The Effect of Halogen-to-Hydrogen Bond Substitution on Human

Subscriber access provided by GAZI UNIV

Letter

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition Jindrich Fanfrlik, Francesc X. Ruiz, Aneta Kadl#íková, Jan #ezá#, Alexandra Cousido-Siah, André Mitschler, Susanta Haldar, Martin Lepsik, Michal H. Kolá#, Pavel Majer, Alberto D. Podjarny, and Pavel Hobza ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/acschembio.5b00151 • Publication Date (Web): 28 Apr 2015 Downloaded from http://pubs.acs.org on May 5, 2015

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

ACS Chemical Biology is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 7

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Chemical Biology

The halogen atom of an aldose reductase inhibitor involved in the halogen bond has been replaced with an amine group that formed a hydrogen bond retaining the binding mode. 39x18mm (600 x 600 DPI)

ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 2 of 7

The Effect of HalogenHalogen-toto-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition Jindřich Fanfrlík,*a Francesc X. Ruiz,b Aneta Kadlčíková,a Jan Řezáč,a Alexandra Cousido-Siah,b André Mitschler,b Susanta Haldar,a Martin Lepšík,a Michal H. Kolář,a,c Pavel Majer,a Alberto D. Podjarny*b and Pavel Hobzaa,d a

Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic b Department of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404 Illkirch CEDEX, France. c Institute of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich d Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic

ABSTRACT:

The effect of halogen-to-hydrogen bond substitution on the binding energetics and biological activity of an aldose reductase inhibitor has been studied using X-ray crystallography, IC50 measurements, advanced binding free energy calculations and simulations. The replacement of Br or I atoms by an amine (NH2) group has not induced changes in the original geometry of the complex, which made it possible to study the isolated features of selected non-covalent interactions, in a biomolecular complex.

A halogen bond (X-bond) is a non-covalent interaction that plays an important role in molecular recognition, crystal engineering1 and interactions of drugs or biological molecules.2-4 Halogens, exhibiting the highest electronegativity in the periodic table, possess a non-uniform electron density distribution. The electrostatic potential (ESP) around a halogen atom is strongly anisotropic due to the unequal occupation of the valence orbitals. Besides the negative areas expected, there is also an area of positive ESP, called a σ-hole.5,6 The X-bond is an interaction between the σ-hole and an X-bond acceptor (an electron donor: O, N, phenyl ring). Since X-bond acceptors can also serve as hydrogen-bond (H-bond) acceptors, X-bonds and Hbonds are mutually interchangeable. This idea has been pursued thoroughly at the level of gas-phase energetics in model complexes, but the implications of X-bond/H-bond substitution in more complex biomolecular systems have not yet been studied. The main reason is that it is difficult to isolate this substitution effect from those intimately linked to it, such as a change in the spatial arrangement of the interacting residues or altered interactions of the X-linked aromatic ring due to perturbed mesomeric effects. It is well known that the strength of an X-bond depends on the properties of the σ-hole, which can be characterized by its

magnitude and size.7,8 The magnitude is defined as the value of the most positive ESP of the electron density surface, and the size as the spatial extent of the positive region. The magnitude of the σ-hole increases with the increasing atomic size, i.e. when passing from chlorine to iodine. Furthermore, it has been shown that the σ-hole magnitude correlates with the strength of the Xbond in structurally similar complexes.7,8 Apart from small molecular complexes, this has also been demonstrated in protein– ligand complexes. Cl replacement by Br and I has enhanced the X-bond in the cathepsin-inhibitor complex and reduced IC50 from 30 nM to 6.5 and 4.3 nM, respectively.9 The strength of the Xbond can also be increased further by substitutions in the vicinity of the halogen. Electron-withdrawing groups make the σ-hole larger and more positive.7,8 It is thus also possible to tune the inhibition activity by modulating the X-bond strength in a protein-ligand (P-L) complex. We have recently reduced the IC50 of aldose reductase (AR) inhibitors from 1900 nM to 190 nM by fluorination close to the halogen atom that is involved in an Xbond.10 Interestingly enough, there was no direct correlation between the magnitude of the σ-hole and the inhibition activity, because the fluorination also changed other properties of the ligand. In our previous work, we speculated that it mainly affected the solvation free energy of the inhibitors.10 While this evidence clearly shows the advantages of X-bonds, it has not been quantified yet what the gain in binding energetics and inhibition activity is when an H-bond is replaced by an X-bond. To study this effect, we opted for the AR-IDD388 complex, which had been extensively studied by the authors and others.10-14 IDD388 is an AR inhibitor containing a Br atom participating in an X-bond with an OG1 atom of the side chain of Thr113 of AR.11 Here, we have replaced this X-bond with an H-bond and examined whether this substitution changes the binding mode. The starting point were the AR inhibitors IDD388 and MK315, containing Br and I, respectively (see Figure 1A), involved in the X-bond. The only option that conserves the linear arrangement of the original X-bond is to introduce an amine (NH2) group that


