Article pubs.acs.org/jnp
Isolation, Structure Elucidation, and Biological Activity of Altersolanol P Using Staphylococcus aureus Fitness Test Based Genome-Wide Screening John Ondeyka,†,§ Alexei V. Buevich,† R. Thomas Williamson,† Deborah L. Zink,† Jon D. Polishook,† James Occi,† Francisca Vicente,‡,⊥ Angela Basilio,‡,⊥ Gerald F. Bills,‡,∥ Robert G. K. Donald,†,▽ John W. Phillips,†,○ Michael A. Goetz,†,§ and Sheo B. Singh*,† †
Merck Research Laboratories, Rahway, New Jersey 07065 and Kenilworth, New Jersey 07033, United States CIBE, Merck Sharp & Dohme de Espana, S. A. Josefa Valcárcel, Madrid, Spain
‡
S Supporting Information *
ABSTRACT: Bacteria continue to evade existing antibiotics by acquiring resistance by various mechanisms, leading to loss of antibiotic effectiveness. To avoid an epidemic from infections of incurable drug-resistant bacteria, new antibiotics with new modes of action are desperately needed. Using a genome-wide mechanism of action-guided whole cell screening approach based on antisense Staphylococcus aureus fitness test technology, we report herein the discovery of altersolanol P (1), a new tetrahydroanthraquinone from an unknown fungus from the Hypocreales isolated from forest litter collected in Puerto Rico. The structure was elucidated by high-resolution mass spectrometry and 2D NMR spectroscopy. Relative stereochemistry was established by NOESY correlations, and absolute configuration was deduced by the application of MPA ester-based methodology. Observed 1H and 13C NMR shifts were well aligned with the corresponding chemical shifts predicted by DFT calculations. Altersolanol P exhibited Gram-positive antibacterial activity (MIC range 1−8 μg/mL) and inhibited the growth of Gram-negative Haemophilus inf luenzae (MIC 2 μg/ mL). The isolation, structure elucidation, and antibacterial activity of altersolanol P are described.
A
from different geographical regions and habitat (including marine microbes) in combination with improved highthroughput fermentation methods.3 These approaches led to the discovery of a series of natural products4−6 including platensimycin7,8 and platencin9,10 using an fabH/fabF-sensitized strain and a number of other new natural products using an rpsD-sensitized antisense strain.11−15 In the past few years, we have extended our antisense-based screening approach to include a Staphylococcus aureus fitness test (SaFT), in which 245 antisense-containing S. aureus strains are used simultaneously to elucidate the mechanism of action of antibacterial compounds.16 As described earlier, this approach allows the grouping of compounds and crude natural product extracts based on SaFT profile comparison in the SaFT profile database,16,19 which when combined with high resolving power accurate mass measurement Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a robust dereplication tool,17,18 as illustrated by the discovery of kibdelomycin and kibdelomycin A.19,20 Acetone extracts of fermentations of the fungal strain (F166,863) screened in the SaFT assay produced a distinct SaFT
ntibiotic-resistant bacteria are ever more common and pose serious threats. Infections caused by methicillinresistant Staphylococcus aureus (MRSA) alone are responsible for about 18 000 deaths per year in the United States.1 While the MRSA report has drawn significant attention, infections by a number of drug-resistant Gram-negative bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii are perhaps even more alarming. Incremental improvements in the lead classes of antibiotics discovered during the Golden Age of antibiotic discovery provide most of the currently used antibiotics. Further progress to improve existing antibiotics is proving to be challenging, and returns on investment in research have significantly diminished. The best way to alleviate this problem is through the discovery of new lead classes of antibacterial agents. Natural products are prolific sources of antibacterial leads. One of the biggest challenges in natural products discovery is how to avoid rediscovery of known compounds and therefore improve the odds for success. In order to address this challenge, new screening technologies and new sources of natural products are needed. We have attempted to address both of these questions through two approaches. First, we introduced an S. aureus target-based antisense whole-cell screening approach that utilizes strains hypersensitive to certain target-based inhibitors and allows for differentiation of antibacterial agents at the crude extract stage.2 Second, we expanded our efforts to isolate microorganisms © 2014 American Chemical Society and American Society of Pharmacognosy
Special Issue: Special Issue in Honor of Otto Sticher Received: September 16, 2013 Published: January 15, 2014 497
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eight carbons were assigned as quaternary (Table 1). Of these, two were indicative of quinone-type carbonyls, one an
profile that did not match other compounds in the profile database. Bioassay-guided fractionation using a simple S. aureus growth inhibition assay led to the isolation of altersolanol P (1), a new member of the altersolanol family of compounds. The isolation, structure elucidation by 2D NMR, mass spectral analysis, DFT calculations, absolute configuration, and antibacterial activity of altersolanol P are described.
