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Article history:
Received 22 November 2013
Revised 13 December 2013
Accepted 14 December 2013
Available online 22 December 2013
a b s t r a c t
Natural products have been a rich source of antibacterial drugs for many decades, but investments in this
area have declined over the past two decades. The purpose of this review article is to provide a recent
survey of new natural product classes and the mechanisms by which they work.
2013 Published by Elsevier Ltd.
Keywords:
Natural products
Antibacterial
Antimicrobial
In the past decade, only seven new chemical entities (NCE) have
been approved for therapy for treatment of bacterial infections.1
The number of approvals are down substantially from the peak
years in the mid-1980s, where on average, four new drugs were
introduced to the market each year.2 The plausible reasons for this
decline are most likely a combination of factors from a changing
regulatory environment, increased drug safety standards, as well
as failure of modern drug discovery techniques, such as high
throughput screening (HTS) against the essential bacterial genome,
to deliver on the promise of large numbers of new and novel targets in antibacterial space.3,4 OShea and Moser have published
on the physical properties of approved antibacterial drugs which
stands in contrast to typical Lipinski-like molecules found in most
company screening collections (e.g., antibacterial drugs with
Gram-negative activity have log D = 2.8 vs 1.6 for non-antibacterial
drugs).5 Aside from being highly polar and zwitterionic in many
cases, many of these are also covalent inhibitors (e.g., b-lactams)
or contain other chemical features postulated to aid in outer membrane penetration of bacteria. In comparison to mammalian cells,
the cell wall of bacteria (especially Gram-negative) present a formidable barrier for traditional small molecule drug-like space
which is typically represented in corporate HTS collections. This
barrier is due to both highly polar outer membranes and prolic
efux pumps that remove foreign compounds.
Of all the drugs currently approved as antibacterial NCEs, a signicant percentage of those are either natural products themselves
Corresponding author. Tel.: +1 781 839 4101; fax: +1 781 839 4390.
E-mail address: dean.brown@astrazeneca.com (D.G. Brown).
0960-894X/$ - see front matter 2013 Published by Elsevier Ltd.
http://dx.doi.org/10.1016/j.bmcl.2013.12.059
414
Me
HO
HO
OH
O
HO
OH
HO 3SO
Me
Me
Me
N
( )13
Me
N
H
OH
H
N
O
N
Me
H
N
O
CO2 H
( )7
Me
NH
O
Me
Me
Me
H
N
HN
H
N
N
Me
O
HO3 S
Me
1, Arylomycin A-C 16
CO2 H
NH
Me
2, Actinocarbasin
CO2H
O
Me
SO 3H
O
NH
SO3 H
O
O O
HN
i-Pr
N
H
HN
O
HO
NH
O
Me
H
N
N
OO
O
Me
NH
H
N
( )n
O
O
NH
NH
i-Pr
Cl
i-Pr
Me Me
O
N
HN
H
N
Cl
O
HO
25
O
NH
O
Et
O Me
NH
OH
H
HN
Me
i-Pr
Me
Me
HN
OMe
OH
14
OH
Me
OH
Me
Me
3, Krisynomycin
4, n = 4, Globomycin
5, n = 8
Figure 1. Type 1 signal peptidase inhibitors arylomycin 1, actinocarbasin 2, & krisynomycin 3. type II signal peptidase inhibitors globomycin 4 and 5 and myxovirescin
scaffolds 6, 7, 8.
415
416
Me
Me
N
Me
Me
O
O
O
HO
OH
t -Bu
N
H
i-Pr
OH
HN
HN
OH
O
HO
9, Orthoformimycin
Me
O
Me
Me
N
H
N
O
H H
N
N
H
N
R
O
O
t-Bu
R
R
F12
R9
V14
Y7
V16
L5
R18
G3
NH2
G2
R1
Protegrin I
NH
NH 2
HN
HN
NH
O
N
H
H
N
N
H
O
H
N
O
N
H
Me
NH
NH2
NH2
DP
LP
NH2
12
11
Peptidomimetics
NH
H 2N
10
O
N
H
Me
O
O 3
H
N
O
N
H
O
H
N
N
H
Me
O
OH
1
Me
NH 2
12
H
N
NH
NH 2
12, L27-11
Position
Compound
10
11
12
L8-1
L19-45
L26-19
L27-11
POL7001
vancomycin, and daptomycin are scarce examples of unadulterated natural product AMPs that have successfully passed clinical
trials and have been commercialized. Although safety remains an
issue with these agents, their potent, broad spectrum activity
and marginal pharmaceutical properties endears them with last
line of defence status for highly drug resistant bacteria (Fig. 3).
