Structure Elucidation of Helical Aromatic Foldamer–Protein Complexes with Large Contact Surface Areas

The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein–protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Ų of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein–foldamer hydrophobic contacts. In addition, foldamer–foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.     

A Study of the Solvation Structure of l‐Leucine in Alcohol–Water Binary Solvents through Molecular Dynamics Simulations and FTIR and NMR Spectroscopy

The solvation structures of l ‐leucine (Leu) in aliphatic‐alcohol–water and fluorinated‐alcohol–water solvents are elucidated for various alcohol contents by using molecular dynamics (MD) simulations and IR, and ¹H and ¹³C NMR spectroscopy. The aliphatic alcohols included methanol, ethanol, and 2‐propanol, whereas the fluorinated alcohols were 2,2,2‐trifluoroethanol and 1,1,1,3,3,3‐hexafluoro‐2‐propanol. The MD results show that the hydrophobic alkyl moiety of Leu is surrounded by the alkyl or fluoroalkyl groups of the alcohol molecules. In particular, TFE and HFIP significantly solvate the alkyl group of Leu. IR spectra reveal that the Leu C?H stretching vibration blueshifts in fluorinated alcohol solutions with increasing alcohol content, whereas the vibration redshifts in aliphatic alcohol solutions. When the C?H stretching vibration blueshifts in the fluorinated alcohol solutions, the hydrogen and carbon atoms of the Leu alkyl group are magnetically shielded. Consequently, TFE and HFIP molecules may solvate the Leu alkyl group through the blue‐shifting hydrogen bonds.     

A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II

We present in this article a case study on the thermodynamics of binding to human carbonic anhydrase II (HCA II) by three well-known inhibitors, viz. (a) acetazolamide (AZM) that directly binds to the catalytic Zn(II) ion at the active site, (b) non-zinc binding 6-hydroxy-2-thioxocoumarin (FC5) (c) 2-[(S)-benzylsulfinyl]benzoic acid (3G1). In each case, the crystal structure or its analogue of inhibitor-bound HCA II has been used to perform classical molecular dynamics (MD) simulation in water till . AZM and FC5 are found to undergo repeated binding and unbinding with markedly different dynamics from the partially buried, substrate-binding hydrophobic pocket near the active site. 3G1, on the other hand, is found to remain mostly at its crystallographic binding site occluded from the active site of HCA II. The associated binding free energies ( ) have been computed using the known MM/GBSA method and compared to the available experimental data. Our results show that encounters several issues including limited sampling of multiple binding sites and incorrect prediction of the affinity of the chosen ligands. Possible use of the simulation results in further construction of Markov state models is also discussed.     

Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution

In the search of molecules that could recognize sizeable areas of protein surfaces, a series of ten helical aromatic oligoamide foldamers was synthesized on solid phase. The foldamers comprise three to five monomers carrying various proteinogenic side chains, and exist as racemic mixtures of interconverting right‐handed and left‐handed helices. Functionalization of the foldamers by a nanomolar ligand of human carbonic anhydrase II (HCA) ensured that they would be held in close proximity to the protein surface. Foldamer–protein interactions were screened by circular dichroism (CD). One foldamer displayed intense CD bands indicating that a preferred helix handedness is induced upon interacting with the protein surface. The crystal structure of the complex between this foldamer and HCA could be resolved at 2.1 Å resolution and revealed a number of unanticipated protein–foldamer, foldamer–foldamer, and protein–protein interactions.     

The binding of human carbonic anhydrase II by functionalized folded polypeptide receptors

Several receptors for human carbonic anhydrase II (HCAII) have been prepared by covalently attaching benzenesulfonamide carboxylates via aliphatic aminocarboxylic acid spacers of variable length to the side chain of a lysine residue in a designed 42 residue helix-loop-helix motif. The sulfonamide group binds to the active site zinc ion of human carbonic anhydrase II located in a 15 A deep cleft. The dissociation constants of the receptor-HCAII complexes were found to be in the range from low micromolar to better than 20 nM, with the lowest affinities found for spacers with less than five methylene groups and the highest affinity found for the spacer with seven methylene groups. The results suggest that the binding is a cooperative event in which both the sulfonamide residue and the helix-loop-helix motif contribute to the overall affinity.     

