N → π? Interactions in N-Acyl Homoserine Lactone Derivatives and Their Effects on Hydrolysis Rates

Article abstract of DOI:10.1021/acs.jpca.8b12266

N-Acyl homoserine lactones (AHLs) mediate population-wide behavioral changes in Gram-negative bacteria through quorum sensing (QS), a process shown to regulate virulence, biofilm formation, and other phenotypes that impact human health. AHLs have been proposed to contain an n → π? interaction that reduces the molecules' susceptibility to signal inactivation via lactone hydrolysis. In this work, seven AHL derivatives were modeled via gas-phase DFT calculations, implicit solvent DFT calculations, and MD simulations. Each derivative was then synthesized and hydrolyzed to probe the relationship between the strength of the orbital interaction and hydrolysis rate. The data obtained support that an increase in n → π? energy (E_n→π?) correlates to a decrease in the hydrolysis rate constant (k_obs). Further, the observed variation in these rates demonstrates that AHL hydrolysis can be modified by manipulating steric and electronic effects that alter the electrophilicity of the lactone carbonyl. These results help to elucidate nature's choice of AHLs as agents of density-dependent bacterial communication and could inform the design of AHL-based quorum sensing modulators.

Full text of DOI:10.1021/acs.jpca.8b12266

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A: Kinetics, Dynamics, Photochemistry, and Excited States
n # #* Interactions in N-Acyl Homoserine Lactone (AHL)
Derivatives and Their Effects on Hydrolysis Rates
Daniel J. Schmucker, Sydney R. Dunbar, Tricia D. Shepherd, and Michael A. Bertucci
J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.8b12266 • Publication Date (Web): 11 Mar 2019
Downloaded from http://pubs.acs.org on March 13, 2019
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n  π* Interactions in N-Acyl Homoserine Lactone (AHL) Derivatives and
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Their Effects on Hydrolysis Rates
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Daniel J. Schmucker , Sydney R. Dunbar , Tricia D. Shepherd , and Michael A. Bertucci*
Department of Chemistry, Moravian College, 1200 Main St., Bethlehem, PA 18018
Department of Chemistry, Hartwick College, 1 Hartwick Dr., Oneonta, NY 13820
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Abstract:
N-acyl homoserine lactones (AHLs) mediate population-wide behavioral changes in gram-
negative bacteria through quorum sensing (QS), a process shown to regulate virulence, biofilm
formation, and other phenotypes that impact human health. AHLs have been proposed to contain
an n → π* interaction that reduces the molecules’ susceptibility to signal inactivation via lactone
hydrolysis. In this work, seven AHL derivatives were modeled via gas-phase DFT calculations,
implicit solvent DFT calculations, and MD simulations. Each derivative was then synthesized
and hydrolyzed to probe the relationship between the strength of the orbital interaction and
hydrolysis rate. The data obtained support that an increase in n → π* energy (En→π*) correlates
to a decrease in the hydrolysis rate constant (kobs). Further, the observed variation in these rates
demonstrates that AHL hydrolysis can be modified by manipulating steric and electronic effects
that alter the electrophilicity of the lactone carbonyl. These results help to elucidate nature’s
choice of AHLs as agents of density-dependent bacterial communication and could inform the
design of AHL-based quorum sensing modulators.