Page 3 of 7

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


forms an H-bond with the same acceptor. Modeling a hydroxyl substitution did not yield an analogous H-bond (not shown). The respective compound was synthesized (AK198) and the X-ray structure of the AR-AK198 complex was determined (PDB ID 4QXI). We found that the binding mode had indeed been conserved. Further, the complex was modeled and scored by an advanced three-layer QM/SQM/MM scoring function15 and complemented by alchemical free energy simulations. Finally, the inhibition activity was characterized by the experimental IC50 value (Table 1). The obtained data on the AR-AK198 complex were compared to the previously studied complexes of IDD388 and MK315.10 The X-ray crystal structure of the AR-AK198 complex was determined at the ultrahigh resolution of 0.87 Å. With such a resolution, the level of the details observed in the best-ordered areas approaches that of small-molecule studies,11 which is the current case (the overall mean B-factor is 13.44 Å2 and the inhibitor mean B-factor is 6.8 Å2). The omit difference map showed very clearly the inhibitor electron density, which was refined to an occupancy of 56 % (see Figure 1A). The alignment of the X-ray crystal structures is shown in Figure 1B and the geometric properties of the X-bond are listed in Table 1. The Xto-N substitution had not changed even the details of the binding mode, confirming our design hypothesis. The X-ray structure proves that the X-bond has been replaced by an H-bond, because the distance between the N atom of AK198 and the oxygen atom of Thr113 is only 2.92 Å. Moreover, a donated-hydrogen electron-density peak can be observed between these two atoms in the difference map (data not shown). To gain further insight into the details of the H-bond, we have refined the crystallographic data with SHELXL,16 keeping the structure rigid with the exception of AK198 and Thr113, which were refined without constraints. The following features have been revealed. Firstly, the C-N bond of the fluoroaniline moiety of AK198 is 1.3877 ± 0.0277 Å, suggesting a neutral, slightly pyramidal NH2. (the C-N bond length for sp2 N, sp3 N and an ammonium salt is known to be 1.355, 1.395 and 1.465 Å, respectively). The neutral form of the amino group will most likely prevail also for the free ligand in solution, given that the experimental pKa of 3fluoroanilin is 3.59.17 Secondly, the CB-OG1 distance of Thr113 is 1.4416 ± 0.0103 Å, which corresponds to a protonated OG1, acting as an H-bond acceptor. The experimental geometries are compared with the QM/SQM/MM-optimized structures in Figure 1B and Table 2. The QM/SQM/MM structures have accurately reproduced the Xbonded complexes. However, the length of the H-bond was by about 10 % longer in the QM/SQM structure than in the X-ray crystal structure. It might be caused by insufficient basis set used in gradient optimization.18 The strength of the H-bond calculated using the larger basis set in single point calculations on the structure with the too long H-bond might thus be underestimated and should be interpreted only as its lower bound. The QMSQM structures were analyzed by the advanced scoring function developed in our laboratory.15 The scoring function has been designed as a sum of terms where each has a physical meaning. The most important ones are the gas-phase interaction energy (∆Eint), changes in the solvation free energy upon complex formation (∆∆Gsolv) and the conformational “free” energy of the ligand (∆G'confw(L)). The scoring results are summarized in Table 1. In the gas phase, the ∆Eint of AK198 is more negative than that of the halogenated compounds IDD388 and MK315 (by about 4.9 and 1.1 kcal mol-1, respectively). In order to see the origin of the change in ∆Eint, we also calculated the interaction energies (at the RI-DFT-D/TPSS/TZVP level)

