Electrostatic complementarity between proteins and ligands. 3. Structural basis

Summary Electrostatic potential complementarity between ligands and their receptor sites is evaluated by the superposition of the electrostatic potential, generated by the receptor, onto the ligand potential over the ligand van der Waals surface. We would like to examine which structural factors generate this pattern of superposition. Example studies suggest that in many ligand-protein pairs, there exist principal formal charges on each molecule, largely responsible for the electrostatic potential complementarity observed. Electrostatic potential complementarity depends on the relative disposition of these principal charges and the ligand van der Waals surface. Simple mathematical models were constructed to predict the complementarity solely from structural considerations. The essential conditions for electrostatic potential complementarity were elucidated. These can be used in ligand design strategies to obtain an electrostatically optimal ligand.     

Analysis of electrostatic and hydrophobic complementarities between chymotrypsin and avian ovomucoid third domains using molecular electrostatic potential: Effect of residue replacements

Electrostatic and hydrophobic complementarities between chymotrypsin and its inhibitor, avian ovomucoid third domains, were evaluated for eight species, which have different amino acid sequences, using molecular electrostatic potential (MEP) and MEP correlation, and the enzyme-inhibitor interaction was analyzed. The changes in the electrostatic and hydrophobic complementarities caused by the amino acid replacements were reflected clearly in the calculated MEP correlation, and it explained the observed binding association constants correctly. The electrostatic complementarity due to arginine at P′₃ strongly promotes the binding process of the inhibitor, while the hydrophobic complementarity in the P₁ and P′₂ positrons also affects the binding process. It was demonstrated that our method is an effective molecular modeling tool in drug design and protein engineering. © 1996 John Wiley & Sons, Inc.     

Structures and Interligand Interaction Pattern of Phosphoramidite Pd Complexes by NMR Spectroscopy: Modulations in Extended Interaction Surfaces as Stereoselection Mode of a Privileged Class of Ligands

During the last decade, phosphoramidites have been established as a so‐called privileged class of ligands in various transition metal catalyses. However, the interactions responsible for their favorable properties have hitherto remained elusive. To address this issue, the formation trends, structural features, and interligand interaction patterns of several trans‐ and cis‐[PdLL′Cl₂] complexes have been investigated by NMR spectroscopy. The energetic contribution of their interligand interactions has been measured experimentally using the supramolecular balance for transition‐metal complexes. The resulting energetics combined with an analysis of the electrostatic potential surfaces reveal that in phosphoramidites not only the aryl groups but the complete (CH)CH₃Ph moieties of the amine side chains form extended quasi‐planar CH‐π and π‐π interaction surfaces. Application of the supramolecular balance has shown that modulations in these extended interaction surfaces cause energetic differences that are relevant to enantioselective catalysis. In addition, the energetics of these interligand interactions are quite independent of the actual structures of the complexes. This is shown by similar formation and aggregation trends of complexes with the same ligand but different structures. The extended quasi‐planar electrostatic interaction surface of the (CH)CH₃Ph moiety explains the known pattern of successful ligand modulation and the substrate specificity of phosphoramidites. Thus, we propose modulations in these extended CH‐π and π‐π interaction areas as a refined stereoselection mode for these ligands. Based on the example of phosphoramidites, this study reveals three general features potentially applicable to various ligands in asymmetric catalysis. First, specific combinations of alkyl and aryl moieties can be used to create extended anisotropic interaction areas. Second, modulations in these interaction surfaces cause energetic differences that are relevant to catalytic applications. Third, bulky substituents with matching complementary interaction surfaces should not only be considered in terms of steric hindrance but also in terms of attractive and repulsive interactions, a feature that may often be underestimated in asymmetric catalysis.     

