Pseudomonas aeruginosa porphobilinogen synthase assembly state regulators: hit discovery and initial SAR studies

Reitz, Allen B.; Ramirez, Ursula D.; Stith, Linda; Du, Yanming; Smith, Garry R.; Jaffe, Eileen K.

doi:10.3998/ark.5550190.0011.815

Cited by 8 publications

(6 citation statements)

References 5 publications

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“…However, the arm-pit of the PBGS hexamer is in a region of the protein that is phylogenetically variable. Hence, a third application is stabilizing the PBGS hexamer of a human pathogen as a new approach to antibiotic discovery (32)(33)(34)(35). In this case, we have learned that many pathogens such a Pseudomonas aeroginosa, Wolbachia endobacteria, and Toxoplasma gondii have evolved their PBGS to avoid formation of the susceptible hexameric assembly.…”

Section: Practical and Health-related Applications Of Small Molecule Perturbation Of The Pbgs Quaternary Structure Equilibriummentioning

confidence: 99%

Porphobilinogen synthase: An equilibrium of different assemblies in human health

Jaffe

2020

Progress in Molecular Biology and Translational Science

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Porphobilinogen synthase (PBGS) is an essential enzyme that catalyzes an early step in heme biosynthesis. An unexpected human PBGS quaternary structure dynamic drove the definition of morpheeins, which are protein multimers that dissociate, change shape, and re-assemble differently with functional consequences. Each PBGS monomer has two domains that can reposition through a hinge motion. Human PBGS exists in an equilibrium among high activity octamer, low activity hexamer, and low mole-fraction dimer in which the hinge motion occurs. The dimer conformation dictates the multimer architecture. An octamer-specific inter-subunit interaction responds to pH, resulting in a pH-dependence to the octamer-hexamer equilibrium. An inborn error of metabolism, ALAD porphyria, is caused by single amino acid substitutions that stabilize the hexamer relative to octamer. Drugs that stabilize the PBGS hexamer result in a drug side effect that can exacerbate porphyria. PBGS is essential for all organisms that require respiration, photosynthesis, or methanogenesis. Consequently, phylogenetic variation in PBGS multimerization equilibria provides insight into how Nature has harnessed oligomeric variation in the control of protein function. The dynamic multimerization of PBGS revealed the morpheein mechanism for allostery, a structural basis for inborn errors of metabolism, a quaternary structure focus for drug discovery and/or drug side effects, and a pathway toward new antibiotics or herbicides. The fortuitous discovery of PBGS quaternary structure dynamics arose from characterization of a low-activity single amino acid variant that dramatically stabilized the hexamer, whose existence had previously gone unnoticed.

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Section: Practical and Health-related Applications Of Small Molecule Perturbation Of The Pbgs Quaternary Structure Equilibriummentioning

confidence: 99%

Porphobilinogen synthase: An equilibrium of different assemblies in human health

Jaffe

2020

Progress in Molecular Biology and Translational Science

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“…In addition, EBS and DPDS can oxidize thiol groups of proteins [3,4,7] as observed in the mammalian enzyme δ-aminolevulinic acid and some bacteria, such as Escherichia coli) [15,18,19], and the Mgdependent enzymes, that are found mainly in plants, protozoa and other bacteria [13,[20][21][22].…”

Section: Introductionmentioning

confidence: 99%

The Se…S/N interactions as a possible mechanism of δ-aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: A computational study