between the inhibitors and the side chains of the amino acids within 4 Å of the inhibitor. Figure 2 shows the difference in the interaction energies (∆∆Eint) for the amino acid side chains with ∆∆Eint larger than 0.5 kcal/mol. Obviously, the H-bond is stronger than the X-bond, and the change in total ∆Eint is caused mainly by weakening the interaction with Thr113. The H-bond with Thr113 was calculated to be by about 3 kcal mol-1 stronger than the X-bond. In fact, ∆Eint of the X-bond is close to zero (∆Eint with Thr113 of 0.6, -0.4 and -3.1 kcal mol-1 for IDD388, MK315 and AK198, respectively), which corresponds to the bent C-X…O angle.19 Optimal arrangement for an X-bond is linear, while the angle in the studied complexes is only about 155 degrees. Upon passing to the solvent, the advantage of the H-bond is offset by the solvation. A quantum chemical approach using the SMD implicit solvent model20,21 shows that the solvation free energy (∆Gsolv) of AK198 is significantly more negative than that of the halogenated compounds IDD388 and MK315 (-70.99, 62.65 and -66.28 kcal mol-1, respectively). Another approach is represented by molecular dynamics (MD) simulations of the ligands surrounded by explicit waters followed by alchemical free energy simulations using fast-growth thermodynamic integration (FGTI). The halogen atoms were treated utilizing an explicit σ-hole (ESH).22,23 The relative ∆Gsolv for AK198-toIDD388, AK198-to-MK315 and IDD388-to-MK315 were calculated to be 6.90±0.03, 5.85±0.11 and -1.21±0.34 kcal mol-1, respectively. Methodologically, this represents very well converged values: the thermodynamic closure of -0.16 kcal mol-1 is close to its theoretical value 0.0 kcal mol-1. These results confirm that the penalty for the ligand desolvation is considerably larger for AK198 than for the two halogenated inhibitors. It is encouraging to see a semiquantitative agreement considering the different approximations in the two approaches. SMD, on the one hand, boasts the accurate quantum-based treatment but suffers from the single-conformational approach;24,25 on the other hand, FGTI is inherently bound by force-field inaccuracies but has the advantage of a multi-conformational treatment. Taken together, both methods provide qualitatively consistent results showing that the amino analog is the best solvated variant, followed by the I- and Br- analogs. These results are consistent with the trend in the ∆∆Gsolv term of the score (with the ∆∆Gsolv term of MK198 being 11.2 and 7.8 kcal mol-1 larger than that of IDD388 and MK315, respectively; see Table 1). In contrast to the ∆Eint and ∆∆Gsolv terms, the ligand conformational change (∆G'confw(L)) did not play an important role here. The simple QM optimizations did not change the conformation of inhibitors and the (∆G'confw(L)) values were close to zero for all the three inhibitors. This is, however, the lower bound of the real values of the conformational change as the global minimum cannot be expected to be reached by a simple optimization.24,25 We have thus carried out a structural analysis of the 20-ns-long MD runs of inhibitors in explicit waters at ambient conditions. Overall, the molecules are unable to undergo any large conformational change. The radii of gyration (Rg) are comparable as seen from the histograms (the mode and the standard deviations of the Rg of AK198, IDD388 and MK315 are 3.91±0.09, 3.96±0.1 and 3.96±0.1 Å, respectively; see Fig. S3). To show this more clearly, we also calculated the corresponding distances between N, Br and I atoms and the two O atoms of the carboxylate group (Figure S3). The average distances are calculated to be about 7.5 Å for all the N...O, Br...O and I...O contacts. From the presented analysis, we may conclude that dynamic ensembles of the ligands in aqueous environment are very similar.