_____________________________________________________________________________
Introduction:
With the emergence of virulent bacterial strains that have developed resistances to current
treatments, as observed in opportunistic human pathogen Pseudomonas aeruginosa, efficacy of
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traditional antibiotics is decreasing.1 Thus, the discovery of new treatments is in high demand
and the movement towards novel antimicrobial strategies has become more prominent.2,3 One
process that has been linked to bacterial virulence is quorum sensing (QS). QS is density-
dependent chemical communication that permits unified gene expression amongst bacteria and
results in such phenotypes as competence, the production of virulence factors, and biofilm
formation.4-7
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In gram-negative bacteria, such as Pseudomonas aeruginosa, QS processes rely on the
self-production of signaling molecules known as N-Acyl-Homoserine Lactones (AHLs) for
intercellular communication.8,9 Amongst the variety present in different species of gram-negative
bacteria, AHLs have been demonstrated to hydrolyze at variable rates.10 This natural control of
signal concentration allows the bacteria to accurately measure the population density in a given
moment and regulate the initiation and duration of the multicellular event. When both the
bacterial cell and unhydrolyzed AHL concentration are sufficiently high (Figure 1, 1), the AHL
binds to its cognate receptor and bacterial communication occurs. As the AHL is hydrolyzed
(Figure 1, 2) and the concentration of the active AHL decreases, the signal cannot bind and
bacterial communication ceases.10,11 This allows the QS mechanism to be controlled and gene
expression to be “switched” on and off based on colony density. Hydrolytic enzymes (e.g. AHL
lactonases) are produced by the quorate-forming bacteria to, in part, catalyze the silencing of QS
Figure 1. AHLs Undergo Hydrolysis. The reaction scheme above displays the hydrolysis of an
AHL found in P.aeruginosa under physiological conditions. When the AHL is hydrolyzed, it is
incapable of binding to its cognate receptor to stimulate gene expression.
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signaling in this manner.12,13 Thus, the stability of the lactone ring and its hydrolysis rate are
critical for effective signaling. Controlling hydrolysis rates could be a strategy for designing
AHL-like modulators to control gram-negative QS and manage its downstream effects, such as
virulence factor production and biofilm formation.14-17
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An n  π* interaction was recently proposed by Newberry and Raines between the lone
pair of the amide O and the C=O π* orbital of the lactone of the AHL (Figure 2).19 The presence
of this orbital overlap was confirmed by a crystal structure of the unbound 3-oxobutanoyl
AHL.20 The n  π* interaction is a weak, attractive interaction that results from a sub-Van der
Waals contact between a filled lone pair and a π antibonding orbital. This overlap has been
implicated in protein folding and structure21,22, RNA synthesis23, and native chemical ligation.24
In these systems, the donation of electron density to the π* orbital of the carbonyl has been
demonstrated to reduce the electrophilicity of the C=O, increasing the energetic barrier for
nucleophilic attack.25
Consequently, it has been hypothesized that the observed n  π* orbital overlap is
responsible for slowing AHL hydrolysis in physiological environments, allowing the signal to
persist during intercellular transport. If so, one should be able to develop AHL derivatives that
enhance or reduce the strength of this key orbital overlap and observe a decrease or increase in
AHL hydrolysis rates. In this work, a small library of AHL derivatives were computationally
modeled, synthesized, and hydrolyzed to evaluate the correlation between n  π* orbital overlap
and AHL hydrolysis rates. Verifying the impact of the n  π* interaction on hydrolysis would
support consideration of the through-space interaction in the design of novel AHL derivatives for
QS modulation.
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A
B
O
O
O
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R
N
H
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= orbital overlap
θ
(3a-3g)
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Figure 2. A Key Orbital Overlap in AHLs. (A) The described n  π* interaction occurs between
the lone pair of the AHL amide oxygen and the π* antibonding orbital of the lactone carbonyl
α
(pink arrow). The dihedral angle for C′i−1−Ni−C −C′i (θ, green) was measured to confirm the
i
viability of an orbital overlap based on the lowest energy conformation. The library of AHL
derivatives (3a-3g) in this study was modeled and synthesized with various aromatic substituents
defined in Table 1. (B) Energy minimized structure of the phenyl substituted AHL with the n 
π* overlap and measured dihedral angle θ indicated.
Experimental Methods:
DFT Calculations. All quantum mechanical calculations were performed by the Gaussian09
package.26 Gas phase and implicit water (PCM27) optimizations were performed at the B3LYP\6-
311+G(2d,p) and RB3LYP\6-31++G(d,p) levels of theory, respectively. The energies of the
resultant structures were corrected by the zero-point vibrational energy and the optimized
structures yielded no imaginary frequencies. In order to obtain values for the contribution of
nπ* overlap, NBO analysis of the optimized conformations was completed at the same level of
theory.28
MD Simulations. The general Amber force field (GAFF)29 was used for MD simulations. Partial
atomic changes were calculated at the HF-6.31G* level following the RESP30 protocol as
implemented in the antechamber module of the AmberTools1831 package. All MD simulations
were performed using AMBER 12 under periodic boundary conditions with 2 fs integration time.
