Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly

Metathesis Reactions of Pyrazolotriazinones Generate Dynamic Combinatorial Libraries

[reaction: see text] Reversible metathesis reactions of pyrazolotriazinones and aliphatic aldehydes or ketones proceed in aqueous, phosphate-buffered media at pH 4 and 40-60 degrees C to generate thermodynamically controlled mixtures of heterocycles.

Template-Directed Synthesis of Multiply Mechanically Interlocked Molecules Under Thermodynamic Control

The template-directed construction of crown-ether-like macrocycles around secondary dialkylammonium ions (R2NH2+) has been utilized for the expedient (one-pot) and high-yielding synthesis of a diverse range of mechanically interlocked molecules. The clipping together of appropriately designed dialdehyde and diamine compounds around R2NH2+-containing dumbbell-shaped components proceeds through the formation, under thermodynamic control, of imine bonds. The reversible nature of this particular reaction confers the benefits of "error-checking" and "proof-reading", which one usually associates with supramolecular chemistry and strict self-assembly processes, upon these wholly molecular systems. Furthermore, these dynamic covalent syntheses exploit the efficient templating effects that the R2NH2+ ions exert on the macrocyclization of the matched dialdehyde and diamine fragments, resulting not only in rapid rates of reaction, but also affording near-quantitative conversion of starting materials into the desired interlocked products. Once assembled, these "dynamic" interlocked compounds can be "fixed" upon reduction of the reversible imine bonds (by using BH3.THF) to give kinetically stable species, a procedure that can be performed in the same reaction vessel as the inital thermodynamically controlled assembly. Isolation and purification of the mechanically interlocked products formed by using this protocol is relatively facile, as no column chromatography is required. Herein, we present the synthesis and characterization of 1) a [2]rotaxane, 2) a [3]rotaxane, 3) a branched [4]rotaxane, 4) a bis [2]rotaxane, and 5) a novel cyclic [4]rotaxane, demonstrating, in incrementally more complex systems, the efficacy of this one-pot strategy for the construction of interlocked molecules.

Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators

Based on the structural characters of PPAR modulators, a virtual combinatorial library containing 1226,625 compounds was constructed using SMILES strings. Selected ADME filters were employed to compel compounds having poor drug-like properties from this library. This library was converted to sdf and mol2 files by CONCORD 4.0, and was then docked to PPARgamma by DOCK 4.0 to identify new chemical entities that may be potential drug leads against type 2 diabetes and other metabolic diseases. The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries.

Receptor-Assisted Combinatorial Chemistry: Thermodynamics and Kinetics in Drug Discovery

Current drug discovery using combinatorial chemistry involves synthesis followed by screening, but emerging methods involve receptor-assistance to combine these steps. Adding stoichiometric amounts of receptor during library synthesis alters the kinetics or thermodynamics of the synthesis in a way that identifies the best-binding library members. Three main methods have emerged thus far in receptor-assisted combinatorial chemistry: dynamic combinatorial libraries, receptor-accelerated synthesis, and a new method, pseudo-dynamic libraries. Pseudo-dynamic libraries apply both thermodynamics and kinetics to amplify library members to easily observable levels, and attain selectivity heretofore unseen in receptor-assisted systems.

Reversible Michael addition of thiols as a new tool for dynamic combinatorial chemistry

The Michael addition of thiols to enones is reported as a new method for dynamic combinatorial library synthesis.

Enhanced Ligand Affinity for Receptors in which Components of the Binding Site Are Independently Mobile

Using calmodulin antagonism as a model, it is demonstrated that, under circumstances in which binding sites are motionally independent, it is possible to create bifunctional ligands that bind with significant affinity enhancement over their monofunctional counterparts. Suitable head groups were identified by using a semiquantitative screen of monofunctional tryptophan analogs. Two bifunctional ligands, which contained two copies of the highest-affinity head group tethered by rigid linkers, were synthesized. The bifunctional ligands bound to calmodulin with a stoichiometry of 1:1 and with an affinity enhancement over their monofunctional counterparts; the latter bound with a stoichiometry of 2:1 ligand:protein. A lower limit to the effective concentrations of the domains of calmodulin relative to each other (0.2-2 mM) was determined. A comparable effective concentration was achieved for bifunctional ligands based on higher-affinity naphthalene sulphonamide derivatives.

