Fluoroalkenes as Peptide Isosteres: Ground State Analog Inhibitors of Thermolysin

Bartlett, Paul A.; Otake, Atsushi

doi:10.1021/jo00115a028

Cited by 146 publications

(77 citation statements)

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“…Instead, we observed an almost opposite correlation where K m dominates the relationship. Indeed, such a relationship has been observed before with the peptidyl fluoroalkane inhibitors of thermolysin where inhibition robustly correlates with K m of the corresponding substrate (44). Our results strongly suggest that for the aminopeptidases, the aminoacyl phosphonates are likely to bind the ground state of the enzyme.…”

Section: Pig Apnsupporting

confidence: 83%

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

Drąg

Bogyo

Ellman

et al. 2010

Journal of Biological Chemistry

119

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Aminopeptidases process the N-terminal amino acids of target substrates by sequential cleavage of one residue at a time. They are found in all cell compartments of prokaryotes and eukaryotes, being implicated in the major proteolytic events of cell survival, defense, growth, and development. We present a new approach for the fast and reliable evaluation of the substrate specificity of individual aminopeptidases. Using solid phase chemistry with the 7-amino-4-carbamoylmethylcoumarin fluorophore, we have synthesized a library of 61 individual natural and unnatural amino acids substrates, chosen to cover a broad spectrum of the possible interactions in the S1 pocket of this type of protease. As proof of concept, we determined the substrate specificity of human, pig, and rat orthologs of aminopeptidase N (CD13), a highly conserved cell surface protease that inactivates enkephalins and other bioactive peptides. Our data reveal a large and hydrophobic character for the S1 pocket of aminopeptidase N that is conserved with aminopeptidase Ns. Our approach, which can be applied in principle to all aminopeptidases, yields useful information for the design of specific inhibitors, and more importantly, reveals a relationship between the kinetics of substrate hydrolysis and the kinetics of enzyme inhibition.The largest group of aminopeptidases, proteases that remove amino acids from the N terminus of target substrates one residue at a time, are members of the metallopeptidases (1). They are found in most cell compartments of prokaryotes and eukaryotes and are implicated in several major cell fates such as maintenance of the differentiated state, defense against pathogens, growth, and development (2-4). A classic aminopeptidase activity is the removal of the N-terminal Met after the initiation of translation by methionine aminopeptidase (5, 6). In addition to their primary proteolytic function, aminopeptidases also play secondary roles as viral or toxin receptors, transcriptional repressors, and vesicular trafficking controllers (7-9). The activity of well known aminopeptidases and the characterization of new aminopeptidases are generally determined using synthetic substrates containing one of a few natural amino acids attached to chromogenic or fluorogenic leaving groups (10, 11). For example, the M1 clan (alanine aminopeptidases) is assayed using fluorogenic peptide substrates containing a P1 Ala, and the M17 clan (leucine aminopeptidases) is assayed using fluorogenic peptide substrates containing a P1 Leu (12-14). However, this type of evaluation of enzyme specificity gives limited information about the profile of the S1 pocket, a primary determinant in the absolute specificity of aminopeptidases for their natural substrates.A number of general substrate-based library screening methods have been developed for the fast and reliable determination of protease specificity (15)(16)(17)(18)(19)(20). Importantly, for the cysteine, serine, and threonine proteases, substrate specificity data provide valuable information that can be ...

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Section: Pig Apnsupporting

confidence: 83%

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

Drąg

Bogyo

Ellman

et al. 2010

Journal of Biological Chemistry

119

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“…Beispiele umfassen 1) die Hydratisierung von a-Fluorcarbonylgruppen, wie anhand vieler Übergangszustandsinhi-bitoren vorgestellt wurde [76] (Abschnitt 3.1), 2) den Einsatz von Vinylfluoriden als Mimetika für die Amidbindung [77] (Abschnitt 3.2) und 3) die Modulation benachbarter Funktionalitäten (Abschnitt 3.3) durch die Einführung von Fluorsubstituenten (Schema 15). [78] …”

Section: Andere Anwendungen Der C-f-bindung In Der Katalyseunclassified

Konformative Fluoreffekte in der Organokatalyse: eine neuartige Strategie zum molekularen Design

