and Compound Z selectively bind to PfGrp94 over its human homologues. Comparatively, Compound Z had a higher affinity for PfGrp94 than Compound S. Further interrogation of the inhibitor binding using molecular dynamics (MD) analysis confirmed that Compound Z formed stable binding poses within the ATP-binding pocket of the PfGrp94 N-terminal domain (NTD) during the 250 ns simulation run. PfGrp94 interacted with Compound Z through hydrogen bonding and hydrophobic interactions with residues Asp 148, Asn 106, Gly 152, Ile 151 and Lys 113. Based on the findings of this study, Compound Z could serve as a competitive and selective inhibitor of PfGrp94 and may be useful as a starting point for the development of a potential drug for malaria.Communicated by Ramaswamy H. Sarma.

2.
ChemMedChem ; 18(7): e202200630, 2023 04 03.
Article in English | MEDLINE | ID: mdl-36749500

ABSTRACT

The research and development of a new antimicrobial drug using a target-based approach raises the question of whether any resulting hits will also show activity against the homologous target in other closely related organisms. While an assessment of the similarities of the predicted interactions between the identified inhibitor and the various targets is an obvious first step in answering this question, no clear and consistent framework has been proposed for how this should be done. Here we developed Multifaceted Target Specificity Analysis (MTSA) and applied it to type III pantothenate kinase (PanKIII ) - an essential enzyme required for coenzyme A biosynthesis in a wide range of pathogenic bacteria - as a case study to establish if targeting a specific organism's PanKIII would lead to a narrow- or broad-spectrum agent. We propose that MTSA is a useful tool and aid for directing new target-based antimicrobial drug development initiatives.


Subject(s)
Anti-Infective Agents , Pantothenic Acid , Pantothenic Acid/pharmacology , Phosphotransferases (Alcohol Group Acceptor) , Bacteria
3.
Gut ; 72(6): 1115-1128, 2023 06.
Article in English | MEDLINE | ID: mdl-36175116

ABSTRACT

OBJECTIVE: In the management of patients with IBD, there is a need to identify prognostic markers and druggable biological pathways to improve mucosal repair and probe the efficacy of tumour necrosis factor alpha biologics. Vnn1 is a pantetheinase that degrades pantetheine to pantothenate (vitamin B5, a precursor of coenzyme A (CoA) biosynthesis) and cysteamine. Vnn1 is overexpressed by inflamed colonocytes. We investigated its contribution to the tolerance of the intestinal mucosa to colitis-induced injury. DESIGN: We performed an RNA sequencing study on colon biopsy samples from patients with IBD stratified according to clinical severity and modalities of treatment. We generated the VIVA mouse transgenic model, which specifically overexpresses Vnn1 on intestinal epithelial cells and explored its susceptibility to colitis. We developed a pharmacological mimicry of Vnn1 overexpression by administration of Vnn1 derivatives. RESULTS: VNN1 overexpression on colonocytes correlates with IBD severity. VIVA mice are resistant to experimentally induced colitis. The pantetheinase activity of Vnn1 is cytoprotective in colon: it enhances CoA regeneration and metabolic adaptation of colonocytes; it favours microbiota-dependent production of short chain fatty acids and mostly butyrate, shown to regulate mucosal energetics and to be reduced in patients with IBD. This prohealing phenotype is recapitulated by treating control mice with the substrate (pantethine) or the products of pantetheinase activity prior to induction of colitis. In severe IBD, the protection conferred by the high induction of VNN1 might be compromised because its enzymatic activity may be limited by lack of available substrates. In addition, we identify the elevation of indoxyl sulfate in urine as a biomarker of Vnn1 overexpression, also detected in patients with IBD. CONCLUSION: The induction of Vnn1/VNN1 during colitis in mouse and human is a compensatory mechanism to reinforce the mucosal barrier. Therefore, enhancement of vitamin B5-driven metabolism should improve mucosal healing and might increase the efficacy of anti-inflammatory therapy.