When electron exchange is chemical exchange-assignment of 1H NMR spectra of paramagnetic cobalt(II)-2,2':6'2''-terpyridine complexes

Electron exchange between [Co(terpy)2]3+ and [Co(terpy)2]2+ can be monitored by 1H NMR exchange spectroscopy and allows the cobalt(II) spectra to be fully assigned.

Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly

Rapid progress in genomics and proteomics has provided a wealth of new targets for the pharmaceutical industry, even as many older targets still remain challenging for small-molecule drug discovery. Fragment-based lead discovery, in which leads are built progressively by expanding or combining small fragments, is a rapidly growing field that offers potential advantages over traditional lead-discovery processes. However, identifying and assembling the fragments themselves can be challenging. Here, we review the concept of site-directed ligand discovery, in which a covalent bond is used to stabilize the interaction between a low-affinity fragment and a target protein. We also describe how this technique can facilitate fragment-based lead discovery and help overcome some of the limitations of traditional screening methods.

Tethering: fragment-based drug discovery

The genomics revolution has provided a deluge of new targets for drug discovery. To facilitate the drug discovery process, many researchers are turning to fragment-based approaches to find lead molecules more efficiently. One such method, Tethering1, allows for the identification of small-molecule fragments that bind to specific regions of a protein target. These fragments can then be elaborated, combined with other molecules, or combined with one another to provide high-affinity drug leads. In this review we describe the background and theory behind Tethering and discuss its use in identifying novel inhibitors for protein targets including interleukin-2 (IL-2), thymidylate synthase (TS), protein tyrosine phosphatase 1B (PTP-1B), and caspases.

Complexes of 5,5′-aminoacido-substituted 2,2′-bipyridyl ligands: control of diastereoselectivity with a pH switch and a chloride-responsive combinatorial library

The synthesis and coordination chemistry of a new chiral ligand, 2,2'-bipyridine substituted at the 5 and 5' positions by N-methyl-L-valine methyl ester (5), is presented. The ligand readily forms complexes [M(5)3]2+ where M = Co(II) and Fe(II) in CH3CN, and the complexation reaction is slightly diastereoselective (d.e. =ca. 20%) in favour of the Delta diastereomer. The addition of six equivalents of HCl to these complexes [M(II)(5)3]2+ leads to formation of Delta-[M(II)(5H2)3]8+ with a d.e. of 100%. This high diastereoselectivity can be reversed by the addition of base i.e. the diastereoselectivity can be controlled by the pH. Delta-[Fe(5H2)3]8+ was found to bind chloride ions in CD3OD-CD3CN (6:1) with a binding constant of 260 M(-1). [Co(II)(5)3]2+ can be oxidised to Delta-[Co(III)(5H2)3]9+. Formation constants for both [Co(II)(5)3]2+ and [Co(II)(5H2)3]8+ in acetonitrile were obtained by spectrophotometric titrations. In the former case, the stability constant, log beta3 = 19.5(8), is very similar to that measured for [Co(II)(bipy)3]2+ (log beta3 = 19.3(7)) but this drops significantly when the amine groups of are protonated (log beta3 = 16.5(2)). A dynamic combinatorial library was prepared by mixing three equivalents of, three equivalents of bipy, and two equivalents of Co(II) in CD3CN. The presence of all possible Delta- and Lambda-[Co(II)(5)x(bipy)(3-x)]2+ complexes was inferred from 1H NMR and ES-MS spectra. Addition of protons to this library reduced the number of components by inducing diastereoselectivity, and presence of chloride further simplified the 1H NMR spectrum, indicating that [Cl2 ligand Delta-[Co(II)(5H2)3]]6+ and [Co(II)(bipy)3]2+ were the dominant products.

