The use of a pharmacophore model for identification of novel ligands for the benzodiazepine binding site of the GABAA receptor

Rational approaches for the design of various GABA modulators and their clinical progression

GABA (γ-amino butyric acid) is an important inhibitory neurotransmitter in the central nervous system. Attenuation of GABAergic neurotransmission plays an important role in the etiology of several neurological disorders including epilepsy, Alzheimer's disease, Huntington's chorea, migraine, Parkinson's disease, neuropathic pain, and depression. Increase in the GABAergic activity may be achieved through direct agonism at the GABAA receptors, inhibition of enzymatic breakdown of GABA, or by inhibition of the GABA transport proteins (GATs). These functionalities make GABA receptor modulators and GATs attractive drug targets in brain disorders associated with decreased GABA activity. There have been several reports of development of GABA modulators (GABA receptors, GABA transporters, and GABAergic enzyme inhibitors) in the past decade. Therefore, the focus of the present review is to provide an overview on various design strategies and synthetic approaches toward developing GABA modulators. Furthermore, mechanistic insights, structure-activity relationships, and molecular modeling inputs for the biologically active derivatives have also been discussed. Summary of the advances made over the past few years in the clinical translation and development of GABA receptor modulators is also provided. This compilation will be of great interest to the researchers working in the field of neuroscience. From the light of detailed literature, it can be concluded that numerous molecules have displayed significant results and their promising potential, clearly placing them ahead as potential future drug candidates.

Ubiquitous Nature of Fluoroquinolones: The Oscillation between Antibacterial and Anticancer Activities

Fluoroquinolones are synthetic antibacterial agents that stabilize the ternary complex of prokaryotic topoisomerase II enzymes (gyrase and Topo IV), leading to extensive DNA fragmentation and bacteria death. Despite the similar structural folds within the critical regions of prokaryotic and eukaryotic topoisomerases, clinically relevant fluoroquinolones display a remarkable selectivity for prokaryotic topoisomerase II, with excellent safety records in humans. Typical agents that target human topoisomerases (such as etoposide, doxorubicin and mitoxantrone) are associated with significant toxicities and secondary malignancies, whereas clinically relevant fluoroquinolones are not known to exhibit such propensities. Although many fluoroquinolones have been shown to display topoisomerase-independent antiproliferative effects against various human cancer cells, those that are significantly active against eukaryotic topoisomerase show the same DNA damaging properties as other topoisomerase poisons. Empirical models also show that fluoroquinolones mediate some unique immunomodulatory activities of suppressing pro-inflammatory cytokines and super-inducing interleukin-2. This article reviews the extended roles of fluoroquinolones and their prospects as lead for the unmet needs of "small and safe" multimodal-targeting drug scaffolds.

Pharmacophore models for GABA(A) modulators: implications in CNS drug discovery

IMPORTANCE OF THE FIELD

GABA(A) ion channel is a validated drug target, implicated in the pathophysiology of various neurological and psychiatric disorders. Structural investigations on GABA(A) are currently precluded in the absence of experimentally resolved structure. Pharmacophore modeling circumvents such issues and proves to be a powerful and successful method in drug discovery.

AREAS COVERED IN THIS REVIEW

The present reviews encompass pharmacophoric models available in the literature for the orthosteric GABA and the allosteric benzodiazepine binding site. Success stories from these simplistic pharmacophore models in scaffold hopping and strategic lead optimization have been highlighted. Recent advances in pharmacophore modeling that can leverage CNS drug discovery programs and deliver astounding results have been reviewed.

WHAT THE READER WILL GAIN

Readers are bound to gain a comprehensive insight on different computational techniques used by different groups to arrive at simple, yet sophisticated pharmacophore models. In the absence of experimentally unresolved active site geometry of GABA(A), these models will provide the reader an opportunity to translate these pharmacophoric features to the microscopic phenomenon of supramolecular ligand interaction.

TAKE HOME MESSAGE

Pharmacophore modeling has now evolved as a mainstay approach for lead generation and optimization in drug discovery programs. Of late, many advances in pharmacophore perception have emerged. Such advancements should be used to confront activity profiling and early stage risk assessment in a high-throughput fashion. Extending such technologies has the potential not only to reduce time and cost, but also to prevent late stage attrition in drug discovery.