Subject(s)
Colitis , Inflammatory Bowel Diseases , Humans , Mice , Animals , Colitis/metabolism , Colon/pathology , Intestinal Mucosa/metabolism , Inflammatory Bowel Diseases/genetics , Fatty Acids, Volatile/metabolism , Vitamins , Dextran Sulfate , Disease Models, Animal
4.
Mol Cell ; 82(14): 2650-2665.e12, 2022 07 21.
Article in English | MEDLINE | ID: mdl-35662397

ABSTRACT

Coenzyme A (CoA) is essential for metabolism and protein acetylation. Current knowledge holds that each cell obtains CoA exclusively through biosynthesis via the canonical five-step pathway, starting with pantothenate uptake. However, recent studies have suggested the presence of additional CoA-generating mechanisms, indicating a more complex system for CoA homeostasis. Here, we uncovered pathways for CoA generation through inter-organismal flows of CoA precursors. Using traceable compounds and fruit flies with a genetic block in CoA biosynthesis, we demonstrate that progeny survive embryonal and early larval development by obtaining CoA precursors from maternal sources. Later in life, the microbiome can provide the essential CoA building blocks to the host, enabling continuation of normal development. A flow of stable, long-lasting CoA precursors between living organisms is revealed. This indicates the presence of complex strategies to maintain CoA homeostasis.


Subject(s)
Coenzyme A , Microbiota , Animals , Coenzyme A/genetics , Coenzyme A/metabolism , Drosophila/metabolism , Female , Humans , Mothers , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Zygote/metabolism
5.
ACS Chem Biol ; 16(11): 2401-2414, 2021 11 19.
Article in English | MEDLINE | ID: mdl-34582681

ABSTRACT

The pantothenate analogue hopantenate (HoPan) is widely used as a modulator of coenzyme A (CoA) levels in cell biology and disease models─especially for pantothenate kinase associated neurodegeneration (PKAN), a genetic disease rooted in impaired CoA metabolism. This use of HoPan was based on reports that it inhibits pantothenate kinase (PanK), the first enzyme of CoA biosynthesis. Using a combination of in vitro enzyme kinetic studies, crystal structure analysis, and experiments in a typical PKAN cell biology model, we demonstrate that instead of inhibiting PanK, HoPan relies on it for metabolic activation. Once phosphorylated, HoPan inhibits the next enzyme in the CoA pathway─phosphopantothenoylcysteine synthetase (PPCS)─through formation of a nonproductive substrate complex. Moreover, the obtained structure of the human PPCS in complex with the inhibitor and activating nucleotide analogue provides new insights into the catalytic mechanism of PPCS enzymes─including the elusive binding mode for cysteine─and reveals the functional implications of mutations in the human PPCS that have been linked to severe dilated cardiomyopathy. Taken together, this study demonstrates that the molecular mechanism of action of HoPan is more complex than previously thought, suggesting that the results of studies in which it is used as a tool compound must be interpreted with care. Moreover, our findings provide a clear framework for evaluating the various factors that contribute to the potency of CoA-directed inhibitors, one that will prove useful in the future rational development of potential therapies of both human genetic and infectious diseases.


Subject(s)
Coenzyme A/metabolism , Enzyme Inhibitors/pharmacology , Pantothenic Acid/analogs & derivatives , Peptide Synthases/antagonists & inhibitors , gamma-Aminobutyric Acid/analogs & derivatives , Amino Acid Sequence , Amino Acid Substitution , Animals , Cells, Cultured , Crystallization , Drosophila melanogaster , Kinetics , Molecular Conformation , Pantothenic Acid/pharmacology , Peptide Synthases/metabolism , Substrate Specificity , gamma-Aminobutyric Acid/pharmacology
6.
Org Biomol Chem ; 19(20): 4515-4519, 2021 05 26.
Article in English | MEDLINE | ID: mdl-33913984

ABSTRACT

Pantothenate synthetase from Escherichia coli (PSE. coli) catalyzes the ATP-dependent condensation of (R)-pantoic acid and ß-alanine to yield (R)-pantothenic acid (vitamin B5), the biosynthetic precursor to coenzyme A. Herein we show that besides the natural amine substrate ß-alanine, the enzyme accepts a wide range of structurally diverse amines including 3-amino-2-fluoropropionic acid, 4-amino-2-hydroxybutyric acid, 4-amino-3-hydroxybutyric acid, and tryptamine for coupling to the native carboxylic acid substrate (R)-pantoic acid to give amide products with up to >99% conversion. The broad amine scope of PSE. coli enabled the efficient synthesis of pharmaceutically-relevant vitamin B5 antimetabolites with excellent isolated yield (up to 89%). This biocatalytic amide synthesis strategy may prove to be useful in the quest for new antimicrobials that target coenzyme A biosynthesis and utilisation.