Self-organization by selection: generation of a metallosupramolecular grid architecture by selection of components in a dynamic library of ligands

Self-organization by selection is implemented in the generation of a tetranuclear [2 x 2] grid-type metallosupramolecular architecture from its components. It occurs through a two-level self-assembly involving two dynamic processes: reversible covalent bound connection and reversible metal ion coordination. Thus, mixing the aminophenol 3, the dialdehyde 4, and zinc acetate generates the grid complex 1a(Zn) via the assembly of the ligand 2a by imine formation and of the grid by zinc(II) binding. When the same process is conducted in a solution containing a mixture of different aminophenol and carbonyl components, the generation of the grid 1a(Zn) drives the selection of the correct components in a virtual dynamic library of ligands, displaying an amplification factor of >100 and a selectivity of >99%. Component exchange as well as reversible protonic modulation of the assembly/disassembly process display the dynamic character of the system and its ability to respond/adapt to changes in environmental conditions. The processes described demonstrate the implementation of a two-level self-organization by selection operating on the dynamic diversity generated by a set of reversibly connected components and driven by the formation of a specific product in a "self-design" fashion.

Generation of an equilibrating collection of crystalline solids from a dynamic combinational library

Thermodynamically controlled crystallization of a copper-containing building block [CuL] (H(2)L = 2-(2'-hydroxyphenyl)-Delta(2)-thiazoline-4-carboxylic acid) from a methanol-ethanol mixture solvent leads to a combinatorial mixture of four crystalline solids, from which each of them is isolated and structurally characterized.

Complexation of phenolic guests by endo- and exo-hydrogen-bonded receptors

This article describes the complexation of phenol derivatives by hydrogen-bonded receptors. These phenol receptors are formed by self-assembly of calix[4]arene dimelamine or tetramelamine derivatives with 5,5-diethylbarbiturate (DEB) or cyanurate derivatives (CYA). The double rosette assemblies 3(3).(DEB)6/(CYA)6 have their phenol-binding functionalities (ureido groups) at the top and at the bottom of the double rosette (exo-receptors). The tetrarosette assemblies 4(3).(DEB)12/(CYA)12 form a cavity with binding sites between the two double rosettes for guest encapsulation (endo-receptors). An intrinsic binding constant Ka of 202 M-1 and 286 M-1 for the binding of 4-nitrophenol to the ureido functionalized exo- and endo-receptors, respectively, was observed. For the exo-receptor a 1:6 stoichiometry was observed while for the endo-receptor 1:4 binding stoichiometry was determined by Job plot and MALDI-TOF MS. The important role that the hydroxy group's acidity plays in the complexation of 4-nitrophenol is clarified by binding studies with different phenol derivatives. The hydrogen-bonded receptors showed a much smaller response towards less acidic phenol derivatives.

Ligand-directed molecular architectures: self-assembly of two-dimensional rectangular metallacycles and three-dimensional trigonal or tetragonal prisms

Three angular ditopic ligands (1,3-bis(benzimidazol-1-ylmethyl)-4,6-dimethylbenzene L(1), 1,3-bis(benzimidazol-1-ylmethyl)-2,4,6-trimethylbenzene L(2), and 1,4-bis(benzimidazol-1-ylmethyl)-2,3,5,6-tetramethylbenzene L(3)) and one tripodal ligand 1,3,5-tris(benzimidazol-1-ylmethyl)-2,4,6-trimethylbenzene L(4) have been prepared. Reaction of these shape-specific designed ligands with different metal salts affords a series of discrete molecular architectures: [Ag(2)L(1)(2)](BF(4))(2) 1, [Ag(2)L(2)(2)](CF(3)SO(3))(2) 2, [CF(3)SO(3)(-) subset Ag(2)L(3)(2)]CF(3)SO(3) 3, [CF(3)SO(3)(-) subset Ag(2)L(3)(3)]CF(3)SO(3) 4, [ClO(4)(-) subset Cu(2)L(2)(4)](ClO(4))(3) 5, [4H(2)O subset Ni(2)L(2)(4)Cl(4)].6H(2)O 6, [BF(4)(-) subset Ag(3)L(4)(2)](BF(4))(2) 7, [ClO(4)(-) subset Ag(3)L(4)(2)](ClO(4))(2) 8, and [CuI(3)(2-) subset Cu(3)L(4)(2)](2)[Cu(2)I(4)] 9. The compounds were characterized by elemental analysis, ESI-MS, IR, and NMR spectroscopy, and X-ray crystallography. 1 is a dinuclear metallacycle with 2-fold rotational symmetry in which two syn-conformational L(1) ligands are connected by two linearly coordinated Ag(+) ions. 2 and 3 are structurally related, consisting of rectangular structures assembled from two linearly coordinated Ag(+) ions and two L(2) or L(3) ligands. The structure of 4 is a trigonal prismatic box consisting of two Ag(+) ions in trigonal planar coordination linked by three L(3) ligands, while the structures of 5 and 6 are tetragonal prismatic cages constructed by two square planar Cu(2+) or Ni(2+) ions linked by four L(2) ligands. The topologies of 7-9 are similar to that of 4; however, these three structures are assembled from three linearly coordinated Ag(+) or Cu(+) ions and two tripodal ligands, representing an alternative strategy to assembling a trigonal prism. (1)H NMR and ESI-MS were utilized to elucidate the solution structures of these macrocycles.

