4.3 Release Mechanisms and Prodrug Design
143
structural determinants could be beneficial in this area since PDF is required to induce
a reaction in the prodrug rather than inhibit it.
There may also be a possibility for the released compound from deformylation
to act as an inhibitor of the next enzyme, methionine amino peptidase, which is
required to remove the methionine unit. This enzyme is an essential one in bacterial
and human cells so the compound would need to have selective inhibition properties,
but this might be possible based on it’s targeted release within the bacterial cell. A
review of advances in this area of bacterial methionine peptidase inhibitors has been
published by Helgren et al. (2016), and from enzyme structural studies significant
differences have been identified between the bacterial and human enzymes (Helgren
et al. 2016).
Another approach to consider is that of using bacterial cell peptidase to activate
a prodrug after assisted transport into the cell. This approach was used successfully
with eneamide prodrugs of inhibitors of the essential bacterial enzyme 1-deoxy-dxylulose-5-phosphate (DXP) synthase. This enzyme is essential in bacterial central
metabolism and is found in most pathogenic bacteria but it is not present in animals.
Work is being undertaken into enamide prodrugs of the selective mechanism-based
acylphosphonate inhibitors of this enzyme as potent antibacterials (Bartee et al.
2019). The prodrug design was based on the natural product dehydrophos and the
peptidic enamide prodrugs were transported into the cell via peptide transporter,
OppA. Inside the cell the peptidase cleaved the peptide units to give an enamine
which could then be hydrolysed to the active acetyl phosphonate DXP inhibitors
(Bartee et al. 2019). This approach has considerable potential for improved intracellular prodrug delivery to bacterial cells via the OppA transporter. Different peptidic
prodrugs could be transported including ones with an additional antibacterial leaving
group appropriately attached to an enamide moiety for the spatio-temporal release
of a dual acting hybrid for synergy with the acetyl phosphonate DXP inhibitor. In
this context a design extension to replace the phosphonate moiety by a boronate unit
could be pursued with a view to potentially increasing DXP inhibitory potency or
invoking a second activity.
Targeting of anaerobic over aerobic bacteria could be achieved with involvement
of nitroreductase in the former for prodrug activation and release of the active component(s). If the actives are only released once inside the bacterium where the bacterial
enzyme resides this will result in selectivity of action, assuming the prodrug is not
affected by external host enzymes or pH and doesn’t have other interactions with nonbacterial targets resulting in unwanted side effects. In this context consideration might
be given to designing a piperazine N-substituted nitro-vinyl ciprofloxacin derivative which could be activated by a bacterial nitroreductase to release ciprofloxacin
plus ultimately an α,β-unsaturated aldehyde. Such an aldehyde might be expected
to covalently interact with a number of intracellular protein sites or other sites, in
addition to the gyrase/topoisomerase targeting ciprofloxacin, providing an expression of multiple activity from the prodrug (Scheme 4.6). Further development of this
conceptual approach might include nitro-azole analogues.
Pretomanid (Fig. 4.6), an orally bioavailable, nitroimidazo-oxazine based
prodrug, is activated by a deazaflavin (cofactor F 420 )-dependent nitroreductase. The
143
structural determinants could be beneficial in this area since PDF is required to induce
a reaction in the prodrug rather than inhibit it.
There may also be a possibility for the released compound from deformylation
to act as an inhibitor of the next enzyme, methionine amino peptidase, which is
required to remove the methionine unit. This enzyme is an essential one in bacterial
and human cells so the compound would need to have selective inhibition properties,
but this might be possible based on it’s targeted release within the bacterial cell. A
review of advances in this area of bacterial methionine peptidase inhibitors has been
published by Helgren et al. (2016), and from enzyme structural studies significant
differences have been identified between the bacterial and human enzymes (Helgren
et al. 2016).
Another approach to consider is that of using bacterial cell peptidase to activate
a prodrug after assisted transport into the cell. This approach was used successfully
with eneamide prodrugs of inhibitors of the essential bacterial enzyme 1-deoxy-dxylulose-5-phosphate (DXP) synthase. This enzyme is essential in bacterial central
metabolism and is found in most pathogenic bacteria but it is not present in animals.
Work is being undertaken into enamide prodrugs of the selective mechanism-based
acylphosphonate inhibitors of this enzyme as potent antibacterials (Bartee et al.
2019). The prodrug design was based on the natural product dehydrophos and the
peptidic enamide prodrugs were transported into the cell via peptide transporter,
OppA. Inside the cell the peptidase cleaved the peptide units to give an enamine
which could then be hydrolysed to the active acetyl phosphonate DXP inhibitors
(Bartee et al. 2019). This approach has considerable potential for improved intracellular prodrug delivery to bacterial cells via the OppA transporter. Different peptidic
prodrugs could be transported including ones with an additional antibacterial leaving
group appropriately attached to an enamide moiety for the spatio-temporal release
of a dual acting hybrid for synergy with the acetyl phosphonate DXP inhibitor. In
this context a design extension to replace the phosphonate moiety by a boronate unit
could be pursued with a view to potentially increasing DXP inhibitory potency or
invoking a second activity.
Targeting of anaerobic over aerobic bacteria could be achieved with involvement
of nitroreductase in the former for prodrug activation and release of the active component(s). If the actives are only released once inside the bacterium where the bacterial
enzyme resides this will result in selectivity of action, assuming the prodrug is not
affected by external host enzymes or pH and doesn’t have other interactions with nonbacterial targets resulting in unwanted side effects. In this context consideration might
be given to designing a piperazine N-substituted nitro-vinyl ciprofloxacin derivative which could be activated by a bacterial nitroreductase to release ciprofloxacin
plus ultimately an α,β-unsaturated aldehyde. Such an aldehyde might be expected
to covalently interact with a number of intracellular protein sites or other sites, in
addition to the gyrase/topoisomerase targeting ciprofloxacin, providing an expression of multiple activity from the prodrug (Scheme 4.6). Further development of this
conceptual approach might include nitro-azole analogues.
Pretomanid (Fig. 4.6), an orally bioavailable, nitroimidazo-oxazine based
prodrug, is activated by a deazaflavin (cofactor F 420 )-dependent nitroreductase. The