Subject(s)
Peptide Synthases
7.
Front Microbiol ; 12: 791756, 2021.
Article in English | MEDLINE | ID: mdl-34987490

ABSTRACT

Mycoplasmas are responsible for a wide range of disease states in both humans and animals, in which their parasitic lifestyle has allowed them to reduce their genome sizes and curtail their biosynthetic capabilities. The subsequent dependence on their host offers a unique opportunity to explore pathways for obtaining and producing cofactors - such as coenzyme A (CoA) - as possible targets for the development of new anti-mycoplasma agents. CoA plays an essential role in energy and fatty acid metabolism and is required for membrane synthesis. However, our current lack of knowledge of the relevance and importance of the CoA biosynthesis pathway in mycoplasmas, and whether it could be bypassed within their pathogenic context, prevents further exploration of the potential of this pathway. In the universal, canonical CoA biosynthesis pathway, five enzymes are responsible for the production of CoA. Given the inconsistent presence of the genes that code for these enzymes across Mycoplasma genomes, this study set out to establish the genetic capacity of mycoplasmas to synthesize their own CoA de novo. Existing functional annotations and sequence, family, motif, and domain analysis of protein products were used to determine the existence of relevant genes in Mycoplasma genomes. We found that most Mycoplasma species do have the genetic capacity to synthesize CoA, but there was a differentiated prevalence of these genes across species. Phylogenetic analysis indicated that the phylogenetic position of a species could not be used to predict its enzyme-encoding gene combinations. Despite this, the final enzyme in the biosynthesis pathway - dephospho-coenzyme A kinase (DPCK) - was found to be the most common among the studied species, suggesting that it has the most potential as a target in the search for new broad-spectrum anti-mycoplasma agents.

8.
ACS Infect Dis ; 6(7): 1844-1854, 2020 07 10.
Article in English | MEDLINE | ID: mdl-32375471

ABSTRACT

Pantothenamides (PanAms) are potent antiplasmodials with low human toxicity currently being investigated as antimalarials with a novel mode of action. These structural analogues of pantothenate, the vitamin precursor of the essential cofactor coenzyme A, are susceptible to degradation by pantetheinase enzymes present in serum. We previously discovered that α-methylation of the ß-alanine moiety of PanAms increases their stability in serum and identified N-phenethyl-α-methyl-pantothenamide as a pantetheinase-resistant PanAm with potent, on-target, and selective antiplasmodial activity. In this study, we performed structure-activity relationship investigations to establish whether stability and potency can be improved further through alternative modification of the scissile amide bond and through substitution/modification of the phenyl ring. Additionally, for the first time, the importance of the stereochemistry of the α-methyl group was evaluated in terms of stability versus potency. Our results demonstrate that α-methylation remains the superior choice for amide modification, and that while monofluoro-substitution of the phenyl ring (that often improves ADME properties) was tolerated, N-phenethyl-α-methyl-pantothenamide remains the most potent analogue. We show that the 2S,2'R-diastereomer is far more potent than the 2R,2'R-diastereomer and that this cannot be attributed to preferential metabolic activation by pantothenate kinase, the first enzyme of the coenzyme A biosynthesis pathway. Unexpectedly, the more potent 2S,2'R-diastereomer is also more prone to pantetheinase-mediated degradation. Finally, the results of in vitro studies to assess permeability and metabolic stability of the 2S,2'R-diastereomer suggested species-dependent degradation via amide hydrolysis. Our study provides important information for the continued development of PanAm-based antimalarials.


Subject(s)
Antimalarials , Antimalarials/pharmacology , Coenzyme A/metabolism , Humans , Pantothenic Acid/analogs & derivatives , Structure-Activity Relationship
9.
Sci Adv ; 6(14): eaay7919, 2020 04.
Article in English | MEDLINE | ID: mdl-32284973

ABSTRACT

Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.


Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Conformation , Protein Interaction Domains and Motifs , Proteins/chemistry , Allosteric Regulation , Ammonia/chemistry , Binding Sites , Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/chemistry , Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/genetics , Catalysis , Mutation , Protein Binding , Proteins/genetics
10.
Front Cell Infect Microbiol ; 10: 605662, 2020.
Article in English | MEDLINE | ID: mdl-33384970

ABSTRACT

Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Antitubercular Agents/pharmacology , Coenzyme A , Humans , Tuberculosis/drug therapy , Vitamins
11.
Medchemcomm ; 10(12): 2118-2125, 2019 Dec 01.
Article in English | MEDLINE | ID: mdl-32206243

ABSTRACT

The biosynthesis of the essential metabolic cofactor coenzyme A (CoA) has been receiving increasing attention as a new target that shows potential to counter the rising resistance to established antimicrobials. In particular, phosphopantothenoylcysteine synthetase (PPCS)-the second CoA biosynthesis enzyme that is found as part of the bifunctional CoaBC protein in bacteria, but is monofunctional in eukaryotes-has been validated as a target through extensive genetic knockdown studies in Mycobacterium tuberculosis. Moreover, it has been identified as the molecular target of the fungal natural product CJ-15,801 that shows selective activity against Staphylococcus aureus and the malaria parasite Plasmodium falciparum. As such, CJ-15,801 and 4'-phospho-CJ-15,801 (its metabolically active form) are excellent tool compounds for use in the development of new antimicrobial PPCS inhibitors. Unfortunately, further study and analysis of CJ-15,801 is currently being hampered by several unique challenges posed by its synthesis. In this study we describe how these challenges were overcome by using a robust palladium-catalyzed coupling to form the key N-acyl vinylogous carbamate moiety with retention of stereochemistry, and by extensive investigation of protecting groups suited to the labile functional group combinations contained in this molecule. We also demonstrate that using TBAF for deprotection causes undesired off-target effects related to the presence of residual tertiary ammonium salts. Finally, we provide a new method for the chemoenzymatic preparation of 4'-phospho-CJ-15,801 on multi-milligram scale, after showing that chemical synthesis of the molecule is not practical. Taken together, the results of this study advances our pursuit to discover new antimicrobials that specifically target CoA biosynthesis and/or utilization.

12.
Life Sci Alliance ; 1(4): e201800073, 2018 Aug.
Article in English | MEDLINE | ID: mdl-30456364

ABSTRACT

Like other tumors, aggressive soft tissue sarcomas (STS) use glycolysis rather than mitochondrial oxidative phosphorylation (OXPHOS) for growth. Given the importance of the cofactor coenzyme A (CoA) in energy metabolism, we investigated the impact of Vnn1 pantetheinase-an enzyme that degrades pantetheine into pantothenate (vitamin B5, the CoA biosynthetic precursor) and cysyteamine-on tumor growth. Using two models, we show that Vnn1+ STS remain differentiated and grow slowly, and that in patients a detectable level of VNN1 expression in STS is associated with an improved prognosis. Increasing pantetheinase activity in aggressive tumors limits their growth. Using combined approaches, we demonstrate that Vnn1 permits restoration of CoA pools, thereby maintaining OXPHOS. The simultaneous production of cysteamine limits glycolysis and release of lactate, resulting in a partial inhibition of STS growth in vitro and in vivo. We propose that the Warburg effect observed in aggressive STS is reversed by induction of Vnn1 pantetheinase and the rewiring of cellular energy metabolism by its products.

13.
Bioorg Med Chem ; 26(22): 5896-5902, 2018 12 01.
Article in English | MEDLINE | ID: mdl-30429095

ABSTRACT

Pantothenate kinase (PanK) catalyzes the transformation of pantothenate to 4'-phosphopantothenate, the first committed step in coenzyme A biosynthesis. While numerous pantothenate antimetabolites and PanK inhibitors have been reported for bacterial type I and type II PanKs, only a few weak inhibitors are known for bacterial type III PanK enzymes. Here, a series of pantothenate analogues were synthesized using convenient synthetic methodology. The compounds were exploited as small organic probes to compare the ligand preferences of the three different types of bacterial PanK. Overall, several new inhibitors and substrates were identified for each type of PanK.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacillus anthracis/drug effects , Phosphotransferases (Alcohol Group Acceptor)/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Bacillus anthracis/enzymology , Crystallography, X-Ray , Dose-Response Relationship, Drug , Ligands , Microbial Sensitivity Tests , Models, Molecular , Molecular Structure , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry , Structure-Activity Relationship
14.
Sci Rep ; 8(1): 14701, 2018 10 02.
Article in English | MEDLINE | ID: mdl-30279472