A single solute molecule was surrounded by a 10 Å box of TIP3P32 water. After minimization
(the steepest descent method for 2000 steps) and equilibration in NVT and NPT ensembles (for
20 and 60 ps, respectively), the simulation was performed at 300 K and at 1 bar for 12 ns. All
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bonds containing hydrogen atoms were constrained using the SHAKE algorithm. A 10 Å cutoff
value was adopted for nonbonded interactions, and long-range electrostatic interactions were
handled with the PME scheme. Langevin dynamics was used to control temperature with a
collision frequency of 2 ps-1 and a pressure coupling with 1 ps time constant.
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Synthesis of N-Acyl Homoserine Lactone (AHL) Derivatives. In a 250-mL round bottom
flask, 0.364 g (2 mmol) of α-amino-γ-butyrolactone hydrobromide was dissolved in 60 mL of
dichloromethane (DCM). A stir bar and 0.836 mL (6 mmol) of triethylamine were added. The
solution was placed on ice and the corresponding benzoyl chloride (2 mmol) was added. After
sitting on ice for 30 mins, the ice bath was removed and the reaction was allowed to run for 4 h.
Thin-layer chromatography (TLC) was used to monitor reaction progression and completion.
Upon completion, the solvent was evaporated under reduced pressure. The reaction mixture was
redissolved in 60 mL of EtOAc and washed in a separatory funnel with 1 M of NaHCO3 (2x),
saturated KOH (2x), and saturated NaCl (2x). The organic layer was collected, dried over
Na2SO4, and concentrated under reduced pressure.33 The product was redissolved in 3 mL of
EtOAc and a silica column was run using a 75:25 EtOAc:Hexane mobile phase. The pure
fractions, as determined by TLC, were combined and concentrated. For the 3-NO2 AHL (3f),
1
further purification via recrystallization in ethanol was required to remove minor impurities. H-
NMR and 13C-NMR spectra were obtained for each product.
Phenyl N-acyl homoserine lactone 3a: Yield 44.7 mg (10.9%); δH (CDCl3, 200MHz)
2.31 (1H, p), 2.83 (1H, m), 4.25-4.49 (2H, t), 4.81-4.90 (1H, m), 7.28-7.45 (4H, m), 7.77-7.81
(2H, d); δc (CDCl3, 50MHz) 176.1, 167.7, 132.9, 132.0, 128.6, 127.2, 66.3, 49.5, 30.0; ESI-TOF-
MS [M+H]+ calc. 205.0739, found 205.0743 (Δ1.94 ppm)
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2-methoxyphenyl N-acyl homoserine lactone 3b: Yield 119 mg (25.4%); δH (CDCl3,
200MHz) 2.15- 2.32 (1H, p), 2.71-2.84 (1H, m), 3.85 (3H, s), 4.22-4.71 (3H, m), 6.8-6.85 (1H,
d), 6.96-7.0 (1H, t), 7.22-7.38 (1H, t), 8.07-8.11 (1H, d) 8.54-8.56 (1H, s); δc (CDCl3, 50MHz)
175.7, 165.4, 157.6, 133.3, 131.9, 121.0, 119.9, 111.2, 66.1, 55.8, 49.4, 29.9; ESI-TOF-MS
[M+H]+ calc. 235.0845, found 235.0853 (Δ3.47 ppm)
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3-methoxyphenyl N-acyl homoserine lactone 3c: Yield 39 mg (8.3%); δH (CD3CN -d3,
