Chem Biol Drug Des. 2013 Feb;81(2):238-49.

Structure-based design and synthesis of benzothiazole phosphonate analogues with inhibitors of human ABAD-Aβ for treatment of Alzheimer’s disease.

Valasani KR, Hu G, Chaney MO, Yan SS.

Department of Pharmacology & Toxicology and Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA.



Amyloid binding alcohol dehydrogenase, a mitochondrial protein, is a cofactor facilitating amyloid-β peptide (Aβ) induced cell stress. Antagonizing Aβ-ABAD interaction protects against aberrant mitochondrial and neuronal function and improves learning memory in the Alzheimer’s disease mouse model. Therefore, it offers a potential target for Alzheimer’s drug design, by identifying potential inhibitors of Aβ-ABAD interaction. 2D QSAR methods were applied to novel compounds with known IC(50) values, which formed a training set. A correlation analysis was carried out comparing the statistics of the measured IC(50) with predicted values. These selectivity-determining descriptors were interpreted graphically in terms of principle component analyses, which are highly informative for the lead optimization process with respect to activity enhancement. A 3D pharmacophore model also was created. The 2D QSAR and 3D pharmacophore models will assist in high-throughput screening. In addition, ADME descriptors were also determined to study their pharmacokinetic properties. Finally, amyloid binding alcohol dehydrogenase molecular docking study of these novel molecules was undertaken to determine whether these compounds exhibit significant binding affinity with the binding site. We have synthesized only the compounds that have shown the best drug-like properties as candidates for further studies.

PMID: 23039767



Amyloid binding alcohol dehydrogenase (ABAD), a mitochondrial enzyme, plays a key role in mitochondrial dysfunction and in the pathogenesis of AD. This enzyme has attracted considerable interest because of its ability to interact with Aβ. Importantly, the interaction of ABAD with Aβ mediates mitochondrial and synaptic dysfunction [1; 2].  Antagonizing Aβ-ABAD interaction with the ABAD decoy peptide that encompasses the amino residues responsible for Aβ binding to ABAD protects against aberrant mitochondrial and neuronal function and improves learning memory in AD transgenic mice [1-3]. Furthermore, interception of Aβ-ABAD interaction also significantly reduces mitochondrial and cerebral Aβ accumulation [3]. These data support that Aβ-ABAD interaction is a potential target of the drug development for treatment of AD.

In this way, the search for inhibitors of Aβ-ABAD interaction has started and using an ELISA-based screening assay, frentizole, an FDA-approved immunosuppressive drug, was identified as a novel inhibitor of Aβ–ABAD interaction. Analyzing the frentizole SAR studies, we have developed novel benzothiazole ureas with a 30-fold improvement in potency[4]. Recently, AG18051 (1-azepan-1-yl-2-phenyl-2-(4-thioxo-1,4-dihydropyrazolo[3,4-d]pyrimidin-5-yl)-ethanone) was also identified as a potent inhibitor of ABAD.[5] However, currently available inhibitors of Aβ-ABAD interaction have the disadvantages of low solubility, poorly crossing the blood brain barrier (BBB), high toxicity, and low cell permeability. Current efforts to design AβABAD inhibitors have been unsuccessful due largely to poor ADME (Absorption, Distribution, Metabolism and Excretion) properties.  To overcome the limitation of currently available ABAD inhibitors, we have designed a new class of small molecular inhibitors of Aβ-ABAD interaction via phosphonate derivatives. The goal of this study is to identify the potential blockers of Aβ-ABAD interaction as therapeutic targets of AD.

In our previous work, we have described the synthesis and evaluation of a novel class of benzothiazole urea derivatives as potent Aß-ABAD inhibitors.[6]  Based on benzothiazole urea and frentizole structure activities studies, we have designed benzothiazole amino and frentizole   phosphonate derivatives. Molecular docking, QSAR studies and pharmacokinetics⁄absorption, distribution, metabolism, and excretion (ADME) prediction for any given scaffold of interest are the most popular methods of computer aided drug design.

Based on the frentizole SAR study and the previous report, we have developed novel benzothiazole ureas with a 30-fold improvement in potency;[4] benzothiazole urea and frentizole analogs provide remarkable enhancements of permeation across biological membranes and of oral bioavailability. Based on frentizole and benzothiazole urea derivatives SAR studies, we  have designed and synthesized novel small drug molecules  as urea and frentizole phosphonate derivatives which might have the capacity to cross the BBB and inhibit Aβ-ABAD interaction. The rational design of phosphonate derivatives had also been strongly supported by known  phosphonate  prodrugs and docking studies showing that Tyr652 and Phe656 play a pivotal role in the ABAD drug binding, by promoting cation-π, π-π, and hydrophobic interactions with the basic nitrogen and aromatic rings of drugs. This might confer the capacity to cross the BBB and to inhibit Aβ-ABAD interaction.

The major novelty of the present approach is the use of a benthiazole phosphonate moiety, which readily penetrates biological membranes such as the blood-brain barrier (BBB) and enters the target organ.[7-9] According, phosphate esters are frequently used as a prodrug strategy, especially for water insoluble compounds, since the phosphate group confers the following characteristic features to the xenobiotic: 1) decreases the adverse effects of the drugs, 2)  help in readily crossing the blood-brain barrier (BBB) and enters the target organ, 3) increases water solubility and thereby enables delivery of the drug parenterally, 4) cleavage of the phosphonate carrier/drug entity in vivo provides a hydrophilic, negatively charged intermediate, which is “locked” in the brain or other organ and which provides significant and sustained delivery of the active drug species to the target organ, 5) as phosphonate moiety induces polar nature to the derivatives, bio transformation ( by Phase I enzymes) is not necessary for drug disposition, thereby reducing  drug-drug interaction.[7; 8; 10-13]

From the docking, 2D QSAR and pharmacophore studies (Figure 1), it is concluded that most of these compounds are reasonable inhibitors of ABAD. The ligand – complexes generated from molecular docking process suggest that the molecules are good ABAD inhibitors as they are showing good binding affinity with the ABAD receptor (Figure 2). This molecular docking study will not be used to screen the molecules that are having inhibitory activity against ABAD, since it is an inefficient.  However, our demonstration of 2D QSAR and 3D pharmacophore models to predict activity should be very useful to screen a huge number of new compounds. We hope to combine these models to give us greater accuracy in the prediction of active candidates for treating AD.

Koteswara Rao Valasani-1Figure 1.  Showing the resulting pharmacophore model (shown as volume sheres) based on the activities (IC50) of 20 compounds in the training set. The various pharmacophore sites are labeled as to the features or properties (H-bond donor, H-bond acceptor, hydrophilic/aromatic and carboxyl acceptor/anion donor).  The 6 top most active ABAD inhibitors from the test set are overlayed with the pharmacophore model.

Koteswara Rao Valasani-2Figure 2.  Binding site for active IC50 compound 1 &2. Compound 1 (left) binding affinity is contributed to 4 H-bonds to Ser 155 Ala 156 and Arg 116, as shown by the dotted yellow interactions. Compound 2 (right) binding affinity is contributed to P-stacking interactions between Lys 172, Arg 116 and a H-bond to Gln 115.



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