2011

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Strategien zum molekularen Design, die von den intrinsischen stereoelektronischen und elektrostatischen Effekten fluorierter organischer Moleküle profitieren, sind bisher hauptsächlich auf die bioorganische Chemie beschränkt. Bei vielen konformativen Fluoreffekten handelt es sich zwar um akademische Kuriositäten ohne unmittelbare Anwendung, die Renaissance der Organokatalyse bietet allerdings die Möglichkeit zur Erforschung vieler dieser ausführlich beschriebenen Phänomene zur molekularen Präorganisation. In diesem Kurzaufsatz werden Beispiele zur Verbesserung von Katalysatoren durch die Einführung einer aliphatischen C‐F‐Bindung erläutert, die als eine chemisch inerte dirigierende Gruppe zur Steuerung der Konformation dient.

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“…In order to recapture amide-like character in an olefinic mimic, dipeptide fluoro- olefin isosteres have been introduced. [19] In this context, it is also increasingly appreciated that the structural features that cause peptides to adopt secondary structures (including bturns) are complex. In addition to hydrogen bonding, [20] allylic strain about the Pro-d-Val amide, [21] dipole neutralization of the Pro-d-Val carbonyl, [22] and n-to-p* donation [23] from the Xaa-Pro carbonyl lone pair to the Pro-Yaa carbonyl may each contribute to the b-turns stability.…”

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confidence: 99%

Functional Analysis of an Aspartate‐Based Epoxidation Catalyst with Amide‐to‐Alkene Peptidomimetic Catalyst Analogues

2008

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Keywordsepoxidation; peptide; asymmetric catalysis; olefin isostere; fluorine; peptidomimetic The biosynthesis of natural products that contain epoxides represents a powerful stimulus for the study of "epoxidase" enzymes. [i] Likewise, these processes have inspired a generation of science focused on small molecule catalysts that mediate selective epoxidations through a variety of mechanisms. [ii] With respect to the naturally occurring epoxidases, the mechanistic basis of O-atom transfer is often associated with the chemistry of either flavinoid cofactors, P450 enzymes containing a heme group, or chloroperoxidases that lead to stepwise ring formation. [iii] In thinking about the known biosynthetic apparatus for epoxide formation, we became curious about an alternative mode for O-atom transferone based on functional groups available in proteins, but perhaps not well-documented in the biosynthesis of epoxides. In particular, we speculated and recently showed that asparticacid-containing peptides (e.g., 1; Figure 1a) might shuttle between the side-chain carboxylic acid and the corresponding peracid (e.g., 2) creating a catalytic cycle competent for asymmetric epoxidation with turnover of the aspartate-derived catalyst. Such an approach is orthogonal to the Julia-Colonna epoxidation, a complementary peptide-based epoxidation based on a nucleophilic mechanism. [iv] Indeed, as shown in Figure 1b, this new electrophilic epoxidation catalytic cycle mediates the asymmetric epoxidation of substrates like 3 to give products like 4 with up to 92% ee. [v] Mechanistic questions abound in this catalytic system. To date, we have identified a number of relevant aspects. For example, we observed off-catalytic cycle intermediates, including catalytically inactive diacyl peroxides (6). [vi] We also showed that these off-cycle intermediates could be reinserted into the productive pathway through the action of nucleophiles such as DMAP or DMAP-N-oxide (7). On the other hand, the basis of stereochemical information transfer was not immediately clear. Indeed, the high precision delineation of the stereochemical mode of action of chiral catalysts is a critical frontier in the discipline of asymmetric catalysis, whether the catalysts are enzymes or small molecules. With this back-drop, we began a detailed study of the mode of action for catalyst 5.The conversion of 3 to 4 was originally undertaken with the hypothesis that substratecatalyst hydrogen bonding might contribute to transition state organization. [vii] Indeed, a substrate lacking obvious H-bonding capability (phenylcyclohexene) was found to undergo epoxidation with catalyst 5 with low enantioselectivity (~10% ee). Thus, we envisioned several potential loci for contacts between 3 and 5 (Figure 2a). Shown in blue is the site that

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Fluoroalkenes as Peptide Isosteres: Ground State Analog Inhibitors of Thermolysin

Cited by 146 publications

References 0 publications

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

Konformative Fluoreffekte in der Organokatalyse: eine neuartige Strategie zum molekularen Design

Functional Analysis of an Aspartate‐Based Epoxidation Catalyst with Amide‐to‐Alkene Peptidomimetic Catalyst Analogues

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