Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity

Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation

TMPRSS2 (transmembrane serine proteinase 2) is a multidomain type II transmembrane serine protease that cleaves the surface glycoprotein HA (haemagglutinin) of influenza viruses with a monobasic cleavage site, which is a prerequisite for virus fusion and propagation. Furthermore, it activates the fusion protein F of the human metapneumovirus and the spike protein S of the SARS-CoV (severe acute respiratory syndrome coronavirus). Increased TMPRSS2 expression was also described in several tumour entities. Therefore TMPRSS2 emerged as a potential target for drug design. The catalytic domain of TMPRSS2 was expressed in Escherichia coli and used for an inhibitor screen with previously synthesized inhibitors of various trypsin-like serine proteases. Two inhibitor types were identified which inhibit TMPRSS2 in the nanomolar range. The first series comprises substrate analogue inhibitors containing a 4-amidinobenzylamide moiety at the P1 position, whereby some of these analogues possess inhibition constants of approximately 20 nM. An improved potency was found for a second type derived from sulfonylated 3-amindinophenylalanylamide derivatives. The most potent derivative of this series inhibits TMPRSS2 with a K(i) value of 0.9 nM and showed an efficient blockage of influenza virus propagation in human airway epithelial cells. On the basis of the inhibitor studies, a series of new fluorogenic substrates containing a D-arginine residue at the P3 position was synthesized, some of them were efficiently cleaved by TMPRSS2.

Anion-π interactions in supramolecular architectures

The study of the noncovalent force between π-acidic aromatic systems and anions, referred to as the anion-π interaction, has recently emerged as a new branch of supramolecular chemistry. The anion-π contact is complementary to the cation-π interaction, a prominent noncovalent force involved in protein structure and enzyme function. Until recently, the scientific community had overlooked the anion-π interaction due to its ostensibly counterintuitive nature. Pioneering theoretical studies in 2002, however, established that anion-π interactions are energetically favorable (~20-70 kJ/mol) and prompted a flurry of reports in support of their existence. The interest in anion-π contacts was further fueled by the importance of anions in key chemical and biological processes and the involvement of π-rings in anion recognition and transport. Anion-π interactions hold great promise for the design of selective anion receptors, hosts or scaffolds, colorimetric sensors, and catalysts and may also affect biological functions. Currently, the area of anion-π research is highly topical in the scientific community and on a meteoric rise in the chemical literature. This Account highlights our leading findings in this burgeoning area. Our work has focused on comprehensive investigations of several unprecedented supramolecular systems, in which the anions and their close anion-π contacts are the driving elements of the final architectures. We surveyed several heterocyclic π-acidic aromatic systems amenable to anion-π contacts and explored the subtle interplay between ligand π-acidity, anion identity, and metal ions in mediating the ensuing self-assembled architectures. The reactions we performed between solvated first-row transition metal ions and the π-acidic ligands bptz (3,6-bis(2-pyridyl)-1,2,4,5-tetrazine) or bmtz (3,6-bis(2-pyrimidyl)-1,2,4,5-tetrazine) resulted in unprecedented metallacycles. Our investigations revealed that the identity of the encapsulated ion dictates the metallacycle nuclearity and close anion-π contacts are critical for the metallacycle stability. Our X-ray crystallographic, NMR spectroscopic, and mass spectrometric (MS) studies demonstrated that the tetrahedral ([BF4](-), [ClO4](-)) and octahedral ([SbF6](-), [AsF6](-), [PF6](-)) anions template discrete molecular squares and pentagons, respectively. The metal ions occupy the vertices, and bptz or bmtz moieties span the edges of the metallacycles. The encapsulated anions occupy the π-acidic cavities of the metallacycles and establish multiple close directional F/O···C(tetrazine) contacts with the edges. The observation of notable (19)F solid-state NMR chemical shifts reflects the short contacts of the encapsulated anions, findings that we corroborated by DFT calculations. The solution NMR data support the conclusion that bona fide metallacycle templation and interconversion between the metallacycles in solution occurs only in the presence of the appropriate anions. The NMR, MS, and CV data underscore the remarkable metallapentacycle stability despite the angle strain inherent in pentagons formed by octahedral metal ions. The low anion activation energies of encapsulation (ΔG(‡) ~ 50 kJ/mol) suggest that anion-π contacts assist the anion templation. We also studied reactions of Ag(I)X (X(-) = [PF6](-), [AsF6](-), [SbF6](-), [BF4](-)) with bptz or bppn (3,6-bis(2-pyridyl)-1,2-pyridazine) to assess the effect of the ligand π-acidity on the preferred structures. The X-ray data revealed that the higher π-acidity of the tetrazine ring in bptz leads to propeller-type products [Ag2(bptz)3](2+) exhibiting prominent short anion-π contacts. By contrast, the less π-acidic bppn preferentially favors grids [Ag4(bppn)4](4+) which exhibit maximized π-π interactions. Finally, we explored the reactions of the extended π-acidic heterocycle HAT(CN)6 (1,4,5,8,9,12-hexaazatriphenylene-hexacarbonitrile) with the Cl(-), Br(-), I(-) ions which lead to highly colored solutions/crystals. X-ray crystallographic studies of the HAT(CN)6/halide complexes revealed unprecedented multisite short peripheral charge-transfer and centroid anion-π contacts. In solution, the charge-transfer contacts were evidenced by electronic absorption, (13)C and halogen NMR, as well as MS data. The distinctly colored complex entities exhibit extraordinarily high association constants, which render them promising for anion-sensing receptor applications.

