Bioorganic & Medicinal Chemistry Letters
New peptide deformylase inhibitors design, synthesis and
pharmacokinetic assessment
a,
Fengping Lv a, Chen Chen a, Yang Tang a, Jianhai Wei a, Tong Zhu b, , Wenhao Hu
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a Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University,
North Zhongshan Road 3663, Shanghai, China
b Department of Physics and State Key Laboratory of Precision Spectroscopy, East China Normal University, North Zhongshan Road 3663, Shanghai 200062, China
a r t i c l e i n f o
a b s t r a c t
Article history:
The docking approach for the screening of designed small molecule ligands, led to the identification of a
critical arginine residue in peptide deformylase for spiro cyclopropyl PDF inhibitor’s extra hydrophobic
binding, providing us a useful tool for searching more efficient PDF inhibitors to fight for horrifying
antibiotics resistance. Further synthetic modification was undertaken to optimize the potency of amide
compounds. To lower metabolic susceptibility and in turn reduce unwanted metabolic toxicity that was
observed clinically, while retaining desired antibacterial activity, the use of azoles as amide bioisosteres
had also been investigated. After the completion of chemical synthesis, all the compounds were evaluated
through in vitro antibacterial activity assay, some of which were further subject to in vivo rat pharma-
cokinetic assessment. Those findings in this letter showed that spiro cyclopropyl proline N-formyl
hydroxylamines, and especially the bioisosteric azoles, can represent a promising class of PDF inhibitors.
Ó 2016 Elsevier Ltd. All rights reserved.
Received 14 March 2016
Revised 12 May 2016
Accepted 27 May 2016
Available online xxxx
Keywords:
PDF inhibitor
Antibacterial drug
Antibiotics resistance
MRSA
Docking study
Amide bioisosteres
The excessive and inappropriate use of antibiotics accelerates
the occurrence of their resistance and nowadays makes the resis-
tance to an appalling situation.1–3 The escalated resistance towards
existing antibiotics, alongside with shortage of new drugs with
novel mechanism of action poses great fear that we are risking fail-
ure in the army race between antibiotics discovery and resistance
evolvement, and stepping into a predicament of post-antibiotics
era where common infections are deadly.4–6
Because of grave concern over the weak pipeline of antibiotics
to fight against the ever-growing bacterial drug resistance, there
is an urgent need for the development of new antibiotics with
novel mechanism of action against multi-drug resistance.7,8
Peptide deformylase (PDF)9,10 has become a promising and
attractive bacterial target to explore for the discovery of new
antibacterial agents, because of difference between bacterial and
mammalian protein synthesis.11,12
Gram-positive and Gram-negative bacteria, due to poor structural
stability and tendency of quick clearance.17 LBM41518–20, the first
candidate recruited to run phase I clinical trial, had potency and
broad spectrum of activity, but was found to have structure-related
safety issue, methemoglobinemia.21 GSK132232222, showed broad
spectrum antibacterial activity against pathogens involved in
respiratory tract infections as well as methicillin-resistant Staphy-
lococcus aureus (MRSA), while potential reactive metabolites led to
a recent termination of its phase II clinical trial.23
Given that the dose-related in vivo toxicity of developed PDF
inhibitors are attributable to metabolic instability and harmful
implication of reactive metabolites, two chemistry strategies could
be undertaken: the synthesis of more peptidyl analogs, with higher
potency over bacterial PDF, and the bioisosteric replacement of
scissile amide bond, using heterocyclic azoles as non-peptide scaf-
folds. In continuation of our efforts to search more PDF inhibi-
tors,24–26 we, on the basis of virtual design and molecular
docking analysis, disclosed spiro cyclopropane-containing N-for-
myl hydroxylamines as a kind of novel and more efficient PDF inhi-
bitors. Besides extensive study on structural modification by
integrating various aromatic amines, especially heterocyclic
aromatic amines into proline’s carboxylic motif, preliminary inves-
tigation on isosteres was also made using different heterocycles as
amide mimics, hoping to mitigate the expected metabolic liability-
induced toxicity to the body. After synthetic completion of all
Numerous kinds of bacterial PDF inhibitors have been invented,
and several of them have even been developed into human clinical
trials (Fig. 1);13,14 however, to date, no effective PDF inhibitors
have been marketed. Actinonin15
, the first discovered PDF
inhibitor,16 could not secure acceptable in vivo antibacterial
activity, though exhibited moderate activity against several
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Corresponding authors. Tel.: +86 18801626247 (T.Z.), +86 13636307166 (W.H.).
(W. Hu).
0960-894X/Ó 2016 Elsevier Ltd. All rights reserved.