Carbonic Anhydrase-Encoded Dynamic Constitutional Libraries: Toward the Discovery of Isozyme-Specific Inhibitors

Constitutional Dynamic Inhibition/Activation of Carbonic Anhydrases

In this review we consider one important member of the metalloenzymes family, the carbonic anhydrase (CA), involved in the treatment of several common diseases. Different approaches have emerged to regulate the activity of CA, mostly acting on the inner catalytic active site or outer microenvironment of the enzyme, leading to inhibition or activation of CA. In recent years, gradually increased attention has focused on the adoption of constitutional dynamic chemistry (CDC) strategies for the screening and discovery of potent inhibitors or activators. The participation of reversible covalent bonds enabled the enzyme itself to select the optimal ligands obtained from diverse building blocks with comparatively higher degree of variety, resulting in the fittest recognition of enzyme ligands from complex dynamic systems. With the increasing implementation of CDC for enzyme targets, it shows great potential for drug discovery or CO₂ capture applications.

Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination

Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.

Overview of Recent Strategic Advances in Medicinal Chemistry

Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.

Chitosan hydrogelation with a phenothiazine based aldehyde: a synthetic approach toward highly luminescent biomaterials

Hydrogelation of chitosan with a photoactive aldehyde via covalent dynamic chemistry proved an original approach towards efficient luminescent biomaterials.

Discovery of novel isatin-based sulfonamides with potent and selective inhibition of the tumor-associated carbonic anhydrase isoforms IX and XII

A series of 2/3/4-[(2-oxo-1,2-dihydro-3H-indol-3-ylidene)amino]benzenesulfonamides, obtained from substituted isatins and 2-, 3- or 4-aminobenzenesulfonamide, showed low nanomolar inhibitory activity against the tumor associated carbonic anhydrase (CA, EC 4.2.1.1) isoforms IX and XII - recently validated antitumor drug targets, being much less effective as inhibitors of the off-target cytosolic isoforms CA I and II.

Synthesis of Schiff base derivatives of 4-(2-aminoethyl)-benzenesulfonamide with inhibitory activity against carbonic anhydrase isoforms I, II, IX and XII

Schiff base derivatives were obtained by reaction of 4-(2-aminoethyl)benzenesulfonamide with aromatic aldehydes. The corresponding secondary amine derivatives were also prepared by reduction of the imine compounds with NaBH4. These derivatives were investigated as inhibitors of four human carbonic anhydrase (CA, EC 4.2.1.1) isoforms, the cytosolic isozymes hCA I and II, as well as, the transmembrane, tumor-associated hCA IX and XII. Some of the newly synthesised compounds showed effective inhibitory activities against these CA isozymes. Many low nanomolar inhibitors were detected against all isoforms among the secondary amines whereas the Schiff bases were by far less active compared to the corresponding reduced derivatives among all investigated isoforms.

Dynamic combinatorial chemistry: a tool to facilitate the identification of inhibitors for protein targets

Dynamic combinatorial chemistry enables efficient identification of protein binder(s) from a library of interconverting compounds. The library responds to the addition of the target by amplifying the strongest binder.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Alternative methods of processing bio-feedstocks in formulated consumer product design

In this work new methods of processing bio-feedstocks in the formulated consumer products industry are discussed. Our current approach to formulated products design is based on heuristic knowledge of formulators that allows selecting individual compounds from a library of available materials with known properties. We speculate that most of the compounds (or functions) that make up the product to be designed can potentially be obtained from a few bio-sources. In this case, it may be possible to design a sequence of transformations required to convert feedstocks into products with desired properties, analogous to a metabolic pathway of a complex organism. We conceptualize some novel approaches to processing bio-feedstocks with the aim of bypassing the step of a fixed library of ingredients. Two approaches are brought forward: one making use of knowledge-based expert systems and the other making use of applications of metabolic engineering and dynamic combinatorial chemistry.

Dominant behaviours in the expression of human carbonic anhydrase hCA I activity

Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.

Discovering isozyme-selective inhibitor scaffolds of human carbonic anhydrases using structural alignment and de novo drug design approaches

The development of isozyme-selective carbonic anhydrase inhibitors is currently still a great challenge. In the present study, protein-ligand complex structures were obtained by AutoDock Vina with SBR ((R)-N-(3-indol-1-yl-2-methyl-propyl)-4-sulfamoyl-benzamide) as the only inhibitor docked into the binding pockets of human isozymes CA I, II, IV, VI, IX, XII, and XIII. To make the spatial structures of complexes comparable, the co-ordinates for CA domains were reassigned based on structural alignments. With preferred docking poses of SBR been reduced to seed structures, the LigBuilder was used to build up inhibitor molecules. The results suggested that sulfonamide derivatives with naphthalene, fluorene, and acridan as the scaffold structures can be the potential isozyme-selective CAIs, especially for isozymes CA II, IV, and IX.

Antifungal vanillin-imino-chitosan biodynameric films

Vanillin-chitosan biodynamers have been prepared and structure-morphology correlations revealed the pathway of progressive incorporation of the aldehyde onto chitosan backbones. Such dynamic biopolymers or biodynamers, generated from reversibly interacting components, offer the possibility to address the dynamic covalent behaviour of the reversible imine-bond formation/hydrolysis equilibria between vanillin and chitosan polymeric backbones. The reaction takes place with very low conversion in acidic aqueous solutions (7-12%), but the imine bond formation is amazingly improved (∼80%) when the reaction takes place while solution-solid state transition and solid state phase-organization events occur. The chitosan-vanillin biopolymeric films described here present interesting Candida albicans antifungal activity compared with other common bacterial strands, which suggests the implementation of these biocompatible materials as thin layer protecting systems for medical devices.

Dynamic combinatorial chemistry at the phospholipid bilayer interface

Background

Molecular recognition at the environment provided by the phospholipid bilayer interface plays an important role in biology and is subject of intense investigation. Dynamic combinatorial chemistry is a powerful approach for exploring molecular recognition, but has thus far not been adapted for use in this special microenvironment.

Results

Thioester exchange was found to be a suitable reversible reaction to achieve rapid equilibration of dynamic combinatorial libraries at the egg phosphatidyl choline bilayer interface. Competing thioester hydrolysis can be minimised by judicial choice of the structure of the thioesters and the experimental conditions. Comparison of the library compositions in bulk solution with those in the presence of egg PC revealed that the latter show a bias towards the formation of library members rich in membrane-bound building blocks. This leads to a shift away from macrocyclic towards linear library members.

Conclusions

The methodology to perform dynamic combinatorial chemistry at the phospholipid bilayer interface has been developed. The spatial confinement of building blocks to the membrane interface can shift the ring-chain equilibrium in favour of chain-like compounds. These results imply that interfaces may be used as a platform to direct systems to the formation of (informational) polymers under conditions where small macrocycles would dominate in the absence of interfacial confinement.