ID-Score: a new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions

Scoring functions have been widely used to assess protein-ligand binding affinity in structure-based drug discovery. However, currently commonly used scoring functions face some challenges including poor correlation between calculated scores and experimental binding affinities, target-dependent performance, and low sensitivity to analogues. In this account, we propose a new empirical scoring function termed ID-Score. ID-Score was established based on a comprehensive set of descriptors related to protein-ligand interactions; these descriptors cover nine categories: van der Waals interaction, hydrogen-bonding interaction, electrostatic interaction, π-system interaction, metal-ligand bonding interaction, desolvation effect, entropic loss effect, shape matching, and surface property matching. A total of 2278 complexes were used as the training set, and a modified support vector regression (SVR) algorithm was used to fit the experimental binding affinities. Evaluation results showed that ID-Score outperformed other selected commonly used scoring functions on a benchmark test set and showed considerable performance on a large independent test set. ID-Score also showed a consistent higher performance across different biological targets. Besides, it could correctly differentiate structurally similar ligands, indicating higher sensitivity to analogues. Collectively, the better performance of ID-Score enables it as a useful tool in assessing protein-ligand binding affinity in structure-based drug discovery as well as in lead optimization.

Halogen bonding (X-bonding): a biological perspective

The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure-energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials.

Competition of hydrogen, halogen, and pnicogen bonds in the complexes of HArF with XH2P (X=F, Cl, and Br)

A theoretical study of the complexes formed between HArF and XH2P (X=F, Cl, and Br) has been carried out using ab initio methods (MP2/aug-cc-pVDZ, MP2/aug-cc-pVTZ, and CCSD(T)/aug-cc-pVTZ). Three minima were found, which correspond to a hydrogen-bonded complex (I), a pnicogen-bonded complex (II), and a halogen-bonded complex (III). The pnicogen-bonded complex is the most stable, followed by the hydrogen-bonded complex, and the halogen-bonded complex is the least stable. The Ar-H bond is enhanced in FH2P-HArF-I complex and exhibits a blue shift, while it is weakened in ClH2P-HArF-I and BrH2P-HArF-I complexes and shows a red shift. A blue shift is also found for the distant Ar-H bond in the halogen-bonded and pnicogen-bonded complexes. These complexes have been understood with the electrostatic potentials and symmetry adapted perturbation theory (SAPT) method.

Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory

In this work we assess the performance of different dispersion-corrected density functional theory (DFT) approaches (M06, M06-2X, DFT-D3, and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers X2···X2 and X2···Ar (for X = F, Cl, Br, and I), as well as the prototype halogen bonded complexes H3CX···OCH2 (X = Cl, Br, I). In spite of the generally good performance of all tested methods for weakly bound systems, their performance for halogen-containing compounds varies largely. We find maximum errors in the energies with respect to the CCSD(T) reference values of 0.13 kcal/mol for DCACP, 0.22 kcal/mol for M06-2X, 0.47 kcal/mol for BLYP-D3, and 0.77 kcal/mol for M06. The root-mean-square deviations are 0.13 kcal/mol for DCACP and M06-2X, 0.44 kcal/mol for M06, and 0.51 kcal/mol for BLYP-D3.

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

We present a set of 40 noncovalent complexes of organic halides, halohydrides, and halogen molecules where the halogens participate in a variety of interaction types. The set, named X40, covers electrostatic interactions, London dispersion, hydrogen bonds, halogen bonding, halogen-π interactions, and stacking of halogenated aromatic molecules. Interaction energies at equilibrium geometries were calculated using a composite CCSD(T)/CBS scheme where the CCSD(T) contribution is calculated using triple-ζ basis sets with diffuse functions on all atoms but hydrogen. For each complex, we also provide 10 points along the dissociation curve calculated at the CCSD(T)/CBS level. We use this accurate reference to assess the accuracy of selected post-HF methods.

Highly enantioselective synthesis of 1,2,3-substituted cyclopropanes by using α-Iodo- and α-chloromethylzinc carbenoids

Herein, we report the enantio- and diastereoselective formation of trans-iodo- and trans-chlorocyclopropanes from α-iodo- and α-chlorozinc carbenoids by using a dioxaborolane-derived chiral ligand. The synthetically useful iodocyclopropane building blocks were derivatized by an electrophilic trapping of the corresponding cyclopropyl lithium species or a Negishi coupling to give access to a variety of enantioenriched 1,2,3-substituted cyclopropanes. The synthetic utility of this method was demonstrated by the formal synthesis of an HIV-1 protease inhibitor. In addition, the related stereoselective bromocyclopropanation was also investigated. New insights about the relative electrophilicity of haloiodomethylzinc carbenoids are also presented.

3D-QSAR based on quantum-chemical molecular fields: toward an improved description of halogen interactions

Current 3D-QSAR methods such as CoMFA or CoMSIA make use of classical force-field approaches for calculating molecular fields. Thus, they can not adequately account for noncovalent interactions involving halogen atoms like halogen bonds or halogen-π interactions. These deficiencies in the underlying force fields result from the lack of treatment of the anisotropy of the electron density distribution of those atoms, known as the "σ-hole", although recent developments have begun to take specific interactions such as halogen bonding into account. We have now replaced classical force field derived molecular fields by local properties such as the local ionization energy, local electron affinity, or local polarizability, calculated using quantum-mechanical (QM) techniques that do not suffer from the above limitation for 3D-QSAR. We first investigate the characteristics of QM-based local property fields to show that they are suitable for statistical analyses after suitable pretreatment. We then analyze these property fields with partial least-squares (PLS) regression to predict biological affinities of two data sets comprising factor Xa and GABA-A/benzodiazepine receptor ligands. While the resulting models perform equally well or even slightly better in terms of consistency and predictivity than the classical CoMFA fields, the most important aspect of these augmented field-types is that the chemical interpretation of resulting QM-based property field models reveals unique SAR trends driven by electrostatic and polarizability effects, which cannot be extracted directly from CoMFA electrostatic maps. Within the factor Xa set, the interaction of chlorine and bromine atoms with a tyrosine side chain in the protease S1 pocket are correctly predicted. Within the GABA-A/benzodiazepine ligand data set, PLS models of high predictivity resulted for our QM-based property fields, providing novel insights into key features of the SAR for two receptor subtypes and cross-receptor selectivity of the ligands. The detailed interpretation of regression models derived using improved QM-derived property fields thus provides a significant advantage by revealing chemically meaningful correlations with biological activity and helps in understanding novel structure-activity relationship features. This will allow such knowledge to be used to design novel molecules on the basis of interactions additional to steric and hydrogen-bonding features.