200MHz) 2.41-2.61 (3H, m), 3.85 (1H, s), 4.30 (1H, m), 4.47 (1H, t), 4.72 (1H, q), 7.10-7.16
(1H, m), 7.38 – 7.49 (4H, m); δc (CD3CN-d3, 50MHz) 175.2, 166.5, 159.8, 135.1, 129.8, 119.2,
117.4, 112.2, 65.7, 55.1, 48.8, 28.1; ESI-TOF-MS [M+H]+ calc. 235.0845, found 235.0852
(Δ3.26 ppm)
4-methoxyphenyl N-acyl homoserine lactone 3d: Yield 46 mg (9.8%); δH (CH3CN,
200MHz) 2.41-2.60 (2H, m), 3.86 (3H, s), 4.32 (1H, m), 4.47 (1H, m), 4.71 (1H, m), 6.98-7.01
(2H, d), 7.38-7.41 (1H, s), 7.80 (2H, d); δc (CDCl3, 50MHz) 175.9, 167.3, 162.7, 129.0, 125.2,
113.9, 66.3, 55.4, 49.7, 30.7; ESI-TOF-MS [M+H]+ calc. 235.0845, found 235.0855 (Δ4.51
ppm)
2-nitrophenyl N-acyl homoserine lactone 3e: Yield 32 mg (6.5%); δH (CD3CN-d3,
200MHz) 2.37-2.51 (1H, m), 2.66 (1H, m), 4.24-4.38 (1H, m), 4.47 (1H, m), 4.62-4.77 (1H, m),
7.52-7.83 (4H, m), 8.04-8.06 (1H, d); δc (CD3CN-d3, 50MHz), 175.9, 167.5, 148.4, 134.9,
132.9, 132.4, 130.2, 125.7, 67.1, 50.3, 29.3; ESI-TOF-MS [M+H]+ calc. 250.0590, found
250.0600 (Δ3.97 ppm)
3-nitrophenyl N-acyl homoserine lactone 3f: Yield 141 mg (28.1%); δH (CD3CN-d3,
200MHz) 2.44 (1H, p), 2.57 (1H, m), 4.29 (1H, m), 4.47 (1H, td), 4.75 (1H, m), 7.72 (2H, t),
8.19 (1H, d), 8.37 (1H, d), 8.62 (1H, s); δc (CD3CN-d3, 50MHz), 176.2, 166.0, 149.6, 136.3,
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134.6, 131.5, 127.6, 123.4, 67.1, 50.3, 29.3; ESI-TOF-MS [M+H]+ calc. 250.0590, found
250.0595 (Δ2.17 ppm)
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4-nitrophenyl N-acyl homoserine lactone 3g: Yield 124 mg (24.7%); δH (acetone-d6,
200MHz) 2.39-2.86 (2H, m), 4.32-4.55 (2H, m), 4.96 (1H, m), 8.16 (2H, d), 8.36 (2H, d), 8.56
(1H, s); δc (acetone-d6, 50MHz), 175.7, 166.2, 151.0, 140.7, 129.9, 124.9, 66.6, 50.3, 29.7; ESI-
TOF-MS [M+H]+ calc. 250.0590, found 250.0591 (Δ0.64 ppm)
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Hydrolysis Rates via HPLC. Standard samples were made in acetonitrile at concentrations of
2.0 mM, 1.0 mM, 0.25 mM, 0.0625 mM, and 0.0156 mM for each AHL derivative through serial
dilution. The samples were utilized to generate a calibration curve for the absorbance of each
AHL at wavelengths of 220 nm and 254 nm.
To monitor the hydrolysis of each AHL derivative, a 50 mM stock solution of each AHL
was prepared in 0.4 mL DMSO. Before the first HPLC injection, 0.08 mL of 50 mM stock
solution was diluted with PBS buffer to 4.0 mL to obtain a final AHL concentration of 1.0 mM.
The solution was immediately transferred to an HPLC vial and injected into the HPLC in 25-
minute intervals to monitor the hydrolysis of the AHL over time at 25°C. The hydrolysis of each
AHL was repeated independently in triplicate and the rate constant obtained from each trial was
averaged to yield the reported kobs value (see Table S2). The product peak in the 3-MeO AHL
(3c) trial was collected to verify the formation of the hydrolysis product by HR-MS ([M+H]+
calc. 253.0950, found 253.0961).