The paradoxical thermodynamic basis for the interaction of ethylene glycol, glycine, and sarcosine chains with bovine carbonic anhydrase II: an unexpected manifestation of enthalpy/entropy compensation

This paper describes a systematic study of the thermodynamics of association of bovine carbonic anhydrase II (BCA) and para-substituted benzenesulfonamides with chains of oligoglycine, oligosarcosine, and oligoethylene glycol of lengths of one to five residues. For all three of these series of ligands, the enthalpy of binding became less favorable, and the entropy less unfavorable, as the chain length of the ligands increased. The dependence on chain length of the enthalpy was almost perfectly compensated by that of the entropy; this compensation resulted in dissociation constants that were independent of chain length for the three series of ligands. Changes in heat capacity were independent of chain length for the three series and revealed that the amount of molecular surface area buried upon protein-ligand complexation did not increase with increasing chain length. Taken together, these data refute a model in which the chains of the ligands interact hydrophobically with the surface of BCA. To explain the data, a model is proposed based on decreasing "tightness" of the protein-ligand interface as the chain length of the ligand increases. This decreasing tightness, as the chain length increases, is reflected in a less favorable enthalpy (due to fewer van der Waals contacts) and a less unfavorable entropy (due to greater mobility of the chain) of binding for ligands with long chains than for those with short chains. Thus, this study demonstrates a surprising example of enthalpy/entropy compensation in a well-defined system. Understanding this compensation is integral to the rational design of high-affinity ligands for proteins.     

A new synthesis of difluoromethanesulfonamides--a novel pharmacophore for carbonic anhydrase inhibition

Preparation of the key intermediate carboxydifluoromethanesulfonamide provides direct synthetic access to a wide range of novel difluoromethanesulfonamides, including the acetazolamide analogue (2-ethanoylamino-1,3,4-thiadiazol-5-yl)-difluoromethanesulfonamide. Their water solubility and stability, ether partition coefficient, pK(a) and submicromolar dissociation constants for human carbonic anhydrase isozyme II (HCA II) make them promising candidates for topical glaucoma therapy.     

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.     

Water‐Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein–ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water‐mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy‐driven or entropy‐driven. Our findings highlight a possible asymmetry in protein–ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.     

A versatile polypeptide platform for integrated recognition and reporting: affinity arrays for protein-ligand interaction analysis

A molecular platform for protein detection and quantification is reported in which recognition has been integrated with direct monitoring of target-protein binding. The platform is based on a versatile 42-residue helix-loop-helix polypeptide that dimerizes to form four-helix bundles and allows site-selective modification with recognition and reporter elements on the side chains of individually addressable lysine residues. The well-characterized interaction between the model target-protein carbonic anhydrase and its inhibitor benzenesulfonamide was used for a proof-of-concept demonstration. An affinity array was designed where benzenesulfonamide derivatives with aliphatic or oligoglycine spacers and a fluorescent dansyl reporter group were introduced into the scaffold. The affinities of the array members for human carbonic anhydrase II (HCAII) were determined by titration with the target protein and were found to be highly affected by the properties of the spacers (dissociation constant Kd=0.02-3 microM). The affinity of HCAII for acetazolamide (Kd=4 nM) was determined in a competition experiment with one of the benzenesulfonamide array members to address the possibility of screening substance libraries for new target-protein binders. Also, successful affinity discrimination between different carbonic anhydrase isozymes highlighted the possibility of performing future isoform-expression profiling. Our platform is predicted to become a flexible tool for a variety of biosensor and protein-microarray applications within biochemistry, diagnostics and pharmaceutical chemistry.     

Protein crystal structures with ferrocene and ruthenocene-based enzyme inhibitors

We have determined the protein X-ray crystal structures of four organometallic inhibitors in complex with their target enzyme carbonic anhydrase II. The barrel-shaped hydrophobic ferrocene and ruthenocene moieties have provided a structure-based avenue to better occupy the hydrophobic binding patch within the enzyme active site.     