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The total scores are summarized in Table 1. The score for AK198 is less negative, and its binding affinity is consequently expected to be weaker. This is consistent with the IC50 measurements. The IC50 value of AK198 is larger (1.3 µM) than the IC50 of IDD388 and MK315 (0.4 and 0.2 µM, respectively). This observed trend in the binding affinities is fully supported by the inhibitor occupancy in the X-ray structures. In the case of the AR-IDD388 and AR-MK315 complexes, the inhibitors have 100% occupancy, whereas the AK198 inhibitor in the AR-AK198 complex has an occupancy of only 56%. The other 44% correspond to the holoenzyme structure, as the B conformation of Leu300 overlaps with the inhibitor and corresponds to the conformation preceding the inhibitor binding. Please, also note that both the AR-MK315 and AR-AK198 complexes were obtained by co-crystallization with 4 mM inhibitor (the ARIDD388 complex was obtained by soaking). We are aware of the small sample size, which complicates generalizations of the obtained results. Unfortunately, the requirement of conserving the binding mode prevents us from generating a broader series. Other groups (like -OH) do not form the respective H-bond. Moreover, even small changes in the remainder of the inhibitor (for example fluorination) change the solvation of the inhibitor,10 which prevents a direct comparison. The limitations of the scoring function used should also be considered. The most important limitation is the treatment of entropy. Only the solvation entropy was considered here, while the vibrational analysis at the MM level was not performed due to the problematic description of halogenated inhibitors. The MD simulations have, however, shown that the behavior of the studied inhibitors in solvent is very similar, and thus the entropy component will probably also be comparable. It should also be noticed that more active H-bonded compounds can be designed when the requirements of the binding mode conservation are lowered. For example, the group of G. Klebe has crystallized an AR inhibitor IDD393 (PDB code: 2IKJ) which is very similar to IDD388. The only difference is the replacement of the 4-Bromo-2-fluoro-phenyl moiety with 3nitrophenyl. The nitro group of IDD393 interacts with the backbone of Leu300 and the side chain of Tyr309, and the ∆Gb° of IDD393 was comparable with that of IDD388 (with the ∆Gb° of IDD393 being less negative by only 0.1 kcal mol-1).13 The structure and properties of the AR-IDD388 X-bond had also been studied by X-ray analysis and isothermal titration calorimetry in the group of G. Klebe.26 The authors constructed a series of single-site AR mutations and showed that the Thr113Ala mutation caused a loss of ∆Gb° of IDD388 to AR by about 1.3 kcal mol-1.26 However, we have shown that this X-bond is particularly weak due to its suboptimal geometric arrangement. This suggests that the loss of ∆Gb° should not be governed by losing this X-bond. This finding might support an alternative hypothesis based on the incorporation of an additional water molecule into the extra space provided by the Thr113Ala mutation.27 In the X-ray crystal structure of the mutated Thr113Ala AR-IDD388 complex (PDB ID 3LQG), a Br ion (product of radiation damage) was found in a position partially occupied by the residue 113 in the wild type AR complexes.26 This could point to the possibility that the same position was occupied by a water molecule in solution. The loss of ∆Gb° could, thus, be caused by the entropy penalty of a buried water molecule with a long residency. Indeed, the results of the calorimetry measurement for the cited mutant showed a loss of entropy of 2.4 kcal mol-1, while the binding enthalpy (∆Hb°) was more negative by 1.3 kcal mol-1 (i.e. it favored the binding).26