Mapping the binding of GluN2B-selective N-methyl-D-aspartate receptor negative allosteric modulators

We have used recent structural advances in our understanding of the N-methyl-d-aspartate (NMDA) receptor amino terminal domain to explore the binding mode of multiple diaryl GluN2B-selective negative allosteric modulators at the interface between the GluN1 and GluN2B amino-terminal domains. We found that interaction of the A ring within the binding pocket seems largely invariant for a variety of structurally distinct ligands. In addition, a range of structurally diverse linkers between the two aryl rings can be accommodated by the binding site, providing a potential opportunity to tune interactions with the ligand binding pocket via changes in hydrogen bond donors, acceptors, as well as stereochemistry. The most diversity in atomic interactions between protein and ligand occur in the B ring, with functional groups that contain electron donors and acceptors providing additional atomic contacts within the pocket. A cluster of residues distant to the binding site also control ligand potency, the degree of inhibition, and show ligand-induced increases in motion during molecular dynamics simulations. Mutations at some of these residues seem to distinguish between structurally distinct ligands and raise the possibility that GluN2B-selective ligands can be divided into multiple classes. These results should help facilitate the development of well tolerated GluN2B subunit-selective antagonists.

The role of structural information in the discovery of direct thrombin and factor Xa inhibitors

The quest for novel medications to treat thromboembolic disorders such as venous thrombosis, pulmonary embolism and stroke received a boost when the 3D structures of two major players in the blood coagulation cascade were determined in 1989 and 1993. Structure-guided design of inhibitors of thrombin (factor IIa, fIIa) and factor Xa (fXa) eventually led to the discovery of potent, selective, efficacious, orally active and safe compounds that proved successful in clinical studies. In 2008, the direct thrombin inhibitor dabigatran etexilate developed by Boehringer Ingelheim became the first novel antithrombotic molecular entity to enter the market in 50 years. Additional compounds targeting factor Xa were subsequently granted marketing authorization or are in late-stage clinical studies. In this review, I use selected case studies to describe the discovery of novel fIIa and fXa inhibitors, with a particular emphasis on the pre-eminent role that structural information played in this process.

Dimerization of β-tryptase inhibitors, does it work for both basic and neutral P1 groups?

The tetrameric folding of β-tryptase and the pair-wise distribution of its substrate binding sites offer a unique opportunity for development of inhibitors that span two adjacent binding sites. A series of dimeric inhibitors with two basic P1 moieties was discovered using this design strategy and exhibited tight-binder characteristics. Using the same strategy, an attempt was made to design and synthesize dimeric inhibitors with two neutral-P1 groups in hope to exploit the dimeric binding mode to achieve a starting point for further optimization. The unsuccessful attempt, however, demonstrated the important role played by Ala190 in neutral-P1 binding and casted further doubt on the possibility of developing neutral-P1 inhibitors for β-tryptase.

Molecular recognition at the active site of factor Xa: cation-π interactions, stacking on planar peptide surfaces, and replacement of structural water

Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.

Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations

Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombinase complex on activated platelets to convert prothrombin to thrombin in coagulation reactions. In the current study, 30-ns MD simulations were performed on both the open and closed states of human FXa. Root mean squares (RMS) fluctuations showed that structural fluctuations concentrated on the loop regions of FXa, and the presence of a ligand in the closed system resulted in larger fluctuations of the gating residues. The open system had a gating distance from 9.23 to 11.33 Å, i.e., significantly larger than that of the closed system (4.69-6.35 Å), which allows diversified substrates of variable size to enter. Although the solvent accessible surface areas (SASA) of FXa remained the same in both systems, the open system generally had a larger total SASA or hydrophobic SASA (or both) for residues surrounding the S4 pocket. Additionally, more hydrogen bonds were formed in the closed state than in the open state of FXa, which is believed to play a significant role in maintaining the closed confirmation of the aryl-binding site. Based on the results of MD simulations, we propose that an induced-fit mechanism governs the functioning of human coagulation FX, which helps provide a better understanding of the interactions between FXa and its substrate, and the mechanism of the conformational changes involved in human coagulation.

Ab initio study of hydroxyl torsional barriers and molecular properties of mono- and di-iodotyrosine

Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.

Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.

Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments

(19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description.