Synthesis,spectroscopic characterization,crystal structure,density functional theory studies and biological properties of coordination complex Ni(II) 2-fluorobenzoate with 3-hydroxypyridine

A novel Ni(II) complex containing 2-fluorobenzoate and 3-hydroxypyridine ligands was synthesized and characterized using elemental analysis, Fourier transform infrared (FT-IR) spectroscopy and single-crystal X-ray diffraction. FT-IR peaks show that the carboxylate group from 2-fluorobenzoate has a monodentate coordination mode. The coordination environment around the Ni²⁺ ion is of distorted octahedral geometry. The octahedral geometry consists of a total of four oxygen atoms from two carboxylate groups of two fluorobenzoate anions, two water molecules and two nitrogen atoms from two 3-hydroxypyridine ligands. The complex shows excellent inhibitory effects against some metabolic enzymes. K_i values for the complex were found as 108.17 ± 25.63, 124.88 ± 36.20, 28.11 ± 2.87, 20.95 ± 5.65 and 32.63 ± 9.67 μM against human carbonic anhydrase I, human carbonic anhydrase II, α-glycosidase, acetylcholinesterase and butyrylcholinesterase, respectively. In addition, geometry optimization and vibration frequencies were calculated, and single point energy was studied based on optimization. Experimental and theoretical data were compared. The B3LYP/6-31G(d,p) basis set was used for all calculations.     

Residual ligand entropy in the binding of p-substituted benzenesulfonamide ligands to bovine carbonic anhydrase II

In studies on the thermodynamics of ligand-protein interactions, it is often assumed that the configurational and conformational entropy of the ligand is zero in the bound state (i.e., the ligand is rigidly fixed in the binding pocket). However, there is little direct experimental evidence for this assumption, and in the case of binding of p-substituted benzenesulfonamide inhibitors to bovine carbonic anhydrase II (BCA II), the observed thermodynamic binding signature derived from isothermal titration calorimetry experiments leads indirectly to the conclusion that a considerable degree of residual entropy remains in the bound ligand. Specifically, the entropy of binding increases with glycine chain length n, and strong evidence exists that this thermodynamic signature is not driven by solvent reorganization. By use of heteronuclear (15)N NMR relaxation measurements in a series (n = 1-6) of (15)N-glycine-enriched ligands, we find that the observed thermodynamic binding signature cannot be explained by residual ligand dynamics in the bound state, but rather results from the indirect influence of ligand chain length on protein dynamics.     

Bicarbonate as a proton donor in catalysis by Zn(II)- and Co(II)-containing carbonic anhydrases.

Catalysis of (18)O exchange between CO(2) and water catalyzed by a Co(II)-substituted mutant of human carbonic anhydrase II is analyzed to show the rate of release of H(2)(18)O from the active site. This rate, measured by mass spectrometry, is dependent on proton transfer to the metal-bound (18)O-labeled hydroxide, and was observed in a site-specific mutant of carbonic anhydrase II in which a prominent proton shuttle residue His64 was replaced by alanine, which does not support proton transport. Upon increasing the concentration of bicarbonate, the rate of release of H(2)(18)O increased in a saturable manner to a maximum of 4 x 10(5) s(-)(1), consistent with proton transfer from bicarbonate to the Co(II)-bound hydroxide. The same mutant of carbonic anhydrase containing Zn(II) had the rate of release of H(2)(18)O smaller by 10-fold, but rate of interconversion of CO(2) and HCO(3)(-) about the same as the Co(II)-containing enzyme. These data as well as solvent hydrogen isotope effects suggest that the bicarbonate transferring the proton is bound to the cobalt in the enzyme. The enhancement of (18)O exchange caused by increasing bicarbonate concentration during catalysis by the Zn(II)-containing carbonic anhydrase from the archaeon Methanosarcina thermophila suggests that a very similar mechanism for proton donation by bicarbonate occurs with this wild-type enzyme.     

A caged hydrophobic inhibitor of carbonic anhydrase II

[formula: see text] A tight-binding, hydrophobic inhibitor of carbonic anhydrase II has been masked with a water-solubilizing, photolabile group derived from o-nitrophenylglycine. This caged inhibitor represents our first effort at the site-specific delivery of prodrugs that can be activated by light. Via this approach, we have begun to address the problems of water insolubility and systemic side effects on administration of tight-binding inhibitors of carbonic anhydrase.     

Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II

In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.     