ABSTRACT

S. cerevisiae Hal3 (ScHal3) is a moonlighting protein that, is in its monomeric state, regulates the Ser/Thr protein phosphatase Ppz1, but also joins ScCab3 (and in some instances the Hal3 paralog Vhs3) to form an unusual heterotrimeric phosphopantothenoylcysteine decarboxylase (PPCDC) enzyme. PPCDC is required for CoA biosynthesis and in most eukaryotes is a homotrimeric complex with three identical catalytic sites at the trimer interfaces. However, in S. cerevisiae the heterotrimeric arrangement results in a single functional catalytic center. Importantly, the specific structural determinants that direct Hal3's oligomeric state and those required for Ppz1 inhibition remain largely unknown. We mutagenized residues in the predicted hydrophobic core of ScHal3 (L403-L405) and the plant Arabidopsis thaliana Hal3 (AtHal3, G115-L117) oligomers and characterized their properties as PPCDC components and, for ScHal3, also as Ppz1 inhibitor. We found that in AtHal3 these changes do not affect trimerization or PPCDC function. Similarly, mutation of ScHal3 L403 has no effect. In contrast, ScHal3 L405E fails to form homotrimers, but retains the capacity to bind Cab3-explaining its ability to rescue a hal3 vhs3 synthetically lethal mutation. Remarkably, the L405E mutation decreases Hal3's ability to interact with and to inhibit Ppz1, confirming the importance of the oligomer/monomer equilibrium in Hal3's Ppz1 regulating function.


Subject(s)
Arabidopsis Proteins/genetics , Carboxy-Lyases/metabolism , Cell Cycle Proteins/genetics , Phosphoprotein Phosphatases/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Arabidopsis Proteins/metabolism , Cell Cycle Proteins/metabolism , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Mutagenesis, Site-Directed , Phosphoprotein Phosphatases/antagonists & inhibitors , Phosphoprotein Phosphatases/genetics , Protein Binding/genetics , Protein Multimerization/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/antagonists & inhibitors , Synthetic Lethal Mutations
15.
Chemistry ; 24(66): 17434-17438, 2018 Nov 27.
Article in English | MEDLINE | ID: mdl-30192043

ABSTRACT

Access to vitamin B5 [(R)-pantothenic acid] and both diastereoisomers of α-methyl-substituted vitamin B5 [(R)- and (S)-3-((R)-2,4-dihydroxy-3,3-dimethylbutanamido)-2-methylpropanoic acid] was achieved using a modular three-step biocatalytic cascade involving 3-methylaspartate ammonia lyase (MAL), aspartate-α-decarboxylase (ADC), ß-methylaspartate-α-decarboxylase (CrpG) or glutamate decarboxylase (GAD), and pantothenate synthetase (PS) enzymes. Starting from simple non-chiral dicarboxylic acids (either fumaric acid or mesaconic acid), vitamin B5 and both diastereoisomers of α-methyl-substituted vitamin B5 , which are valuable precursors for promising antimicrobials against Plasmodium falciparum and multidrug-resistant Staphylococcus aureus, can be generated in good yields (up to 70 %) and excellent enantiopurity (>99 % ee). This newly developed cascade process may be tailored and used for the biocatalytic production of various vitamin B5 derivatives by modifying the pantoyl or ß-alanine moiety.


Subject(s)
Ammonia-Lyases/metabolism , Glutamate Decarboxylase/metabolism , Pantothenic Acid/biosynthesis , Peptide Synthases/metabolism , Adenosine Triphosphate/metabolism , Anti-Infective Agents/chemistry , Anti-Infective Agents/metabolism , Anti-Infective Agents/pharmacology , Biocatalysis , Escherichia coli/metabolism , Methicillin-Resistant Staphylococcus aureus/drug effects , Pantothenic Acid/analogs & derivatives , Pantothenic Acid/pharmacology , Plasmodium falciparum/drug effects , Stereoisomerism , beta-Alanine/chemistry , beta-Alanine/metabolism
16.
PLoS Pathog ; 14(4): e1006918, 2018 04.
Article in English | MEDLINE | ID: mdl-29614109