Topoisomerase inhibitors Type II topoisomerase is a clinically
validated antibacterial drug target and inhibition blocks DNA synthesis. At least two pathways involving this protein are known;
namely, disrupting the topoisomerase-DNA complex (so-called
topoisomerase poisons) and/or interrupting catalytic turnover
417
Gram-positive bacteria (MIC = 2.0 and 0.5 lg/mL for S. aureus and
MRSA, respectively). Moderate levels of inhibition were also
observed in a TolC efux pump mutant of E. coli (MIC = 32 lg/
mL), but no activity against wild type Gram-negative pathogens
was evident (E. coli MIC >64 lg/mL), likely due to poor permeability and/or efux. The activity associated with kibdelomycin is
similar to that observed in the structurally unrelated natural products, novobiocin (14) and clorobiocin (15).32 The mechanism of
action is hypothesized to involve inhibition of the ATPase activity
of type II DNA topoisomerases, which leads to obstruction of
DNA synthesis and cell death.
Independently, researchers at AstraZeneca discovered pyrrolamide 16 through a fragment-based lead generation approach
(FBLG).33 X-ray co-crystallography of early pyrrole containing hits
from the FBLG in the S. aureus GyrB N-terminal ATP binding
domain showed a hydrogen bond between the pyrrole-NH and
aspartic acid-81. In an effort to improve potency of these early hits,
a 3,4-dichloro substituent was installed on the pyrrole to increase
hydrophobic interactions in the adenine pocket and to reduce the
pKa of the NH group to make it a better hydrogen bond donor. This
modication lead to >150 fold increase in potency over the initial
hit. Pyrrolamide 16 exhibits single digit micromolar MIC activity
across a range of Gram-positive bacteria. This represents an interesting example whereby the properties of a fully synthetic DNA
gyrase inhibitor drug candidate were altered by the incorporation
of a functional group (3,4-dichloropyrrole amide) that was subsequently identied as a component of a natural product that exhibits the same mode of action; thus medicinal chemistry mimicking
nature in parallel discovery pathways (Fig. 4).
Emerging classes of new natural product space Despite the decline in research dedicated to natural products discovery and
development, natural products with compelling biological proles
and new structural diversity continue to be discovered as exemplied by the following two recent examples (Fig. 5).
In 2011, Rene De Mot and co-workers at the Katholieke Universiteit Leuven disclosed a new amphipathic salicylate containing
antibiotic, promysalin (17).34 Promysalin is uniquely comprised of
a 2-pyrroline carboxylate that bridges a single salicylic acid moiety
and a 2,8-dihydroxymyristamide side chain. These three distinct
structural features are derived from three different central metabolites that are elaborated and combined by a previously unknown
gene cluster combination. Produced by Pseudomonas putida, promysalin facilitates swarming characteristics and biolm formation in
the producing strain, but is antagonistic to other Pseudomonads
including MDR clinical isolates of P. aeruginosa (IC50 = 0.16 lg/mL
and minimum bactericidal activity (MBC) = 100 lg/mL against
PA14). Indeed, of the 16 Pseudomonas species tested, 12 had sensitive strains, and in a broader panel of P. aeruginosa environmental
and clinical isolates, all 83 were sensitive. This intriguing microbiological prole warrants further investigation, and additional work
is required to elucidate the absolute stereochemistry, mechanism of
action and structure activity relationships of promysalin.
At the 53rd ICAAC meeting (Denver, Colorado 2013) a group of
researchers from Fundacion Medina, Cubist Pharmaceuticals and
the University of California, San Diego presented a poster
disclosing a family of novel natural product antibiotics (MDN
005760).35 Isolated from the crude fermentation extract of a lamentous fungus, these natural products possess two isonitrile
functional groups, which although rarely found in natural products, are not unprecedented. Indeed, MK4588, an antibiotic natural
product isolated from Leptospaeria fungus by Gomi and co-workers
in 1990, would appear to be related.36 MDN-0057 exhibits potent
broad spectrum Gram-negative activity with MIC ranging
0.2564 lg/mL against E. coli, Acinetobacter baumannii, P. aeruginosa
and K. pneumonia clinical isolates. MIC values are signicantly lower in efux pump mutant or permeabalized strains of these organisms indicating a propensity for efux and poor permeability for
this chemotype. MDN-0057 did not inhibit S. aureus (>128 lg/
mL) or eukaryotic cell growth (HepG2 and Fa2N4 >512 lg/mL)
and was inactive in the hERG K channel at 50 lM. A study of the
impact of MDN-0057 on macromolecular synthesis indicated a
concentration dependant inhibition of cell wall synthesis, but not
RNA, DNA, protein or lipid synthesis. Additionally, cytology experiments showed that incubation of E. coli cells with MDN-0057 rendered the cells more permeable to DAPI and sytox green (dyes)
thus reinforcing a cell wall target related mode of action.
In summary, natural product research continues to be an important cornerstone for antibacterial drug discovery. With modern advances in selective organic synthesis, ribosome crystallography,
chemical biology tools for target elucidation, and novel methods
for uncovering new natural products, this area can continue to
provide new medicines towards unmet patient needs.
O
O
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13, Kibdelomycin
14, Novobiocin
15, Clorobiocin
Figure 4. Topoisomerase inhibitors from natural sources (13, 14, and 15) and synthetic preparation (16).