Dual pH‐ and Temperature‐Responsive Metallosupramolecular Block Copolymers with Tunable Critical Micelle Temperature by Modulation of the Self‐Assembly of NIR‐Emissive Alkynylplatinum(II) Complexes Induced by Changes in Hydrophilicity and Electrostatic Effects

Terpyridylplatinum(II)‐based metallosupramolecular triblock copolymers with hydrophilic alkynyl ligands have been synthesised and characterised. As a result of the intrinsic properties of Pluronics, reversible temperature‐induced micellisation occurred at high temperature leading to aggregation of the platinum(II) complex moieties through Pt???Pt and π–π interactions, resulting in significant UV/Vis absorption and near‐infrared (NIR) emission spectral changes. The critical micelle temperatures of the complexes were found to vary from 21 to 30 °C due to differences in the hydrophilicity of the alkynyl ligands and the electrostatic repulsions between the positively charged platinum(II) complex moieties. One of the complexes with pH‐responsive CH₂NMe₂ groups on the alkynyl ligand was found to show NIR emission that is sensitive to both pH and temperature. Such dual‐responsive behaviour has been ascribed to the modulation of the self‐assembly of the complex moieties by temperature‐induced micellisation and the changes in the hydrophilicity as well as electrostatic interactions upon protonation/deprotonation of the CH₂NMe₂ groups on the alkynyl ligand.     

Improvement of Ligand Affinity and Thermodynamic Properties by NMR‐Based Evaluation of Local Dynamics and Surface Complementarity in the Receptor‐Bound State

The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand–receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak‐affinity ligands in the receptor‐bound state by forbidden coherence transfer analysis in free‐bound exchange systems (Ex‐FCT), using the interaction between a ligand, a myocyte‐enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system. The Ex‐FCT analyses successfully provided information for the rational design of a ligand with higher affinity and preferable thermodynamic properties for p38α.     

Molecular complexity and its impact on the probability of finding leads for drug discovery.

Using a simple model of ligand-receptor interactions, the interactions between ligands and receptors of varying complexities are studied and the probabilities of binding calculated. It is observed that as the systems become more complex the chance of observing a useful interaction for a randomly chosen ligand falls dramatically. The implications of this for the design of combinatorial libraries is explored. A large set of drug leads and optimized compounds is profiled using several different properties relevant to molecular recognition. The changes observed for these properties during the drug optimization phase support the hypothesis that less complex molecules are more common starting points for the discovery of drugs. An extreme example of the use of simple molecules for directed screening against thrombin is provided.     

A fast and efficient method to generate biologically relevant conformations

Summary Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformation space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography, the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.     

Molecular Simulations using Spherical Harmonics

Computer-aided drug design is to develop a chemical that binds to a target macromolecule known to play a key role in a disease state. In recognition of ligands by their protein receptors, molecular surfaces are often used because they represent the in-teracting part of molecules and they should reflex the comple-mentarity between ligand and receptor. However, assessing the surface complementarity by searching all relative position of two surfaces is often computationally expensive. The comple-mentarity of lobe-hole is very important in protein-ligand inter-actions. Spherical harmonic models based on expansions of spherical harmonic functions were used as a f‘mgerprint to ap-proximate the binding cavity and the ligand, respectively. This defines a new way to identify the complementarity between lobes and holes. The advantage of this method is that two spherical harmonic surfaces to be compared can be defined sep-arately. This method can be used as a filter to eliminate candi-dates among a large number of conformations, and it will speed up the docking procedure. Therefore, it is possible to select complementary ligands or complementary conformations of a ligand and the macromolecules, by comparing their fingerprints previously stored in a database.     