Table 1. 1H (600 MHz) and 13C (150 MHz) NMR Assignment of Altersolanol P (1) in CDCl3 no. 1
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RESULTS AND DISCUSSIONS The producing strain (F-166,863, Figure S1, Supporting Information) was isolated from forest leaf litter collected at Bosque de Tabanuco, Caribbean National Forest, in Puerto Rico using a particle filtration method.21 In culture, the fungus produced simple to sparsely branched phialidic conidiogenous cells on the aerial hyphae, which in turn produced elliptical, single-celled hyaline conidia, and therefore would fit the definition of the form genus Acremonium. However, a revision of generic concepts among fungi classified as Acremonium has confirmed the long-recognized phylogenetic heterogeneity of the genus and has designated A. alternatum as the type species for the genus.22 Sequence homology searches in public databases (www.fungalbarcoding.org, NCBI) indicated that the fungus was unrelated to A. alternatum but instead exhibited affinities to various genera in the Cordycipataceae, Clavicipitaceae, Ophiocordycipitaceae, Nectriaceae, and other families of the Hypocreales. However, overall sequence homologies to authentically named taxa were low, and any clear association with a monophyletic lineage within the Hypocreales was weak. The most similar D1−D2 regions of the 28S rDNA sequences were those of Metacordyceps chlamydosporia (95% similarity). For the intertranscribed spacer rDNA sequences, the most similar matches were several Cosmospora species (88% similarity). Such low similarity scores and its ambiguous association with any known family within the relatively wellstudied Hypocreales indicate that this fungus may belong to a yet uncharacterized phylogenetic lineage (see Figure S2, Supporting Information). The submerged production stage fermentation broth of this fungal species was extracted with an equal volume of acetone and was partitioned with EtOAc. Chromatographic separation of the EtOAc extract by gel permeation on Sephadex LH20 followed by reverse-phase HPLC led to the isolation of homogeneous altersolanol P (18 mg, 18 mg/L) as a gum. Electrospray ionization (ESI) mass spectral analysis of 1 yielded m/z 297 [M + Na]+ and m/z 273 [M − H]+. ESI FTICR MS analysis of 1 yielded a fragment ion at m/z 257.0807 due to loss of a molecule of water, [M + H]+ − H2O with an accurate mass measurement providing the formula C15H13O4. The UV spectrum of 1 showed absorption maxima at 210 and 270 nm, and the IR spectrum showed absorption bands for hydroxy groups (3400 cm−1) and a conjugated ketone (1660 cm−1). The 13C NMR spectrum of 1 in CDCl3 showed 15 distinct resonances. Analysis of the DEPT spectrum suggested the presence of a methyl, two methylene, and an oxymethine group and three olefinic methines. The remaining
type
δC, ppm
CH2
21.0
2
CH2
30.9
3 4
C CH
69.0 69.6
5 6 7 8 9 10 1a 4a 9a 10a 11 3-OH 4-OH 8-OH
CH CH CH C C C C C C C CH3
119.2 136.4 124.6 161.5 189.8 185.9 146.2 142.4 114.8 132.0 25.4
δH in ppm, mult (J in Hz)
HMBC (H→C)
H1, 2.82, dddd (20.3, 8.2, 5.8, 2.3) H1′, 2.62, dddd (20.3, 5.6, 5.5, 1.5) H2, 2.06, dt (13.8, 5.6) H2′, 1.66, ddd (13.5, 8.2, 5.9)
2, 3, 9, 1a, 4a
4.26, s
1a, 4a, 2, 3, 10, 11 7, 10, 9a 8, 10a 5, 8, 9a, 10a
7.62, m 7.61, m 7.26, m
1.34, s 2.89, brs 4.08, d (2.8) 11.98, s
2, 3, 9, 1a, 4a 1, 3, 4, 11, 1a 1, 3, 4, 11, 1a
1, 2, 3, 4 3, 4 6, 7, 8, 9, 9a