Results & Discussion:
We sought to design a model system that would allow methodical evaluation of the
influence of structural and electronic effects on the strength of the n  π* overlap. Seven
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aromatic AHL derivatives were considered, paralleling recently discovered agonists and
antagonists of QS in P.aeruginosa and other gram-negative bacteria.34,35,36 Phenyl AHL
derivatives are not representative of the tremendous variety of QS modulators that have been
developed nor do they represent the most potent inhibitors; however, employing them as our
model system permits the synthesis and systematic evaluation of the n  π* energy in
regioisomers (i.e. – ortho, meta, para) with defined Hammett parameters. As inductive effects
have already been indicated to influence the strength of the n  π* overlap, we reasoned that
simply incorporating electronegative substituents iteratively distanced from the acyl moiety
would lead to a systematic increase in the orbital interaction.37,38 To assess the impact of both
inductive and resonance effects, methoxy (-OMe) and nitro (-NO2) groups were chosen as
substituents due to differences in their corresponding Hammett parameters σp and σm (Table 1).
For instance, para –OMe, which has been shown to behave as either donor or acceptor based on
its orientation39, provides a net electron-donating effect to an adjacent π-system (σp = -0.27);
para –NO2 is electron-withdrawing (σp = +0.78). Finally, the –OMe and –NO2 groups have
notably different contributions with regards to steric strain, with experimentally determined A-
values for -OMe = 0.75 kcal/mol and -NO2 = 1.13 kcal/mol.40 Our library contains regioisomers
in which steric strain is elevated, like the 2-MeO and 2-NO2 derivatives, allowing us to
determine the role steric effects play in disrupting the key orbital overlap.
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Gas-phase DFT calculations were completed on each library member at the B3LYP\6-
311+G(2d,p) level of theory to obtain optimized conformations for each derivative and affirm the
presence of an n  π* interaction. The n  π* overlap in the lowest energy conformation was
obtained using natural bond orbital (NBO) analysis. Across the library, Enπ* were obtained
from 0.60 to 0.76 kcal/mol and, in the case of the ortho and meta-substituted AHLs, were
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detected in more than one optimized conformational state. The variation in conformation
originated from changes in the O=C-C=C dihedral angle between the amide and phenyl moieties
and the resultant orientation of the -NO2 or -OMe substituent (see Table S3). The obtained Enπ*
values are in agreement with the magnitudes reported by Newberry and Raines for such orbital
interactions in their N-trimethyl and N-tribromo AHL derivatives.19 Likewise, the On---C=O*
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α
distances and C′i−1−Ni−C −C′i dihedral angles served as reliable indicators of the n  π*
i
α
interaction. The calculated C′i−1−Ni−C −C′i dihedral angles ranged from 54.8° to 60.5° holding
i
the distance between the donor oxygen and the carbonyl carbon of the lactone between 2.93 and
2.99 angstroms, an acceptable proximity for the proposed van der Waals contact to occur. To
test for the possible disruption of the torsional profiles under a different DFT functional, the
calculations were re-run under dispersion-corrected conditions (Empirical Dispersion = GD3).
The dihedral angles persisted without significant change (see Table S4).
Despite evidence of the interaction in the gas-phase, the impact of the n  π* overlap on
AHL confirmation in the presence of explicit solvent molecules has not been explored.
Consequently, classical molecular dynamics (MD) simulations of each derivative in a box of
water were performed to test the interaction’s influence and resilience in this medium. All seven
of the AHL derivatives adopted and held conformational states indicative of n  π* orbital
overlap for varying lengths of time (see Supporting Information). These states were not the
dominant conformations during the MD simulation, indicating that intermolecular forces from
explicit solvent will compete with the n  π* overlap in solution. A selection of frames
containing conformations that appeared to demonstrate the desired through-space interaction
α
were analyzed. The characteristic On---C=O* distances and C′i−1−Ni−C −C′i dihedral angles
i
observed in the gas-phase and solvation DFT calculations were detected. Further, subsequent
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snapshot quantum calculations revealed Enπ* values, validating the presence of through-space
interaction.