418
R
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OH
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O
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OH
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17, Promysalin
NH2
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18, MDN-0057, R = OH
19, MDN-0059, R = H
OMe
22. For a review, see: Poehlsgaard, J.; Douthwaite, S. Nat. Rev. Microbiol. 2005, 3,
870.
23. (a) Ban, N.; Nissen, P.; Hansen, J.; Moore, P. B.; Steitz, T. A. Science 2000, 289,
905; (b) Wimberly, B.; Brodersen, D. E.; Clemons, W. M., Jr.; Morgan-Warren, R.
J.; Carter, A. P.; Vonrhein, C.; Hartsch, T.; Ramakrishnan, V. Nature 2000, 407,
327; (c) Schuwirth, B. S.; Borovinskaya, M. A.; Hau, C. W.; Zhang, W.; VilaSanjurjo, A.; Holton, J. M.; Doudna Cate, J. H. Science 2005, 310, 827.
24. Mafoli, S. I.; Fabbretti, A.; Brandi, L.; Savelsbergh, A.; Monciardini, P.; Abbondi,
M.; Rossi, R.; Donadio, S.; Gualerzi, C. O. ACS Chem. Biol. 1939, 2013, 8.
25. Shimamura, H.; Gouda, H.; Nagai, T.; Hirose, M.; Ichioka, M.; Furuya, Y.;
Kobayashi, Y.; Hirono, S.; Sunazuka, T.; Omura, S. Angew. Chem., Int. Ed. 2009,
48, 914.
26. Kobayashi, Y.; Ichioka, M.; Hirose, T.; Nagai, K.; Matsumoto, A.; Matsui, H.;
Hanaki, H.; Masuma, R.; Takahashi, Y.; Omura, S.; Sunazuka, T. Bioorg. Med.
Chem. Lett. 2010, 20, 6116.
27. Crone, W. J. K.; Leeper, F. J.; Truman, A. W. Chem. Sci. 2012, 3, 3516.
28. Nguyen, L. T.; Haney, E. F.; Vogel, H. J. Trends Biotechol. 2011, 29, 464.
29. Srinivas, N.; Jetter, P.; Ueberbacher, B. J.; Werneburg, M.; Zerbe, K.; Steinmann,
J.; Van der Meijden, B.; Bernardini, F.; Lederer, A.; Dias, R. L. A.; Misson, P. E.;
Henze, H.; Zumbrunn, J.; Gombert, F. O.; Obrecht, D.; Hunziker, P.; Schauer, S.;
Ziegler, U.; Kch, A.; Eberl, L.; Riedel, K.; DeMarco, S. J.; Robinson, J. A. Science
2010, 327, 1010.
30. Bisacchi, G. S.; Dumas, J. Ann. Rep. Med. Chem. 2009, 44, 379.
31. Phillips, J. W.; Goetz, M. A.; Smith, S. K.; Zink, D. L.; Polishook, J.; Onishi, R.;
Salowe, S.; Wiltsie, J.; Allocco, J.; Sigmund, J.; Dorso, K.; Lee, S.; Skwish, S.; de la
Cruz, M.; Martin, J.; Vicente, F.; Genilloud, O.; Lu, J.; Painter, R. E.; Young, K.;
Overbye, K.; Donald, R. G. K.; Singh, S. B. Chem Biol. 2011, 18, 955.
32. (a) Li, S.-M.; Heide, L. Curr. Med. Chem. Anti-Infect. Agents 2004, 3, 279; (b)
Heide, L.; Gust, B.; Anderle, C.; Li, S.-M. Curr. Top. Med. Chem. 2008, 8, 667.
33. Eakin, A. E.; Green, O.; Hales, N.; Walkup, G. K.; Bist, S.; Singh, A.; Mullen, G.;
Bryant, J.; Embrey, K.; Gao, N.; Breeze, A.; Timms, D.; Andrews, B.; UriaNickelsen, M.; Demeritt, J.; Loch, J. T., III; Hull, K.; Blodgett, A.; Illingworth, R.
N.; Prince, B.; Boriack-Sjodin, P. A.; Hauck, S.; MacPherson, L. J.; Ni, H.; Sherer,
B. Antimicrob. Agents Chemother. 2012, 56, 1240.
34. Li, W.; Estrada-de los Santos, P.; Matthijs, S.; Xie, G.-L.; Busson, R.; Cornelis, P.;
Rozenski, J.; De Mot, R. Chem. Biol. 2011, 18, 1320.
35. Genilloud, O.; Vicente, F.; Reyes, F.; Bills, G.; De la Cruz, M.; Tormo, J.; Martin, J.;
Gonzalez, V.; El Aouad, N.; de Pedro, N.; Perez del Palacio, J.; Diaz, C.; Monteiro,
M.; Conrad, M.; Cassidy, K.; Cotroneo, N.; Cappellucci, L.; Knight-Connoni, V.
Conf. Antimicrob. Agents Chemother 2013, 89. Presentation F1215.
36. Itoh, J.; Takeuchi, Y.; Gomi, S.; Inouye, S.; Mikawa, T.; Yoshikawa, N.; Ohishi, H.
J. Antibiotics 1990, 43, 456.