oxygenated downfield-shifted olefinic carbon, and another an oxygen-bearing aliphatic carbon. COSY correlations suggested three contiguous aromatic methines. They also indicated that both methylene moieties were coupled only to each other. The oxygenated methine appeared as a singlet (δH 4.26, δC 69.6). The methyl singlet (δH 1.34) showed HMBC correlations to C2 (δC 30.9), C-3 (δC 69.0), and C-4 (δC 69.6), thus establishing the connectivity of the upfield C1−C4 carbons. H-4 exhibited HMBC correlations to C-1a (δC 146.2), C-4a (δC 142.4), C-3, and C-10 (δC 185.9), establishing connectivity to the central ring. The HMBC correlations of H-5 to C-10; H-6 to C-8 (δC 161.5); H-7 to C-9a (δC 114.8); and H-1 to C-9 established the tetrahydroanthraquinone structure 1 for altersolanol P. To confirm resonance assignments of 1, proton and carbon chemical shifts were analyzed by the density functional theory (DFT) method with the MPW1PW91 functional and 631G(d,p) basis set. Prior to chemical shift calculations, the molecular geometry of 1 was optimized by the DFT calculations at the B3LYP/6-31G(d) level of theory. All quantum mechanical calculations in the present study were carried out with the Gaussian 09 software package.23 Excellent agreement between experimental and calculated chemical shifts was confirmed by nearly ideal linear regressions described by the 1.065 slope, 0.07 ppm intercept coefficient, 0.9970 correlation coefficient, and 0.27 ppm standard error for 1H chemical shifts (Figure 1a) and by the 0.970 slope, 3.28 ppm intercept coefficient, 0.9994 correlation coefficient, and 1.89 ppm standard error for 13C chemical shifts (Figure 1b). Interestingly, the intramolecular hydrogen bond between the phenolic OH at C-8 and the oxygen of the quinone carbonyl at C-9 was well reproduced by the DFT calculations. Thus, the predicted 13.02 ppm shift for the δH OH-8 proton and 187.5 498
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Figure 1. Comparison of the DFT-calculated (MPW1PW91/6-31G(d,p)) vs measured 1H (a) and 13C (b) chemical shifts for altersolanol P (1).
Figure 2. Conformational equilibrium of altersolanol P. Red arrows show NOEs used for stereochemical analysis. Analysis of trans-3JHH couplings between the H-1 and H-2 protons (Table 2) predicted the 65:35 ratio of A to B.
ppm for the δC C-9 carbonyl carbon were in good agreement with experimental values of 11.97 and 189.8 ppm, respectively. In the case of no intramolecular hydrogen bond, the DFTcalculated prediction for the C-8 hydroxyl δH is 4.8 ppm and that for the C-9 carbonyl δC is 180.3 ppm. The only outlier in the correlation plot of proton chemical shifts is the C-4 hydroxyl (δH 4.08 experimental vs δH 5.15 calculated). This discrepancy can be explained on the basis of conformational analysis, which is discussed below. The relative stereochemistry between C-3 and C-4 was established by 2D NOESY data. The cis-orientation of the H-4 and CH3-11 was confirmed by a strong NOE between the H-4 and H-2′ and between CH3-11 and H-2′ protons (Figure 2). Simultaneous observation of long-range NOEs between the CH3-11 and H-1′ and between the H-4 and H-2′ also suggested that 1 undergoes fast conformational exchange between conformations A and B with pseudoaxial conformations of H4 and CH3-11, respectively (Figure 2). The ratio of conformations A and B in 1 was estimated from the analysis of experimental trans-3JH1′,H2 and trans-3JH1,H2′ couplings. Each of these couplings is an average value that can be described by eq 1: J exp = pA JA + pB JB
method was used at the B3LYP/6-311+G(d,p) level of theory. Specifically, the unconstructed basis set with additionally tightened s and d functions for calculating Fermi contact components was used as previously described.24 Prior to Jcoupling calculations, the conformation geometries were optimized by DFT at the B3LYP/6-31G(d) level of theory. Then we applied least-squares minimization to find probabilities pA and pB, which produced the best fit of both trans-3Jcouplings (Jcalc) to their corresponding experimental values (Jexp). Relatively small, 0.17 Hz root-mean-square deviation of that analysis ensured high accuracy of estimated pA and pB values, whose 65:35 ratio is well consistent with the observed NOEs. Results of a conformational analysis of 1 are summarized in Table 2. The discrepancy between