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Table 1: Implicit solvent energy-minimized conformational data for AHL derivatives
AHL
R
σa
0.0
-
θ (degrees)b d (angstroms) θp (degrees)c
Enπ*
(kcal/mol)
1.11
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3a
Ph
53.8
53.9
53.8
53.2
54.5
54.2
53.8
53.8
53.8
54.0
54.6
54.4
55.3
56.4
53.9
54.1
53.9
2.90
2.89
2.86
2.85
2.92
2.91
2.93
2.89
2.89
2.91
2.91
2.89
2.94
2.97
2.90
2.91
2.91
α
25.4
-27.5
180
58.4
-56.6
-48.6
59.1
150
0.99
1.20
1.14
1.01
0.96
0.86
1.10
1.08
1.12
1.09
1.15
0.88
0.84
1.02
0.93
0.98
3b
2-MeOPh
3c
3d
3e
3-MeOPh
4-MeOPh
2-NO2Ph
0.12
-0.27
-
-27
-21.1
-23.1
-54.9
64.6
-54.0
-27.5
26.7
-30.3
3f
3-NO2Ph
4-NO2Ph
0.71
0.78
3g
aValues obtained from reference 41; bθ represents the C′i−1−Ni−C −C′i dihedral angle; cθp represents the (O=C-
i
C=C) amide-phenyl dihedral angle
With support for the through-space interaction in a dynamic solvent environment, we
sought to obtain Enπ* values that more closely described the AHL derivatives in water. The
coordinates of the n  π*-containing conformations identified in the MD simulations were
employed as the initial conformations for optimization calculations under implicit solvent
conditions. Energy values corresponding to the predicted On---C=O* orbital overlap were again
detected in at least two different conformational states for each of the AHL derivatives, except
the 4-NO2 AHL, which only yielded one minimum (Table 1). These Enπ* values were larger
than the gas-phase values, supported by the observed decrease in On---C=O* distances and
α
C′i−1−Ni−C −C′i dihedral angles. Importantly, the average increase was consistent across all
i
seven of the AHL analogs. As we hypothesized, the proximity of the -NO2 and -OMe groups to
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the N-acyl moiety influenced the Enπ*. The ortho-substituted derivatives (compounds 3b and
3e) displayed the largest number of conformations containing the n  π* interaction. They had
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the largest range of C′i−1−Ni−C −C′i dihedral angles and Oi-1---C’i=Oi distances, and
i
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consequently the greatest variety of Enπ* values. Thus, the influence of sterics is evident as it
had an observable effect on the magnitude of the n  π* interaction. The results for the
remaining AHL derivatives reveal the significant, differential impact the methoxy and nitro
groups have on the orbital interaction. They displayed Enπ* values that moderately correlated to
the known sigma values for each substituent and conformations that allow conjugation of the aryl
ring and the adjacent carbonyl. If the largest observed Enπ* is considered, compound 3d (4-
MeO) has the strongest orbital overlap; it is the only member of the library that has a negative, or
net electron-donating, Hammett parameter. Next in sequence is the phenyl AHL 3a, with an
Enπ* = 1.11 kcal/mol, followed by the net electron-withdrawing methoxy and nitro
regioisomers, 3c, 3f, and 3g.
With computational evidence of the n  π* interaction and its magnitude in each
derivative, we sought to experimentally determine its relationship to AHL hydrolysis. The seven
AHL derivatives were synthesized by combining α-amino-γ-butyrolactone with a functionalized
benzoyl chloride in the presence of base to establish the characteristic N-acyl bond (see
Experimental Section). To simulate an extracellular physiological environment, PBS at pH = 7.4
was employed as the hydrolytic media. Each AHL was then dissolved in the buffer to an initial
concentration of 1.0 mM and the resultant solution was injected at timed intervals into a RP-
HPLC. Peaks corresponding to the AHL and the hydrolysis product were both monitored over
time and, through a standard curve, the concentration of the AHL at each time point was
determined (Figure 3). By fitting the acquired data, we confirmed that the hydrolysis proceeds
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under pseudo-first order conditions and identified kobs values for the hydrolysis of each AHL
derivative (see Supporting Information).
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B
C
Figure 3. Monitoring AHL Hydrolysis. Hydrolysis of each AHL derivative was monitored
overtime by RP-HPLC. The peaks with a retention time of 3.6 and 9.9 min correspond to the
hydrolyzed and unhydrolyzed forms of the 3-MeO AHL (3c), respectively at (A) 7 min, (B) 232
min, and (C) 482 min.