Page 4 of 7

Finally, the weak stabilization energy of this X-bond might also help to explain the presence of two conformations of the OG1 atom in the crystal structure of the Thr113Ser AR mutant with bound IDD388. In this complex, a “void” conformation was enabled by the missing methyl group. If the X-bond were stronger, the OG1 atom should be selectively oriented towards the Br atom. However, a kind of compromise was seen in the Xray crystal structure (PDB ID 3LZ3), as OG1 was scattered over two orientations, one forming, the other avoiding the X-bond.26 To summarize, we designed an X-to-H-bond substitution (Br or I atoms to an NH2 group) in AR inhibitors. The combination of X-ray, advanced QM/SQM/MM scoring, molecular dynamicsbased free energy simulations and IC50 measurement have shown that 1) the geometry of the complex has been conserved; 2) the X-bond has been replaced with an H-bond; 3) although in the vacuum, the H-bond is significantly stronger than the original Xbond, the total binding affinity decreased due to the larger desolvation penalty of the NH2 group. It has thus been revealed that the solvent plays a very important role in the X-bonding of P-L complexes. An important conclusion is that the H-to-X-bond substitution might be used under suitable geometrical conditions to increase the ligand–binding affinity. METHODS IC50 determination The IC50-activity assays were carried out based on the quantification of the NADPH consumption that takes place when the enzyme catalyzes the conversion of glyceraldehyde into glycerol. The assays were performed at 25 ℃ in a 100 mM sodium phosphate buffer (pH 7.0), with the AR protein amount reaching the Vmax, and 0.2 mM NADPH, and the final reaction volume was 500 µL per reaction. The compound was dissolved in dimethyl sulfoxide, and the corresponding solution was added to the cell and incubated for 5 min at 25 ℃ prior to the addition of the substrate. The reaction was initiated by the addition of 1 mM glyceraldehyde, and the decrease in optical density at 340 nm was monitored for 3 min at 25 ℃ in a UV–vis spectrophotometer (UV-1700 PharmaSpec, Shimadzu). The IC50 value was determined as the compound concentration that inhibits the enzymatic activity by 50%. IC50 was calculated using the Grafit program (version 5.0; Erithacus Software) and the values were determined as the mean of three experiments ± the standard error. Crystallization, Structure Determination, and Refinement The crystal of AR:NADP+:AK198 was obtained by cocrystallization (4 mM inhibitor) under the published conditions28 (50 mM ammonium citrate, pH 5.0, 20% polyethylene glycol (PEG) 6000) by the hanging-drop vapor-diffusion method at 24 °C. The data collection was performed on the synchrotron X06DA beamline at the Swiss Light Source. The crystals belong to the P21 space group, with one protein molecule in the asymmetric unit. The atomic coordinates of the human AR:NADP+:IDD594 complex (the PDB code: 1US0), were used to solve the structure of the AR ternary complex. Crystallographic refinement involved repeated cycles of conjugate gradient energy minimization and temperature factor refinement, performed with the CCP4 suite29 and Phenix.30 The final Fo–Fc map indicated clear electron density for AK198. The data collection and the refinement statistics are listed in Table S1. The atomic coordinates have been deposited in the PDB (code: 4QXI). Molecular Modeling and Calculations


Page 5 of 7

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The protein-ligand (P–L) complexes were modeled from the X-ray structure taken from the PDB (PDB code: 2IKI).13 We employed the triple (QM/SQM/MM)-layer subtractive scheme. It couples the small QM region treated at the DFT-D (TPSS/TZVP//B-LYP/SVP) level of theory and the large SQM region treated by PM6-D3H4X31-32 with an MM description for the rest of the system. A detailed description of the QM/SQM/MM setup can be found in the SI part. Scoring terms: The gas-phase interaction energy (∆Eint) was calculated using the QM/SQM/MM method (see above). The solvation free energy of the protein (∆Gsolv) was determined by the generalized Born (GB) solvent model33 SMD/HF/6-31G*20 was used to calculate the solvation free energy of the ligand in order to increase the accuracy of the ∆Gsolv term.25 The ∆G'confw(L) term is the “free” energy change between the ligand in the ligand conformation adopted in the P-L complex and its optimal solution structure. For the evaluation of the change of the conformational “free” energy of ligand (∆G'confw(L)) the gas– phase DFT-D (TPSS/TZVP//B-LYP/SVP) energy is combined with the SMD solvation free energy. A detailed description of all the terms can be found in Refs. 10 and 15. The MD and free energy simulations were performed using an explicit σ-hole (ESH).22,23 A detailed description of the simulations can be found in the SI part.

MK315

I

2.91

156.6

134.9

AK198

N

3.24

144.4

127.6

Figure 1. A) AK198 omit difference map displaying the inhibitor electron density calculated with a 5σ cutoff (H atoms not shown), and the structural formula of the studied inhibitors. X stands for Br, I and NH2. In compounds IDD388, MK315 and AK198, respectively; B) Aligment of the AR-inhibitor complexes based on X-ray and QM/SQM/MM optimized structures (coloring code IDD388:yellow, MK315:orange and AK198:blue).

Organic synthesis A detailed characterization of the synthesized compounds along with the description of the synthesis is available in SI. Table 1. The calculated gas-phase interaction energy (∆Eint), interaction desolvation free energy (∆∆Gsolv), scores, experimental ∆Gb° (calculated by ∆Gb° = RT*ln(IC50/2))[a] and IC50 of the studied inhibitors (Fig. 1A). Energies and IC50 in kcal mol-1 and µM, respectively. Inhibitor AK198

X

∆E int ∆∆Gsolv Score ∆Gb°

NH2 –86.9 [b]

IDD388

Br

–82.0

IC50

45.6

–41.3 –8.4

1.3 ± 0.2

34.3

–47.6 –9.1

0.40 ± 0.02

[b]