Spacer-dependent structural and physicochemical diversity in copper(II) complexes with salicyloyl hydrazones: a monomer and soluble polymers

Complexation of copper(II) with a series of heterodonor chelating Schiff bases (LL) of salicylic acid hydrazide and aliphatic or cycloaliphatic ketones affords soluble one-dimensional (1D) metallopolymers containing Schiff bases as bridging ligands. Single-crystal X-ray diffraction results reveal nanometer-sized metallopolymeric wires [Cu(μ-LL)(2)](n) with off-axis linkers and a zigzag geometry. Octahedrally coordinated copper centers, exhibiting a Jahn-Teller distortion, are doubly bridged by two Schiff-base molecules in the μ(2)-η(1),η(2) coordination mode. The use of dibutylketone with long alkyl chains as a component for Schiff base formation leads to a distorted square planar monomeric copper(II) complex [Cu(LL)(2)], as evidenced by its X-ray crystal structure. The compounds are characterized by elemental analyses and IR and UV-vis spectroscopy, as well as magnetic susceptibility and cyclic voltammetry measurements. Electrochemical studies on the complexes reveal an existence of polymeric and monomeric forms in solution and the dependence of Cu(II)/Cu(I) reduction potentials on alkyl groups of salicyloyl hydrazone ligands. Polymeric complexes form conducting films on Pt electrodes upon multicycle potential sweeps.     

2,5-双取代烷基苯磺酸钠胶束微结构的1H NMR研究

利用核磁共振化学位移变化, 自旋-自旋弛豫和2D NOESY(two-dimensional nuclear Overhauser enhancement spectroscopy)研究了一系列新合成的双取代烷基苯磺酸盐的胶束化. 结果表明, 邻位取代的是正烷烃链, 间位取代的是支烷烃链. 而且, 邻位取代的烷烃链越长, 参与形成胶束疏水核表面层的亚甲基个数越多. 因此, 每个分子在饱和吸附的油水界面上的面积越大. 间位取代的分支链在胶束疏水核中堆积得没有邻位取代的正烷烃链紧密. 分支链越短, 堆积得越不紧密. 描述了胶束中分子的相对排列.     

A selectivity study of benzenesulfonamide derivatives on human carbonic anhydrase II/IX by 3D-QSAR,Molecular Docking and Molecular Dynamics Simulation

Nowadays, different approaches have been pursued with the intent to develop sulfonamide-like carbonic anhydrase inhibitors that possess better selectivity profiles toward the different human isoforms of the enzyme. Here, we used conventional 3D-QSAR methods, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and Topomer CoMFA, to construct three-dimensional quantitative structure-activity relationship (3D-QSAR) models for benzenesulfonamide derivatives as human carbonic anhydrase (hCA) II/IX inhibitors. The theoretical models had good reliability (R²>0.75) and predictability (Q²>0.55), and the contour maps could graphically present the contributions of the force fields for activity and identify the structural divergence between human carbonic anhydrase II inhibitors and human carbonic anhydrase IX inhibitors. Consequently, we explored the selectivity of inhibitor for human carbonic anhydrase II and IX through molecular docking, and the difference of activity coincides with the potential binding mode well. According to the results of the predicted values and the molecule docking, we found that the inhibitors published in the literature had stronger inhibition on the hCA IX; based on the theoretical models, we designed seven new compounds with good potential activity and reasonably good ADMET profile, which could selectively inhibit hCA IX. Molecular Dynamics Simulation showed that newly-designed compound D7 had good selectivity on hCA IX. The findings from 3D-QSAR and docking studies maybe helpful in the rational drug design of isoform-selective inhibitors.     

Studying how different terminal groups change the motion of H2NSO2C6H4CONH(EG)3R when bound to the active site of human carbonic anhydrase II

Molecular dynamics simulations have been used to explore the motions of series of ligands containing coupled benzenesulfonamide and oligoethylene glycol moieties (H2NSO2C6H4CONH(CH2-CH2OCH2CH2OCH2CH2)R+; R+ = NH3+, NHCOCH2NH3+, NHCOCH(CH2Ph)NH3+) bound at the active site of human carbonic anhydrase II (HCAII; E.C. 4.2.1.1). These complexes have been examined previously by X-ray crystallography; the locations of the terminal groups of these ligands were not defined in the crystal structures. These stimulations, carried out in the presence of water, provide dynamic information about the motion of the bound ligand that supplements the quasistatic information from crystallography. Our results suggested that the Gly and Phe groups of these ligands interacted weakly with the protein adjacent to the active site. Quantitative estimates of energies of binding did not correlate usefully with observed free energies of binding, but in the absence of information about entropies, it is not possible to tell if the lack of correlation between calculated energies and observed free energies represents inaccuracies in the energies, or a compensation between enthalpies and entropies. When the terminal Phe group was placed near a previously identified hydrophobic patch in the active site (Phe20 and Pro202) the average conformation of the ligand inferred from this simulation was inconsistent with that from the crystal structure; this result illustrates the problems of misleading local minima in these types of simulations.