ABSTRACT

The malaria-causing blood stage of Plasmodium falciparum requires extracellular pantothenate for proliferation. The parasite converts pantothenate into coenzyme A (CoA) via five enzymes, the first being a pantothenate kinase (PfPanK). Multiple antiplasmodial pantothenate analogues, including pantothenol and CJ-15,801, kill the parasite by targeting CoA biosynthesis/utilisation. Their mechanism of action, however, remains unknown. Here, we show that parasites pressured with pantothenol or CJ-15,801 become resistant to these analogues. Whole-genome sequencing revealed mutations in one of two putative PanK genes (Pfpank1) in each resistant line. These mutations significantly alter PfPanK activity, with two conferring a fitness cost, consistent with Pfpank1 coding for a functional PanK that is essential for normal growth. The mutants exhibit a different sensitivity profile to recently-described, potent, antiplasmodial pantothenate analogues, with one line being hypersensitive. We provide evidence consistent with different pantothenate analogue classes having different mechanisms of action: some inhibit CoA biosynthesis while others inhibit CoA-utilising enzymes.


Subject(s)
Antimalarials/pharmacology , Drug Resistance , Malaria/drug therapy , Mutation , Pantothenic Acid/analogs & derivatives , Phosphotransferases (Alcohol Group Acceptor)/genetics , Plasmodium falciparum/drug effects , Animals , Coenzyme A/biosynthesis , Erythrocytes/parasitology , Malaria/parasitology , Pantothenic Acid/pharmacology , Parasitic Sensitivity Tests , Phosphorylation , Protozoan Proteins/genetics
17.
ACS Infect Dis ; 4(5): 736-743, 2018 05 11.
Article in English | MEDLINE | ID: mdl-29332383

ABSTRACT

Pantothenamides (PanAms) are analogues of pantothenate, the biosynthetic precursor of coenzyme A (CoA), and show potent antimicrobial activity against several bacteria and the malaria parasite in vitro. However, pantetheinase enzymes that normally degrade pantetheine in human serum also act on the PanAms, thereby reducing their potency. In this study, we designed analogues of the known antibacterial PanAm N-heptylpantothenamide (N7-Pan) to be resistant to pantetheinase by using three complementary structural modification strategies. We show that, while two of these are effective in imparting resistance, the introduced modifications have an impact on the analogues' interaction with pantothenate kinase (PanK, the first CoA biosynthetic enzyme), which acts as a metabolic activator and/or target of the PanAms. This, in turn, directly affects their mode of action. Importantly, we discover that the phosphorylated version of N7-Pan shows pantetheinase resistance and antistaphylococcal activity, providing a lead for future studies in the ongoing search of PanAm analogues that show in vivo efficacy.


Subject(s)
Amidohydrolases/chemistry , Amidohydrolases/metabolism , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial , Pantothenic Acid/chemistry , Pantothenic Acid/pharmacology , Drug Discovery , Enzyme Activation , Humans , Kinetics , Molecular Structure , Pantothenic Acid/analogs & derivatives , Structure-Activity Relationship , Substrate Specificity
18.
ACS Infect Dis ; 3(7): 527-541, 2017 07 14.
Article in English | MEDLINE | ID: mdl-28437604

ABSTRACT

N-Substituted pantothenamides (PanAms) are pantothenate analogues with up to nanomolar potency against blood-stage Plasmodium falciparum (the most virulent species responsible for malaria). Although these compounds are known to target coenzyme A (CoA) biosynthesis and/or utilization, their exact mode of action (MoA) is still unknown. Importantly, PanAms that retain the natural ß-alanine moiety are more potent than other variants, consistent with the involvement of processes that are selective for pantothenate (the precursor of CoA) or its derivatives. The transport of pantothenate and its phosphorylation by P. falciparum pantothenate kinase (PfPanK, the first enzyme of CoA biosynthesis) are two such processes previously highlighted as potential targets for the PanAms' antiplasmodial action. In this study, we investigated the effect of PanAms on these processes using their radiolabeled versions (synthesized here for the first time), which made possible the direct measurement of PanAm uptake by isolated blood-stage parasites and PanAm phosphorylation by PfPanK present in parasite lysates. We found that the MoA of PanAms does not involve interference with pantothenate transport and that inhibition of PfPanK-mediated pantothenate phosphorylation does not correlate with PanAm antiplasmodial activity. Instead, PanAms that retain the ß-alanine moiety were found to be metabolically activated by PfPanK in a selective manner, forming phosphorylated products that likely inhibit other steps in CoA biosynthesis or are transformed into CoA antimetabolites that can interfere with CoA utilization. These findings provide direction for the ongoing development of CoA-targeted inhibitors as antiplasmodial agents with clinical potential.


