Carbonic anhydrase II-induced selection of inhibitors from a dynamic combinatorial library of Schiff’s bases

Sulfinamide Crossover Reaction

This study unveils a new catalytic crossover reaction of sulfinamides. Leveraging mild acid catalysis, the reaction demonstrates a high tolerance to structural variations, yielding equimolar products across diverse sulfinamide substrates. Notably, small sulfinamide libraries can be selectively oxidized to sulfonamides, providing a new platform for ligand optimization and discovery in medicinal chemistry. This crossover chemotype provides a new tool for high-throughput experimentation in discovery chemistry.

Abdel-Aziz A, Bua S, Nocentini A, Bakheit AH, Alkahtani HM, Hefnawy MM, Supuran CT. Design, synthesis, and carbonic anhydrase inhibition activities of Schiff bases incorporating benzenesulfonamide scaffold: Molecular docking application

In this study, The inhibitory actions of human carbonic anhydrase (CA, EC 4.2.1.1) (hCA) isoforms I, II, IX, and XII are being examined using recently synthesized substituted hydroxyl Schiff derivatives based on the quinazoline scaffold 4-22. Quinazolines 2, 3, 4, 5, 7, 10, 15, and 18 reduce the activity of hCA I isoform effectively to a Ki of 87.6-692.3 nM, which is nearly equivalent to or more potent than that of the standard drug AAZ (Ki, 250.0 nM). Similarly, quinazolines 2, 3, and 5 and quinazoline 14 effectively decrease the inhibitory activity of the hCA II isoform to a KI of 16.9-29.7 nM, comparable to that of AAZ (Ki, 12.0 nM). The hCA IX isoform activity is substantially diminished by quinazolines 2-12 and 14-21 (Ki, 8.9-88.3 nM against AAZ (Ki, 25.0 nM). Further, the activity of the hCA XII isoform is markedly inhibited by the quinazolines 3, 5, 7, 14, and 16 (Ki, 5.4-19.5 nM). Significant selectivity levels are demonstrated for inhibiting tumour-associated isoforms hCA IX over hCAI, for sulfonamide derivatives 6-15 (SI; 10.68-186.29), and 17-22 (SI; 12.52-57.65) compared to AAZ (SI; 10.0). Sulfonamide derivatives 4-22 (SI; 0.50-20.77) demonstrated a unique selectivity in the concurrent inhibition of hCA IX over hCA II compared to AAZ (SI; 0.48). Simultaneously, benzenesulfonamide derivative 14 revealed excellent selectivity for inhibiting hCA XII over hCA I (SI; 60.35), whereas compounds 5-8, 12-14, 16, and 18-22 demonstrated remarkable selectivity for hCA XII inhibitory activity over hCA II (SI; 2.09-7.27) compared to AAZ (SI; 43.86 and 2.10, respectively). Molecular docking studies additionally support 8 to hCA IX and XII binding, thus indicating its potential as a lead compound for inhibitor development.

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.

Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery

Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.

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.

Synthesis and comparative carbonic anhydrase inhibition of new Schiff's bases incorporating benzenesulfonamide, methanesulfonamide, and methylsulfonylbenzene scaffolds

Herein, we report the synthesis, characterization, and carbonic anhydrase (CA) inhibition of the newly synthesized Schiff's bases 4-18 with benzenesulfonamide, methanesulfonamide, and methylsulfonylbenzene scaffolds. The compound inhibition profiles against human CA (hCA) isoforms I, II, IX, and XII were compared to those of the standard inhibitors, acetazolamide (AAZ) and SLC-0111 (a CA inhibitor in Phase II clinical trials for the treatment of hypoxic tumors). The hCA I was inhibited by compounds 4a-8a with inhibition constants (KI) in the range 93.5-428.1 nM (AAZ and SLC-0111: KI, 250.0 and 5080.0 nM, respectively). Compounds 4a-8a proved to be effective hCA II inhibitors, with KI ranging from 18.2 to 133.3 nM (AAZ and SLC-0111: KI, 12.0 and 960.0 nM, respectively). Compounds 4a-8a effectively inhibited hCA IX, with KI in the range 8.5-24.9 nM; these values are superior or equivalent to that of AAZ and SLC-0111 (KI, 25.0 and 45.0 nM, respectively). Compounds 4a-8a displayed effective hCA XII inhibitory activity with KI values ranging from 8.6 to 43.2 nM (AAZ and SLC-0111: KI, 5.7 and 4.5 nM, respectively). However, compounds 9b-13b and 14c-18c were found to be micromolar CA inhibitors. For molecular docking studies, compounds 5a, 6a, and 8a were selected.

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.

Crystal structure of 1,1'-{(dodecane-1,12-di-yl)bis-[(aza-niumylyl-idene)methanylyl-idene]}bis-(naphthalen-2-olate)

The title compound, C34H40N2O2, exists in an extended conformation and has crystallographically imposed centrosymmetry. The crystal packing can be described as being composed of parallel layers stacked along [010]. The zwitterionic structure is stabilized by an intra-molecular N-H⋯O hydrogen-bond inter-action.

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.

Synthesis, characterization and in vitro biological evaluation of some novel 1,3,5-triazine-Schiff base conjugates as potential antimycobacterial agents

A series of some novel 1,3,5-triazine-Schiff base conjugates (1-32) have been synthesized and evaluated for their in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv using Alamar Blue assay and the activity expressed as the minimum inhibitory concentration (MIC) in μg/mL. Compounds 4 (4-Methoxy-6-methyl-N-(3,4,5-trimethoxybenzylidene)-1,3,5-triazin-2-amine), 11 (4-Methoxy-6-methyl-N-(2-hydroxy-3-bromo-5-chloro-benzylidene)-1,3,5-triazin-2-amine) and 24 (4-Methoxy-6-methyl-N-(1-(2,5-dihydroxyphenyl)ethylidene)-1,3,5-triazin-2-amine) exhibited a significant activity at 3.125, 6.25 and 6.25μg/mL, respectively, when compared with the antitubercular drugs such as ethambutol (3.125μg/mL), pyrazinamide (6.25μg/mL) and streptomycin (6.25μg/mL) and it could be a potential starting point to develop new lead compounds in the fight against Mycobacterium tuberculosis H37Rv.

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.

A class of novel Schiff's bases: Synthesis, therapeutic action for chronic pain, anti-inflammation and 3D QSAR analysis

To discover analgesics for treating chronic pain 17 novel Schiff's bases, N,N'-(Z-allylidene-1,3-diyl)bisamino acid methyl esters were prepared from 1,1,3,3,-tetramethoxypropane and amino acid methyl esters. On tail-flick mouse model 20 micromol/kg of these Schiff's bases were orally administered, the analgesic action started 30 min after administration, reached the maximum 120 min after administration, and at 180 min this action was still observed. On a xylene-induced ear edema mouse model 20 micromol/kg of these Schiff's bases exhibited desirable anti-inflammation. Thus the present Schiff's bases are able to treat chronic pain from inflammation. The effect of the side chains of the amino acid residues of these Schiff's bases on the analgesic activity was explained with 3D QSAR.