Optimizing the reversibility of hydrazone formation for dynamic combinatorial chemistry

Hydrazones from hydrazines bearing electron withdrawing groups, and aromatic or aliphatic aldehydes form and hydrolyse rapidly in water at neutral pH.

In situ assembly of enzyme inhibitors using extended tethering

Cysteine aspartyl protease-3 (caspase-3) is a mediator of apoptosis and a therapeutic target for a wide range of diseases. Using a dynamic combinatorial technology, 'extended tethering', we identified unique nonpeptidic inhibitors for this enzyme. Extended tethering allowed the identification of ligands that bind to discrete regions of caspase-3 and also helped direct the assembly of these ligands into small-molecule inhibitors. We first designed a small-molecule 'extender' that irreversibly alkylates the cysteine residue of caspase-3 and also contains a thiol group. The modified protein was then screened against a library of disulfide-containing small-molecule fragments. Mass-spectrometry was used to identify ligands that bind noncovalently to the protein and that also form a disulfide linkage with the extender. Linking the selected fragments with binding elements from the extenders generates reversible, tight-binding molecules that are druglike and distinct from known inhibitors. One molecule derived from this approach inhibited apoptosis in cells.

Emerging biological materials through molecular self-assembly

Understanding of new materials at the molecular level has become increasingly critical for a new generation of nanomaterials for nanotechnology, namely, the design, synthesis and fabrication of nanodevices at the molecular scale. New technology through molecular self-assembly as a fabrication tool will become tremendously important in the coming decades. Basic engineering principles for microfabrication can be learned by understanding the molecular self-assembly phenomena. Self-assembly phenomenon is ubiquitous in nature. The key elements in molecular self-assembly are chemical complementarity and structural compatibility through noncovalent interactions. We have defined the path to understand these principles. Numerous self-assembling systems have been developed ranging from models to the study of protein folding and protein conformational diseases, to molecular electronics, surface engineering, and nanotechnology. Several distinctive types of self-assembling peptide systems have been developed. Type I, "molecular Lego" forms a hydrogel scaffold for tissue engineering; Type II, "molecular switch" as a molecular actuator; Type III, "molecular hook" and "molecular velcro" for surface engineering; Type IV, peptide nanotubes and nanovesicles, or "molecular capsule" for protein and gene deliveries and Type V, "molecular cavity" for biomineralization. These self-assembling peptide systems are simple, versatile and easy to produce. These self-assembly systems represent a significant advance in the molecular engineering for diverse technological innovations.

Selection and amplification of hosts from dynamic combinatorial libraries of macrocyclic disulfides

We have discovered two receptors for two different guests from a single dynamic combinatorial library. Each of the two guests amplifies the formation of a tightly binding host at the expense of unfit library members. Small differences in host-guest binding translate into useful differences in amplification. The selected hosts could be readily synthesized using biased dynamic libraries that contain only the right ratio of those building blocks that were selected by the guests. These results establish dynamic combinatorial chemistry as a practical method not only for the discovery but also for the synthesis of new receptors.