Nogara

Orian

Rocha

2020

Computational Toxicology

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Organoselenium compounds present many pharmacological properties and are promising drugs. However, toxicological effects associated with inhibition of thiol-containing enzymes, such as the δ-aminolevulinic acid dehydratase (δ-AlaD), have been described. The molecular mechanism(s) by which they inhibit thiol-containing enzymes at the atomic level, is still not well known. The use of computational methods to understand the physical-chemical properties and biological activity of chemicals is essential to the rational design of new drugs. In this work, we propose an in silico study to understand the δ-AlaD inhibition mechanism by diphenyl diselenide (DPDS) and its putative metabolite, phenylseleninic acid (PSA), using δ-AlaD enzymes from Homo sapiens (Hsδ-AlaD), Drosophila melanogaster (Dmδ-AlaD) and Cucumis sativus (Csδ-AlaD). Protein modeling homology, molecular docking, and DFT calculations are combined in this study. According to the molecular docking, DPDS and PSA might bind in the Hsδ-AlaD and Dmδ-AlaD active sites interacting with the cysteine residues by Se … S interactions. On the other hand, the DPDS does not access the active site of the Csδ-AlaD (a non-thiol protein), while the PSA interacts with the amino acids residues from the active site, such as the Lys291. These interactions might lead to the formation of a covalent bond, and consequently, to the enzyme inhibition. In fact, DFT calculations (mPW1PW91/def2TZVP) demonstrated that the selenylamide bond formation is energetically favored. The in silico data showed here are in accordance with previous experimental studies, and help us to understand the reactivity and biological activity of organoselenium compounds. dehydratase (mδ-AlaD) or porphobilinogen synthase (PBGS) (EC 4.2.1.24). Since the δ-AlaD is an important enzyme involved in the porphyrins' synthesis, its inhibition can have toxicological consequences [8][9][10][11]. The δ-AlaD catalyzes the asymmetric condensation of two molecules of 5-aminolevulinic acid (δ-aminolevulinic acid -5-Ala), forming the porphobilinogen (PBG), which is the precursor of porphyrins' synthesis (Fig. 1B). In the enzyme active site, each substrate binds at two different subsites (A and P), leading to the regioselective product PBG. The acetic acid and propanoic acid side-chains of PBG originate from the subsites A and P, respectively [12][13][14]. Porphyrins are essential to living beings, particularly to the aerobic life, due to the heme prosthetic group, which is involved in the transport of oxygen (hemoglobin and myoglobin), xenobiotic metabolism (cytochrome P450), protection against peroxides (peroxidases and catalases), and chlorophyll synthesis [13,[15][16][17]. There are two major classes of δ-AlaD: the Zn-dependent enzymes (that are present in mammals, fungi

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“…In contrast to previously described morphlocks, which inhibit by stabilizing inactive PBGS assemblies, 26 , 31 − 33 most stimulatory influence on the protein is mediated via an induction of the highly enzymatically active octameric assembly, as is the case for allosteric Mg 2+ and K + binding (see structural representation in Figure S8 ), active site binding of 5-ALA 8 , 30 and high protein concentrations (a phenomenon known as protein concentration-dependent specific activity 12 , 13 , 20 , 30 ). In order to achieve a stimulatory effect, wALADin1 must bind to and stabilize the octamers (or pro-octamer dimers) of group Y PBGS orthologs, and it is plausible that the stimulatory effect of wALADin1 is also mediated by stabilization of octamers.…”

Section: Discussionmentioning

confidence: 79%

“…Among group Y PBGS orthologs, the E. coli enzyme requires catalytic Zn B ( Figure S1 24 ) while the other proteins do not require catalytic divalent cations ( Figure S1 4 , 10 , 14 , 25 ). The pattern of oligomeric states sampled by these orthologs is also inconsistent, e.g., dimer and octamer for P. aeruginosa ( 26 ) and T. gondii , 4 while the E. coli ( 25 ) and Y. enterocolitica proteins (E.K. Jaffe, unpublished observation) can sample the hexamer.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, wALADin1 can be classified as a “morphlock” inhibitor that locks a morpheein in its inactive assembly state and thus confers inhibition . Such molecules have previously been detected by targeted in silico screening ,, or screening in an in vitro gel shift assay . In contrast, wALADin1 was originally identified by an unbiased enzymatic assay screening for inhibitors .…”

Section: Discussionmentioning

confidence: 99%

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wALADin Benzimidazoles Differentially Modulate the Function of Porphobilinogen Synthase Orthologs

et al. 2014

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The heme biosynthesis enzyme porphobilinogen synthase (PBGS) is a potential drug target in several human pathogens. wALADin1-benzimidazoles have emerged as species-selective PBGS inhibitors against Wolbachia endobacteria of filarial worms. In the present study, we have systematically tested wALADins against PBGS orthologs from bacteria, protozoa, metazoa and plants to elucidate the inhibitory spectrum. However, the effect of wALADin1 on different PBGS orthologs was not limited to inhibition; several orthologs were stimulated by wALADin1; others remained unaffected. We demonstrate that wALADins allosterically modulate the PBGS homooligomeric equilibrium with inhibition mediated by favoring low-activity oligomers, while 5-aminolevulinic acid, Mg2+ or K+ stabilized high-activity oligomers. Pseudomonas aeruginosa PBGS could be inhibited or stimulated by wALADin1 depending on these factors and pH. We have defined the wALADin chemotypes responsible for either inhibition or stimulation, facilitating the design of tailored PBGS modulators for potential applications as antimicrobial agents, herbicides or drugs for porphyric disorders.

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Pseudomonas aeruginosa porphobilinogen synthase assembly state regulators: hit discovery and initial SAR studies

Cited by 8 publications

References 5 publications

Porphobilinogen synthase: An equilibrium of different assemblies in human health

Porphobilinogen synthase: An equilibrium of different assemblies in human health

The Se…S/N interactions as a possible mechanism of δ-aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: A computational study

wALADin Benzimidazoles Differentially Modulate the Function of Porphobilinogen Synthase Orthologs

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