MK315 I –85.8 37.8 –48.0 –9.6 0.19 ±0.09 ° ∆Gb refers to free energy for the reaction under standard conditions of all the reactants and products at concentrations of 1.0 M; [b] Data taken from Ref. 10. [a]

Table 2. Geometrical properties of the X-bond and H-bond in the studied complexes. Distances in Å and angles in degrees. distance Inhibitor

angle

X X...O

C-X...O

X...O-CA

X-ray IDD388

Br

2.90

154.5

132.2

MK315

I

2.95

158.1

130.2

AK198

N

2.92

146.7

124.9

QM/SQM/MM IDD388

Br

2.92

153.1

132.6



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Figure 2. The change in interaction energy (∆∆ Eint) between the inhibitor and amino acid side chains within 4 Å of the inhibitor. ∆∆ Eint in kcal mol-1.

ASSOCIATED CONTENT Supporting Information

The refinement statistics, the characterization of synthesized compounds along with the description of synthesis and molecular dynamics based-methods available free of charge via the Internet http://pubs.acs.org.

the the are at

AUTHOR INFORMATION Corresponding Author *Email: [email protected], [email protected]

ACKNOWLEDGMENT This work was funded by the CNRS, the INSERM, the Université de Strasbourg, the Region Alsace, the Hopital Civil de Strasbourg, Instruct (part of the European Strategy Forum of Research Infrastructures; ESFRI), the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01 and the Fondation pour la Recherche Medicale (Code FRM: SPF20121226275). The crystallographic experiments were performed on the X06DA beamline at the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. In particular, we thank E. Panepucci and V. Olieric for their help on the beamline. This work was supported by the research project RVO 61388963, awarded by the Academy of Sciences of the Czech Republic. JF, JŘ, ML and PH acknowledge the financial support of the Czech Science Foundation (grant number P208/12/G016). We also thank the Gilead Sciences and IOCB Research Center for financial support. This work was also supported by the Operational Program Research and Development for Innovations—European Science Fund (grant number CZ.1.05/2.1.00/03.0058). MHK acknowledges the kind support provided by the Alexander von Humboldt Foundation.