The results displayed substantial differences in the hydrolysis rate constants of the AHL
derivatives (Table 2). With reaction conditions remaining constant across all trials (i.e.
temperature, pH, etc), only intrinsic properties should impact the hydrolysis rate constant. As the
lactone itself is too many atoms removed from the substituent to influence hydrolysis in a
through-bond manner, the variation in rate constant is evidence of a through-space effect, such as
Table 2. Rate constants for hydrolysis of AHL derivatives
Compound
R
kobsa(min-1)
Compound
R
kobsa(min-1)
3a
3b
3c
3d
Ph
0.236
3e
3f
2-NO2Ph
3-NO2Ph
4-NO2Ph
0.345
2-MeOPh
3-MeOPh
4-MeOPh
0.354
0.318
0.250
3g
0.381
0.224
aAll kobs values shown are equal to the number displayed x10-3 min-1. Hydrolysis of each AHL derivative was
completed in triplicate.
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the n  π* interaction. The only AHL derivative with a larger Enπ* than the phenyl AHL (3a)
is compound 3d. The results of our kinetics experiments demonstrate that 3d has the smallest
rate constant, supporting the hypothesis that the n  π* interaction reduces the electrophilicity
of the lactone. The kobs values for the –OMe substituted AHLs decrease from compound 3c to
3d. This parallels the computed increase in the Enπ* as the methoxy group is moved further
from the N-acyl lactone. Likewise, the NO2-functionalized AHLs 3f and 3g with weaker nπ*
energies hydrolyzed faster. Notably, compound 3g was more susceptible to hydrolysis than 3b
and 3e, despite the influence of steric effects that led to significant variability in calculated Enπ*
values for 3b and 3e. However, the large positive σp value of 3g supports the derivative as being
the most electron-withdrawing regioisomer or the regioisomer that provides the least electron
density to π*C=O. Thus, the stability of a single conformation in 3g may amplify the impact of
the -NO2 electronic effects in enhancing the electrophilicity of the lactone C=O.
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With more than one optimized confirmation identified for six of the AHL derivatives
under implicit solvent conditions, the contribution of each to the observed hydrolysis rate is
uncertain. However, for AHL analogs with two such conformations, it was observed that one of
the Enπ* values almost perfectly aligned with the obtained hydrolysis rate. The result is a clear
progression from increased Enπ* and reduced kobs to decreased Enπ* and enhanced kobs for the
phenyl, meta-substituted and para-substituted AHLs (Table 3). Thus, a direct correlation is
present between the implicit Enπ* values and hydrolysis rate. In addition, as the Enπ* of
Table 3. Implicit solvent data for lowest energy conformations of AHL derivatives
R
θ (degrees)
d (angstroms)
Enπ* (kcal/mol)
kobs (min-1)
4-MeOPh
Ph
54.0
2.89
1.12
1.11
1.10
1.02
0.98
0.224
53.9
2.89
0.236
3-MeOPh
3-NO2Ph
4-NO2Ph
53.9
2.89
0.250
53.9
2.90
0.318
53.9
2.91
0.381
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specific confirmations correlated most strongly to the observed hydrolysis rates, it can be
inferred those conformations may be the dominant n  π* confirmations in solution. We
refrained from selecting a single Enπ* for the ortho-substituted derivatives due to the increased
number of optimized structures identified.
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The magnitude of the rate constants obtained must also be noted. The hydrolysis rates of
the library as a whole were quite slow, with the fastest derivative (3g) reaching only 6.1 – 7.9%
completion after 3 hours. Nature’s selection of AHLs as the key messenger for QS is at first
perplexing as γ-butyrolactone alone has been shown to be resistant to hydrolysis at neutral pH.42
This would be detrimental to a dynamic system like QS that requires timely activation and
termination of colony-wide gene expression. On the other hand, the presence of an α-amino
group substantially increases hydrolysis of the γ-butyrolactone (34% conversion in 4.25 h, Figure
S1) due to inductive effects. AHLs are a unique class that are resistant to rapid hydrolysis,
supporting the intercellular function of AHLs. Yet, AHLs are reactive enough to allow
progressive silencing of the QS event they regulate, even in the absence of hydrolytic enzymes
like AHL lactonases and acylases, that have been shown to mediate signal termination.10,11,13 Our
data supports the conclusion that the source of this balance is in part due to the nπ* interaction.