The size-selective synthesis of folded oligomers by dynamic templation

A dynamic pool of m-phenylene ethynylene oligomers generated by sequence ligation using the imine metathesis reaction was equilibrated under a variety of conditions, and the mixture of products was analyzed by HPLC. The equilibration was performed in the presence and absence of rodlike ligand 2b, which exhibits an affinity for the helical oligomers that is very length specific. Among the eight oligomers generated during metathesis equilibrium, the formation of 22-mer 6b was enhanced in acetonitrile in the presence of 2b. This particular oligomer has the highest binding affinity for 2b. Quantitative analysis by HPLC of the products indicated that 6b was produced in 66% yield in the presence of 2 equiv 2b while a 37% yield was produced in the absence of 2b. Judging from the binding affinities of oligomers 6 with 2b, the equilibrium shifting was driven by the selective binding of 6b with 2b.

Target-induced formation of neuraminidase inhibitors from in vitro virtual combinatorial libraries

Neuraminidase, a key enzyme responsible for influenza virus propagation, has been used as a template for selective synthesis of small subsets of its own inhibitors from theoretically highly diverse dynamic combinatorial libraries. We show that the library building blocks, aldehydes and amines, form significant amounts of the library components resulting from their coupling by reductive amination only in the presence of the enzyme. The target amplifies the best hits at least 120-fold. The dynamic libraries synthesized and screened in such an in vitro virtual mode form the components that possess high inhibitory activity, as confirmed by enzyme assays with independently synthesized individual compounds.

Dynamic covalent chemistry

Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.

How to synthesize macrocycles efficiently by using virtual combinatorial libraries

The selection of different diimines 4 a-c by alkaline earth ions from a virtual combinatorial library (VCL) is described. The products were stabilized by reduction to the diamines 6 a-c; this allowed easy analysis. The library can be directed toward different target molecules 6 a-c upon addition of alkaline earth ions with different radii. Competition experiments show the possibility of synthesizing the macrocycles 6 a, 6 b, and 6 c simultaneously when using Mg(2+), Ca(2+), and Ba(2+) as template ions. The scope of this thermodynamically controlled, reversible approach for macrocycle syntheses is illustrated.

Spectroscopic anatomy of molecular-imprinting of cyclodextrin. Evidence for preferential formation of ordered cyclodextrin assemblies

The processes of molecular-imprinting of beta-cyclodextrin (beta-CyD) with cholesterol and stigmasterol (cross-linking agent = diisocyanate) have been analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy. These templates enormously promote the formation of dimers and trimers of beta-CyD, which are only inefficiently formed in their absence. These ordered assemblies are the guest-binding sites, in which two or three beta-CyD molecules cooperate to bind large steroids. Ordered assemblies are also formed when 2,6-di-O-methyl-beta-cyclodextrin is used in place of beta-CyD. Direct spectroscopic evidence for molecular-imprinting effect has been obtained. Molecular imprinting of CyDs is potent for tailor-made preparation of synthetic receptors for nanometer-scaled guests.

Dynamic combinatorial chemistry

A combinatorial library that responds to its target by increasing the concentration of strong binders at the expense of weak binders sounds ideal. Dynamic combinatorial chemistry has the potential to achieve exactly this. In this review, we will highlight the unique features that distinguish dynamic combinatorial chemistry from traditional combinatorial chemistry, and that could make a useful addition to the set of combinatorial techniques used in drug discovery.

Drug discovery by dynamic combinatorial libraries

Dynamic combinatorial chemistry is a recently introduced supramolecular approach that uses self-assembly processes to generate libraries of chemical compounds. In contrast to the stepwise methodology of classical combinatorial techniques, dynamic combinatorial chemistry allows for the generation of libraries based on the continuous interconversion between the library constituents. Spontaneous assembly of the building blocks through reversible chemical reactions virtually encompasses all possible combinations, and allows the establishment of adaptive processes owing to the dynamic interchange of the library constituents. Addition of the target ligand or receptor creates a driving force that favours the formation of the best-binding constituent--a self-screening process that is capable, in principle, of accelerating the identification of lead compounds for drug discovery.