Subject(s)
Antimalarials/pharmacology , Coenzyme A/antagonists & inhibitors , Pantothenic Acid/pharmacology , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Plasmodium falciparum/drug effects , Protozoan Proteins/metabolism , beta-Alanine/pharmacology , Antimalarials/chemical synthesis , Antimalarials/metabolism , Antimetabolites/metabolism , Antimetabolites/pharmacology , Biotransformation , Carbon Radioisotopes , Coenzyme A/biosynthesis , Erythrocytes/drug effects , Erythrocytes/parasitology , Humans , Kinetics , Models, Molecular , Pantothenic Acid/analogs & derivatives , Pantothenic Acid/metabolism , Parasitic Sensitivity Tests , Phosphorylation , Plasmodium falciparum/growth & development , Plasmodium falciparum/metabolism , Protein Binding , Structure-Activity Relationship , beta-Alanine/analogs & derivatives , beta-Alanine/metabolism
19.
ACS Infect Dis ; 2(9): 627-641, 2016 09 09.
Article in English | MEDLINE | ID: mdl-27759386

ABSTRACT

The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanKII), the first enzyme of coenzyme A biosynthesis. This mechanism of action follows from SaPanKII having a binding mode for PanAms that is distinct from those of other PanKs. To dissect the molecular interactions responsible for PanAm inhibitory activity, we conducted a mini SAR study in tandem with the cocrystallization of SaPanKII with two classic PanAms (N5-Pan and N7-Pan), culminating in the synthesis and characterization of two new PanAms, N-Pip-PanAm and MeO-N5-PanAm. The cocrystal structures showed that all of the PanAms are phosphorylated by SaPanKII but remain bound at the active site; this occurs primarily through interactions with Tyr240' and Thr172'. Kinetic analysis showed a strong correlation between kcat (slow PanAm turnover) and IC50 (inhibition of pantothenate phosphorylation) values, suggesting that SaPanKII inhibition occurs via a delay in product release. In-depth analysis of the PanAm-bound structures showed that the capacity for accepting a hydrogen bond from the amide of Thr172' was a stronger determinant for PanAm potency than the capacity to π-stack with Tyr240'. The two new PanAms, N-Pip-PanAm and MeO-N5-PanAm, effectively combine both hydrogen bonding and hydrophobic interactions, resulting in the most potent SaPanKII inhibition described to date. Taken together, our results are consistent with an inhibition mechanism wherein PanAms act as SaPanKII substrates that remain bound upon phosphorylation. The phospho-PanAm-SaPanKII interactions described herein may help future antistaphylococcal drug development.


Subject(s)
Bacterial Proteins/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Phosphotransferases (Alcohol Group Acceptor)/antagonists & inhibitors , Staphylococcal Infections/microbiology , Staphylococcus aureus/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Enzyme Inhibitors/pharmacology , Kinetics , Models, Molecular , Phosphorylation , Phosphotransferases (Alcohol Group Acceptor)/genetics , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Staphylococcus aureus/drug effects , Staphylococcus aureus/genetics , Structure-Activity Relationship
20.
Nat Rev Mol Cell Biol ; 17(10): 605-6, 2016 10.
Article in English | MEDLINE | ID: mdl-27552973

ABSTRACT

The consensus has been that intracellular coenzyme A (CoA) is obtained exclusively by de novo biosynthesis via a universal, conserved five-step pathway in the cell cytosol. However, old and new evidence suggest that cells (and some microorganisms) have several strategies to obtain CoA, with 4'-phosphopantetheine (P-PantSH; the fourth intermediate in the canonical CoA biosynthetic pathway) serving as a 'nexus' metabolite.


Subject(s)
Coenzyme A/biosynthesis , Pantetheine/analogs & derivatives , Animals , Biological Transport , Biosynthetic Pathways , Cell Membrane Permeability , Humans , Pantetheine/metabolism
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