Through independent work published in 2011, Mattmann and colleagues screened 3d and
3g in E.coli reporter strains harboring QscR and LasR expression vectors to assess the agonism
and antagonism of those AHL analogues at each receptor site. The 4-MeO substituted 3d
displayed 62% inhibition at QscR and 11% inhibition at LasR while in the presence of the native
ligand. The 4-NO2 substituted 3g displayed 52% inhibition and 4 % inhibition at QscR and
LasR, respectively.29 These modest differences in inhibitory potency between the AHL
derivatives correlate with our results. However, it is difficult to determine the impact of AHL
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hydrolysis in this comparison. The assay completed by Mattmann et al. was only run for 4 - 6
hours, a timeframe in which the impact of signal degradation would only be 6.7 – 11.4%
complete based on our observed rates for these AHL derivatives. In addition, previous work has
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α
identified a re-orientation of the AHL C′i−1−Ni−C −C′i dihedral angle and breaking of the nπ*
i
interaction that occurs upon receptor binding. Our MD data shows that interconversion between
conformations containing and not containing the nπ* interaction is common in explicit
solvent, but aligning differences in Enπ* with differences target binding affinity would require
further modeling and experimentation.19
Strengthening the nπ* interaction could provide a different advantage. This added
stability may positively impact the pharmacokinetic profile of synthetic analogs designed for
prophylaxis or infection treatment, a noted setback towards developing QS therapeutics.43 In
addition, strengthening the nπ* interaction allows the native lactone moiety to be preserved
while minimizing QS inactivation by hydrolysis. This may preserve key AHL-receptor
interactions as opposed to replacing the lactone with a non-hydrolyzable functionality. Thus,
manipulating the strength of the orbital overlap to increase the lifetime of the unhydrolyzed form
while maintaining the optimal conformational flexibility and connectivity for binding may aid in
developing more potent QS modulators.
Conclusions:
Our acquired computational data combined with our experimental results strongly
support the presence of an nπ* interaction in AHLs in a dynamic, solvated environment, and
demonstrate the variability of the interaction’s magnitude based on the functionalization of the
N-acyl moiety. By modeling a series of AHL derivatives in accordance with defined Hammett
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parameters, Enπ* values were obtained in both gas-phase and solvation models display the
impact of electronic and steric effects on the donation of the oxygen lone pair to the lactone
carbonyl. These energy values correlated with the derivatives’ hydrolysis rates at pH = 7.4 for
selected conformations. Obtained kobs values varied from 0.224 x 10-3 to 0.381 x 10-3 min-1, even
within our small seven-membered model system. Thus, we have demonstrated that hydrolysis
rate will vary depending on the functionalities incorporated into AHL derivatives, in part due to
through-space orbital interactions. Consideration of these interactions (i.e. - nπ*) in the design
of QS inhibitors may enhance their longevity in physiological environments, but they must
remain weak enough to permit conformational modification for binding. We believe that
evidence of this relationship will help inform those seeking to develop viable QS inhibitors for
combating bacterial infectivity and resistance formation.
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Supporting Information:
Procedures for synthesis of the AHL derivatives as well as data regarding kinetics experiments,
HR-MS, NMR, MD and DFT calculations. This information is available free of charge via the
Internet at http://pubs.acs.org.
Author Information:
Corresponding author: bertuccim@moravian.edu
Acknowledgements:
We would like to express our appreciation to Prof. Carl Salter at Moravian College and Prof.
John Dudek at Hartwick College for helpful conversations as well as the department of chemistry
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at University of Nevada, Reno for use of the TOF LC/MS spectrometer to acquire HR-MS data.
This research was financially supported by departmental and start-up funds at Hartwick and
Moravian College. Computational resources were provided in part by the MERCURY
consortium (http://mercuryconsortium.org/) under NSF grants CHE-1229354 and CHE-1662030.
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