experimental and calculated proton chemical shifts of the C-4 hydroxyl is now explained by the conformational equilibrium of 1. The correlation plots in Figure 1 were based on chemical shifts of the dominant conformation A. Conformational equilibrium had little effect on chemical shifts except for the C-4 hydroxyl. Thus, taking into consideration the 65:35 ratio of conformations A and B and the DFT-predicted chemical shift for OH-4 in A and B, 5.15 and 2.97 ppm, respectively, the average value of δH OH-4 is estimated to be 4.39 ppm, which correlated much better with the experimental observed value of 4.08 ppm (see complete table of chemical shifts for conformations A and B (Supporting Information)). The absolute configuration of altersolanol P (1) was determined thorough derivatization with (R)-(−)-methoxyphe-
(1)
where Jexp is the experimentally observed J-coupling, JA and JB are corresponding J-couplings in conformations A and B, and pA and pB are probabilities of conformations A and B. Since probabilities are normalized (pA + pB = 1), only one of them need be determined. To calculate JA and JB couplings, the DFT 499
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Table 3. In Vitro Antibacterial Activity and Spectrum of Altersolanol P (MIC, μg/mL)a
Table 2. Conformational Analysis of Altersolanol P Based on Experimental and DFT-Calculated (B3LYP/6-311+G(d,p)) trans-3JHH Couplings
JH1,H2′, Hz JH1′,H2, Hz RMSD, Hzb pA:pB
JA
JB
exptl
calcda
12.1 1.6
1.9 12.8
8.2 5.6 0.17 65:35
8.37 5.77
strainb S. aureus Smith strain S. aureus Smith strain 50% human serum S. pneumoniaec S. pneumoniaed E. faecalis VSE B. subtilis E. coli (wt) E. coli (envA/tolC) H. inf luenzae C. albicans
strain no.
1
penicillin G
MB2865 MB2865
4 (2) >64
64 32 2 8
90% conversion. The product was analyzed directly without further purification. 1H NMR (600 MHz, CDCl3, 300 K) δ 11.91 (s, 1H, OH), 7.58 (dd, J = 8.4, 7.5 Hz, 1H), 7.46−7.40 (m, 2H), 7.38−7.22 (m, 5H), 5.97 (s, 1H), 4.85 (s, 1H), 3.42 (s, 3H), 2.97−2.90 (m, 1H), 2.60−2.45 (m, 1H), 1.90 (ddd, J = 13.5, 9.4, 5.9 Hz, 1H), 1.76−1.69 (m, 1H), 1.17 (s, 3H); HRESIMS m/z 423.1452 (C24H22O7 + H, calcd for M + H, 423.1444). Minimum Inhibitory Concentration (MIC). The MIC against each of the strains was determined using the method of National Committee for Clinical laboratory Standards (NCCLS; now called the Clinical Laboratory Standards Institute (CLSI)) by the 2-fold serial
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ASSOCIATED CONTENT
S Supporting Information *
Photographs of the fungus, phylogenetic tree, 1H, 13C, COSY, NOESY, HSQC, and HMBC NMR spectra of 1, and 1H and HSQC NMR spectra of MPA ester 2. This material is available free of charge via the Internet at http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Present Addresses
§ Natural Products Discovery Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, USA. ⊥ Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucia,́ Avenida Conocimiento 3, Parque Tecnológico Ciencias de la Salud, 18100 Armilla, Granada, Spain. ∥ The Brown Foundation of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, USA. ▽ Pfizer Vaccine Research, 401 N. Middletown Road, Pearl River, New York 10965, USA. ○ Allen Institute for Brain Science, Seattle, Washington 98103, USA.
Author Contributions
The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS The authors acknowledge generous help from Tom J. Novak for obtaining accurate mass data on the MPA-ester, Gary E. Martin for proofreading the manuscript, and Jesus Martin for initial dereplication.
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DEDICATION Dedicated to Prof. Dr. Otto Sticher, of ETH-Zurich, Zurich, Switzerland, for his pioneering work in pharmacognosy and phytochemistry.
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REFERENCES
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