Exploring Supramolecular Self‐Assembly of Tetraarylporphyrins by Halogen Bonding: Crystal Engineering with Diversely Functionalized Six‐Coordinate Tin(L)2–Porphyrin Tectons

This study targets the construction of porphyrin assemblies directed by halogen bonds, by utilizing a series of purposely synthesized Sn(axial ligand)₂–(5,10,15,20‐tetraarylporphyrin) [Sn(L)₂‐TArP] complexes as building units. The porphyrin moiety and the axial ligands in these compounds contain different combinations of complimentary molecular recognition functions. The former bears p‐iodophenyl, p‐bromophenyl, 4′‐pyridyl, or 3′‐pyridyl substituents at the meso positions of the porphyrin ring. The latter comprises either a carboxylate or hydroxy anchor for attachment to the porphyrin‐inserted tin ion and a pyridyl‐, benzotriazole‐, or halophenyl‐type aromatic residue as the potential binding site. The various complexes were structurally analyzed by single‐crystal X‐ray diffraction, accompanied by computational modeling evaluations. Halogen‐bonding interactions between the lateral aryl substituents of one unit of the porphyrin complex and the axial ligands of neighboring moieties was successfully expressed in several of the resulting samples. Their occurrence is affected by structural (for example, specific geometry of the six‐coordinate complexes) and electronic effects (for example, charge densities and electrostatic potentials). The shortest intermolecular I???N halogen‐bonding distance of 2.991 Å was observed between iodophenyl (porphyrin) and benzotriazole (axial ligand) moieties. Manifestation of halogen bonds in these relatively bulky compounds without further activation of the halophenyl donor groups by electron‐withdrawing substituents is particularly remarkable.     

Specific Electrostatic Molecular Recognition in Water

The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure‐biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide–peptide interactions could conveniently be observed by clustering of the small, fluorescently labeled target beads on the surface of larger ligand‐containing beads. Sequences of isolated hits were determined by MS/MS. The interactions of the complex showing the highest affinity were investigated by a novel single‐bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen‐bond complementarities. From MD simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured.     

The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity

Summary Three previous papers in this series have outlined an optimization method for atom assignment in drug design using fragment placement. In this paper the procedure is rigorously tested on a selection of five ligand-protein co-crystals. The algorithm is presented with the molecular graph of the ligand, and the electrostatic/hydrophobic potential of the site, with the aim of creating a placement on the molecular graph which is as electrostatically complementary or hydrophobically similar to the site as possible. Various designer options were tested, including, where appropriate, hydrogen bonding and a restricted number of halogens. In most cases, the placement obtained was at least as good as the native ligand, if not significantly better.     

Ligand atom partial charges assignment for complementary electrostatic potentials

Summary The design of molecules to fit into the active site of receptors is a rapidly developing area of pharmacology and medicinal chemistry. A good ligand needs a suitable geometry and also appropriate electrostatic properties. The electrostatic properties of the ligand should complement those of the receptor. We present a method for the assignment of atom-centred point charges for a ligand, based on the electrostatic potential of the receptor. These point charges are chosen to give the best possible complementarity to the receptor electrostatic potential over the van der Waals surface of the ligand. We demonstrate that point charges can be chosen to give good electrostatic complementarity, and suggest that a molecule with similar electrostatic properties should bind well to the receptor.     

Dibenzoeilatin: a novel ligand exhibiting remarkable complementary pi-pi stacking interactions

The complex [Ru(bpy)2(dbneil)][PF6]2 forms discrete dimers in solution held by strong pi-pi stacking interactions via its distorted dibenzoeilatin ligand, indicating that planarity is not an obligatory requirement for achieving strong pi-stacking, as long as complementarity between the stacking moieties can be achieved.     

Modelling drugs and receptors using potentials: examples in the GPCRs' domain

Shape complementarity, electrostatic and hydrophobic matching, were used to model drugs and receptors. From known experimental data on alpha1A/alpha2A-adrenergic ligands and alpha1A/alpha2A-adrenoceptors, a model for the ligand binding sites, based on the structure of bacteriorhodopsin as a template, was proposed and built. Agonists and antagonists have overlapping but different binding sites. Emphasis was given on the role of the disulphide bridge and on the role of the sodium site. The model was extended to other G-protein coupled receptors.     

