Phage Display on the Anti‐infective Target 1‐Deoxy‐<scp>d</scp>‐xylulose‐5‐phosphate Synthase Leads to an Acceptor–Substrate Competitive Peptidic Inhibitor

Marcozzi, Alessio; Masini, Tiziana; Zhu, Di; Pesce, Diego; Illarionov, Boris; Fischer, Markus; Herrmann, Andreas; Hirsch, Anna K. H.

doi:10.1002/cbic.201700402

Cited by 7 publications

(9 citation statements)

References 48 publications

(91 reference statements)

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“…However, off-target activity in bacteria is likely due to the reactive catechol functionality. Using phage display, the Hirsch lab has discovered the first peptide-based d -GAP competitive inhibitor ( 11 ), 40 albeit with weak enzyme inhibitory activity ( K i = 113 μM).…”

Section: Selective Inhibition Of Dxp Synthasementioning

confidence: 99%

Toward Understanding the Chemistry and Biology of 1-Deoxy-d-xylulose 5-Phosphate (DXP) Synthase: A Unique Antimicrobial Target at the Heart of Bacterial Metabolism

Bartee

Meyers

2018

Acc. Chem. Res.

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Antibiotics are the cornerstone of modern healthcare. The 20th century discovery of sulfonamides and β-lactam antibiotics altered human society immensely. Simple bacterial infections were no longer a leading cause of morbidity and mortality, and antibiotic prophylaxis greatly reduced the risk of infection from surgery. The current healthcare system requires effective antibiotics to function. However, antibiotic-resistant infections are becoming increasingly prevalent, threatening the emergence of a postantibiotic era. To prevent this public health crisis, antibiotics with novel modes of action are needed. Currently available antibiotics target just a few cellular processes to exert their activity: DNA, RNA, protein, and cell wall biosynthesis. Bacterial central metabolism is underexploited, offering a wealth of potential new targets that can be pursued toward expanding the armamentarium against microbial infections. Discovered in 1997 as the first enzyme in the methylerythritol phosphate (MEP) pathway, 1-deoxy-d-xylulose 5-phosphate (DXP) synthase is a thiamine diphosphate (ThDP)-dependent enzyme that catalyzes the decarboxylative condensation of pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) to form DXP. This five-carbon metabolite feeds into three separate essential pathways for bacterial central metabolism: ThDP synthesis, pyridoxal phosphate (PLP) synthesis, and the MEP pathway for isoprenoid synthesis. While it has long been identified as a target for the development of antimicrobial agents, limited progress has been made toward developing selective inhibitors of the enzyme. This Account highlights advances from our lab over the past decade to understand this important and unique enzyme. Unlike all other known ThDP-dependent enzymes, DXP synthase uses a random-sequential mechanism that requires the formation of a ternary complex prior to decarboxylation of the lactyl-ThDP intermediate. Its large active site accommodates a variety of acceptor substrates, lending itself to a number of alternative activities, such as the production of α-hydroxy ketones, hydroxamates, amides, acetolactate, and peracetate. Knowledge gained from mechanistic and substrate-specificity studies has guided the development of selective inhibitors with antibacterial activity and provides a biochemical foundation toward understanding DXP synthase function in bacterial cells. Although it is a promising drug target, the centrality of DXP synthase in bacterial metabolism imparts specific challenges to assessing antibacterial activity of DXP synthase inhibitors, and the susceptibility of most bacteria to current DXP synthase inhibitors is remarkably culture-medium-dependent. Despite these challenges, the study of DXP synthase is poised to reveal the role of DXP synthase in bacterial metabolic adaptability during infection, ultimately providing a more complete picture of how inhibiting this crucial enzyme can be used to develop novel antibiotics.

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Section: Selective Inhibition Of Dxp Synthasementioning

confidence: 99%

Toward Understanding the Chemistry and Biology of 1-Deoxy-d-xylulose 5-Phosphate (DXP) Synthase: A Unique Antimicrobial Target at the Heart of Bacterial Metabolism

Bartee

Meyers

2018

Acc. Chem. Res.