REFERENCES

Page 6 of 7

1. Metrangolo, P., and Resnati, G. (2001) Halogen bonding: A paradigm in supramolecular chemistry. Chem. Eur. J. 7, 2511-2519. 2. Lu, Y., Liu, Y., Xu, Z., Li, H., Liu, H., and Zhu, W. (2012) Halogen bonding for rational drug design and new drug discovery. Expert Opin. Drug Discov., 7, 375-383 3. Wilcken, R, Zimmermann, M. O., Lange, A., Joerger A.C., and Boeckler F. M. (2013) Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology, J. Med. Chem. 56, 13631388 4. Scholfield, M. R., Zanden, C. M. V., Carter M., and Ho P. S. (2013) Halogen bonding (X-bonding): A biological perspective, Protein Sci., 22, 139-152. 5. Clark, T., Hennemann, M., Murray, J. S., and Politzer P. (2007) Halogen bonding: The σ-hole. J. Mol. Model. 13, 291-296 6. Kolář, M. H., Carloni, P., and Hobza, P. Phys Chem Chem Phys (2014) Statistical analysis of σ-holes: a novel complementary view on halogen bonding 16, 19111-19114. 7. Riley, K. E., Murray, J. S., Fanfrlík, J., Řezáč, J., Solá, R. J., Concha, M. C., Ramos, F. M. , and Politzer, P. (2011) Halogen bond tunability I: The effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine, J. Mol. Model. 17, 3309–3318. 8. Kolář, M., Hostaš, J., and Hobza, P. (2014) The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole. Phys, Chem. Chem. Phys, 16, 9987-9996. 9. Hardegger, L. A., Kuhn, B., Spinnler, B., Anselm, L., Ecabert, R., Stihle, M., Gsell, B., Thoma, R., Diez, J., Benz, J., et al. (2011) Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions, Angew. Chem. 123, 329-334; Angew. Chem. Int. Ed. 50, 314318. 10. Fanfrlík, J., Kolář, M., Kamlar, M., Hurny, D., Ruiz, F. X., Cousido-Siah, A. Mitschler, A., Řezáč, J., Munusamy, E., Lepšík M., et al. (2013) The modulation of aldose reductase inhibition by halogen bond tuning, ACS Chem. Biol., 2013, 8, 2484-2492. 11. Podjarny, A., Cachau, R. E., Schneider, T., Van Zandt, M., and Joachimiak, A. (2004) Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding, Cell Mol. Life Sci. 61, 763–773. 12. Albert, A., and Serjeant, E. P. (1962) Ionization Constants of Acids and Bases; Methuen: London. 13. Steuber, H., Heine A., and Klebe, G. (2007) Structural and Thermodynamic Study on Aldose Reductase: Nitro-substituted Inhibitors with Strong Enthalpic Binding Contribution, J. Mol. Biol. 368, 618–638. 14. Muzet N, Guillot B, Jelsch C, Howard E, and Lecomte C. (2003) Electrostatic complementarity in an aldose reductase complex from ultrahigh-resolution crystallography and first-principles calculations. Proc Natl Acad Sci U S A. 100, 8742-8747. 15. Lepšík, M., Řezáč, J., Kolář, M., Pecina, A., Hobza P., Fanfrlík, J. (2013) The semiempirical quantum mechanical scoring function for in silico drug design, ChemPlusChem, 78, 921-931. 16. Sheldrick, G.M. & Schneider, T.R. (1997) SHELXL: Highresolution refinement. Methods Enzymol. 277, 319-343. 17. Albert, A., and Serjeant, E. P. (1962) Ionization Constants of Acids and Bases; Methuen: London. 18. Riley E. K., Pitonak, M., Jurecka, P., and Hobza, P. (2010) Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories, Chem. Rev., 110, 5023-5063. 19. Riley, K. E., Murray, J. S., Politzer, P., Concha, M. C., and Hobza, P. (2009) Br...O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone, J. Chem. Theory Comput. 5, 155-163. 20. Marenich, A. V., Cramer, C. J., and Truhlar, D. G. (2009) Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions, J. Phys. Chem. B 113, 6378−6396. 21. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., et al. Gaussian 09, Inc., Wallingford CT, 2009. 22. Kolář, M., Hobza, P. (2012) On extension of the current biomolecular empirical force field for the description of halogen bonds, J. Chem. Theory Comput. 8, 1325-1333.


Page 7 of 7

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


23. Kolář, M., Hobza, P., Bronowska, A. K. (2013) Chem. Commun. Plugging the explicit σ-holes in molecular docking, 49, 981-983. 24. Kolář, M., Fanfrlík, J. and Hobza, P. (2011) Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation, J. Phys. Chem. B, 115, 4718-4724. 25. Kolář, M., Fanfrlík, J., Lepšík,M., Forti, F., Luque, J. F. and Hobza, P. (2013) Assessing the accuracy and performance of implicit solvent models for drug molecules: Conformational ensemble approaches, J. Phys. Chem. B, 117, 5950-5962. 26. Koch, C., Heine, A., and Klebe, G. (2011), Tracing the Detail: How Mutations Affect Binding Modes and Thermodynamics Signatures of Closely Related Aldose Reductase Inhibitors, J. Mol. Biol. 406, 700-712. 27. Koch, C., Heinea, A., and Klebe, G. (2011), Radiation Damage reveals promising interaction position. J Synchrotron Radiat. 18, 782-789. 28. Howard, E. I., Sanishvili, R., Cachau, R. E., Mitschler, A., Chevrier, B., Barth, P., Lamour, V., Van Zandt, M., Sibley, E., Bon, C., et al. (2004) Ultrahigh resolution drug design I: Details of interactions in human aldose reductase-inhibitor complex at 0.66 A, Proteins, 55, 792– 804. 29. Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242. 30. Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., GrosseKunstleve, R. W., et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr. 66, 213-221. 31. Rezac, J., and Hobza, P. (2012) Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods, J. Chem. Theory Comput. 8, 141–151. 32. Rezac, J., and Hobza, P. (2011) A halogen-bonding correction for the semiempirical PM6 method, Chemical Physics Letters 506, 286–289. 33. Tsui, V., and Case, D. A. (2000) Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model, J. Am. Chem. Soc. 122, 2489-2498.


The Effect of Halogen-to-Hydrogen Bond Substitution on Human

Recommend Documents