The N?H Functional Group in Organometallic Catalysis

The organometallic approach is one of the most active topics in catalysis. The application of NH functionality in organometallic catalysis has become an important and attractive concept in catalyst design. NH moieties in the modifiers of organometallic catalysts have been shown to have various beneficial functions in catalysis by molecular recognition through hydrogen bonding to give catalyst–substrate, ligand–ligand, ligand–catalyst, and catalyst–catalyst interactions. This Review summarizes recent progress in the development of the organometallic catalysts based on the concept of cooperative catalysis by focusing on the NH moiety.     

Charge optimization of the interface between protein kinases and their ligands

Examining the potential for electrostatic complementarity between a ligand and a receptor is a useful technique for rational drug design, and can demonstrate how a system prioritizes interactions when allowed to optimize its charge distribution. In this computational study, we implemented the previously developed, continuum solvent-based charge optimization theory with a simple, quadratic programming algorithm and the UHBD Poisson-Boltzmann solver. This method allows one to compute the best set of point charges for a ligand or ligand region based on the ligand and receptor shape, and the receptor partial charges, by optimizing the binding free energy obtained from a continuum-solvent model. We applied charge optimization to a fragment of the heat-stable protein kinase inhibitor (PKI) of protein kinase A (PKA), to three flavopiridol inhibitors of CDK2, and to cyclin A which interacts with CDK2 to regulate the cell cycle. We found that a combination of global (involving every charge) and local (involving only charges in a local region) optimization can give useful hints for designing better inhibitors. Although some parts of an inhibitor may already contribute significantly to binding, we found that they could still be the most important targets for modifications to obtain stronger binders. In studying the binding of flavopiridol inhibitors to CDK2, comparable binding affinity could be obtained regardless of whether the net charges of the inhibitors were constrained to -2, -1, 0, 1, or 2 during the optimization. This provides flexibility in inhibitor design when a certain net charge of the inhibitor is desired in addition to strong binding affinity. For the study of the PKA-PKI and CDK2-cyclin A interfaces, we identified residues whose charge distributions are already close to optimal and those whose charge distributions could be refined to further improve binding.     

配体分子结构对Pd(Ⅱ)-Phen-PCA体系堆积作用的影响

用pH电位滴定法测定了含l，10-邻菲咯啉(Phen)和羧酸(CA)配体的三元混配配合物Pd(Phen)(CA)体系的稳定常数，比较和讨论了各种三元混配配合物之间的稳定性差异．实验结果表明，在三元混配配合物Pd(Phen)(PCA)中(PCA为苯基羧酸)存在分子内芳环堆积作用，堆积程度依赖于苯基和配位的羧酸根之间的亚甲基数目，其中以2-苯乙酸和3-苯丙酸与邻菲咯啉为最佳堆积．     

Synthesis and characterization of bioorganometallic conjugates composed of NCN-pincer platinum(II) complexes and uracil derivatives

The conjugation of the NCN-pincer platinum(II) complexes as an oraganometallic compound and the uracil derivatives as a nucleobase was demonstrated to give the corresponding bioorganometallics. The NCN-pincer ligands bearing the 6-ethynyl-1-octyluracil, 5-ethynyl-1-octyluracil, and the furanopyrimidine moiety were synthesized. In a crystal state, the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety was found to form a hydrogen-bonded dimer through intermolecular hydrogen bonds between the uracil moieties, which was connected through π-π interaction between the uracil and benzene moieties of the NCN-pincer ligand. The reaction of the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety with [Pt(tolyl-4)₂(SEt₂)]₂ led to the formation of the NCN-pincer platinum(II) complex bearing the 6-ethynyl-1-octyluracil moiety. The NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety was obtained by the reaction of the NCN-pincer ligand bearing the furanopyrimidine moiety with [Pt(tolyl-4)₂(SEt₂)]₂. The single-crystal X-ray structure determination of the NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety revealed the formation of the furanopyrimidine ring and the π stack dimer between the furanopyrimidine and benzene moieties of the NCN-pincer ligand in the crystal packing. The NCN-pincer platinum(II) complexes bearing the 6-ethynyl-1-octyluracil moiety or the furanopyrimidine moiety exhibited emission in both solution and solid states.