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“…The rational development of D-GAP competitive inhibitors has been more challenging with both known D-GAP competitive inhibitors emerging from screening approaches. 20,21…”

Section: Introductionmentioning

confidence: 99%

“…Inhibitors of DXP synthase resembling the substrate or cofactor have been pursued. − Among these are the alkylacetylphosphonates (alkylAPs), which are known to inhibit ThDP-dependent pyruvate decarboxylase enzymes. , The acetylphosphonate moiety mimics the natural ketoacid substrate, pyruvate, to form a reversible covalent phosphonolactyl ThDP intermediate [PLThDP (Figure )]. ,, While methylacetylphosphonate (MAP) and its structural analogue, acetylphosphinate (AcPhi), have been useful mechanistic probes in ThDP enzymology, a lack of potency and poor selectivity have limited their usefulness as antimicrobial agents. The rational development of d -GAP competitive inhibitors has been more challenging with both known d -GAP competitive inhibitors emerging from screening approaches. , …”

mentioning

confidence: 99%

“…The rational development of D-GAP competitive inhibitors has been more challenging with both known D-GAP competitive inhibitors emerging from screening approaches. 20,21 Until recently, the conserved nature of ThDP-dependent catalytic mechanisms and the ubiquity of pyruvate as a substrate for ThDP enzymes in mammals and pathogens suggested that targeting DXP synthase selectively would be challenging. Fortunately, work by our group 22−24 and others 25−27 has shown that DXP synthase is unique among ThDP-dependent enzymes.…”

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confidence: 99%

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Targeting the Unique Mechanism of Bacterial 1-Deoxy-d-xylulose-5-phosphate Synthase

Bartee

Meyers

2018

Biochemistry

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The bacterial metabolite 1-deoxy-d-xyulose 5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism that requires formation of a ternary complex among pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), d-glyceraldehyde 3-phosphate (d-GAP), and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of d-GAP, designed to target the unique form of DXP synthase that binds LThDP and d-GAP in a ternary complex. A d-phenylalanine-derived triazole acetylphosphonate (d-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow, tight-binding inhibition with a K* of 90 ± 10 nM, forward ( k) and reverse ( k) isomerization rates of 1.1 and 0.14 min, respectively, and exquisite selectivity (>15000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. d-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.

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“…Moreover, they have been explored as therapeutic agents, such as vaccines, [20] immunotherapy agents, [21] and inhibitors of a target protein. [22][23][24][25] For example, the world's best-selling drug, HUMIRA, was discovered using the phage display technology. We recently developed a novel biopanning strategy to discover small peptides that can specifically bind to programmed death-ligand 1 (PD-L1) and block its interaction with the programmed cell death 1 (PD-1).…”

Section: Introductionmentioning

confidence: 99%

Discovery of Small Anti‐ACE2 Peptides to Inhibit SARS‐CoV‐2 Infectivity

Adhikary

Kandel

Mamani

et al. 2021

Advanced Therapeutics

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COVID‐19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), which infects host cells by binding its viral spike protein receptor‐binding domain (RBD) to the angiotensin converting enzyme 2 (ACE2) on host cells. Blocking the SARS‐CoV‐2‐RBD/ACE2 interaction is, therefore, a potential strategy to inhibit viral infections. Using a novel biopanning strategy, a small anti‐ACE2 peptide is discovered, which shows high affinity and specificity to human ACE2. It blocks not only the SARS‐CoV‐2‐RBD/ACE2 interaction but also the SARS‐CoV‐1‐RBD/ACE2 interaction. Moreover, it inhibits SARS‐CoV‐2 infection in Vero‐E6 cells. The peptide shows negligible cytotoxicity in Vero‐E6 cells and Huh7 cells. In vivo short‐term lung toxicity study also demonstrates a good safety of the peptide after intratracheal administration. The anti‐ACE2 peptide can be potentially used as a prophylactic or therapeutic agent for SARS‐CoV‐2 or other ACE2‐mediated viruses. The strategy used in this study also provides a fast‐track platform to discover other antiviral peptides, which will prepare the world for future pandemics.

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Phage Display on the Anti‐infective Target 1‐Deoxy‐d‐xylulose‐5‐phosphate Synthase Leads to an Acceptor–Substrate Competitive Peptidic Inhibitor

Cited by 7 publications

References 48 publications

Toward Understanding the Chemistry and Biology of 1-Deoxy-d-xylulose 5-Phosphate (DXP) Synthase: A Unique Antimicrobial Target at the Heart of Bacterial Metabolism

Toward Understanding the Chemistry and Biology of 1-Deoxy-d-xylulose 5-Phosphate (DXP) Synthase: A Unique Antimicrobial Target at the Heart of Bacterial Metabolism

Targeting the Unique Mechanism of Bacterial 1-Deoxy-d-xylulose-5-phosphate Synthase

Discovery of Small Anti‐ACE2 Peptides to Inhibit SARS‐CoV‐2 Infectivity

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