Insights into the structure and pharmacology of GABA(A) receptors

GABA is the major inhibitory neurotransmitter in the adult mammalian CNS. The ionotropic GABA type A receptors (GABA(A)Rs) belong to the Cys-loop family of receptors. Each member of the family is a large pentameric protein in which each subunit traverses the cell membrane four times. Within this family, the GABA type A receptors are particularly important for their rich pharmacology as they are targets for a range of therapeutically important drugs, including the benzodiazepines, barbiturates, neuroactive steroids and anesthetics. This review discusses new insights into receptor properties that allow us to begin to relate the structure of an individual receptor to its functional and pharmacological properties.

Discovery of potential integrin VLA-4 antagonists using pharmacophore modeling, virtual screening and molecular docking studies

Very late antigen-4 (VLA-4) is an integrin protein, and its antagonists are useful as anti-inflammatory drugs. The aim of this study is to discover novel virtual lead compounds to use them in designing potent VLA-4 antagonists. A best pharmacophore model was generated with correlation coefficient of 0.935, large cost difference of 114.078, comprising two hydrogen bond acceptors and three hydrophobic features. It was further validated and used in database screening for potential VLA-4 antagonists. A homology model of VLA-4 was built and employed in molecular docking of screened hit compounds. Finally, two compounds were identified as potential virtual leads to be deployed in the designing of novel potent VLA-4 antagonists.

Pharmacophore mapping of arylamino-substituted benzo[b]thiophenes as free radical scavengers

Predictive pharmacophore models have been developed for a series of arylamino-substituted benzo[b]thiophenes exhibiting free radical scavenging activity. 3D pharmacophore models were generated using a set of 20 training set compounds and subsequently validated by mapping 6 test set compounds using Discovery Studio 2.1 software. Further model validation was performed by randomizing the data using Fischer's validation technique at the 95% confidence level. The most predictive pharmacophore model developed using the conformers obtained from the BEST method showed a correlation coefficient (r) of 0.942 and consisted of three features: hydrogen bond donor, hydrogen bond acceptor and aromatic ring. Acceptable values of external validation parameters, like R2pred (0.853) and r2m(test) (0.844), also implied that the external predictivity of the model was significant. The development of further pharmacophore models using conformers obtained from the FAST method yielded a few models with good predictivity, with the best one (r=0.904) consisting of two features: hydrogen bond donor and hydrogen bond acceptor. Significant values of external validation parameters, R2pred (0.913) and r2m(test) (0.821), also reflect the high predictive ability of the model. Again, Fischer validation results implied that the models developed were robust enough and their good results were not based on mere chance. These validation approaches indicate the reliability of the predictive abilities of the 3D pharmacophore models developed here, which may thus be further utilized as a 3D query tool in the virtual screening of new chemical entities with potent antioxidant activities.

Synthesis and biological evaluation of flavan-3-ol derivatives as positive modulators of GABAA receptors

We herein describe the synthesis and positive modulatory activities of a small library of flavan-3-ol derivatives on alpha(1)beta(2)gamma(2L) GABA(A) receptors. Structure-activity relationships of various substituents on the A, B and C rings were evaluated in a functional electrophysiological assay. A trans configuration and a 3-acetoxy moiety are essential for activity. Substitution of the B ring appears to be well tolerated, with substituents on the A ring playing a major role in determining activity.

A Synthesis of 4H-1, 4-Benzothiazines

A convenient synthesis of 4H-1, 4-benzothiazines is described. The key step is the coupling between 2-amino-5-chlorophenyl disulfide (3) and ethyl acetylenecarboxylate (4) in the presence of CuI as a catalyst or by microwave irradiation in moderate yield.

Structural basis for ligand recognition at the benzodiazepine binding site of GABAA alpha 3 receptor, and pharmacophore-based virtual screening approach

Given the heterogeneity of GABA(A) receptor, the pharmacological significance of identifying subtype selective modulators is increasingly being recognized. Thus, drugs selective for GABA(A) alpha(3) receptors are expected to display fewer side effects than the drugs presently in clinical use. Hence we carried out 3D QSAR (three-dimensional quantitative structure-activity relationship) studies on a series of novel GABA(A) alpha(3) subtype selective modulators to gain more insight into subtype affinity. To identify the 3D functional attributes required for subtype selectivity, a chemical feature-based pharmacophore, primarily based on selective ligands representing diverse structural classes was generated. The obtained pseudo receptor model of the benzodiazepine binding site revealed a binding mode akin to "Message-Address" concept. Scaffold hopping was carried out across multi-conformational May Bridge database for the identification of novel chemotypes. Further a focused data reduction approach was employed to choose a subset of enriched compounds based on "Drug likeness" and "Similarity-based" methods. These results taken together could provide impetus for rational design and optimization of more selective and high affinity leads with a potential to have decreased adverse effects.

Pharmacophore identification and virtual screening for methionyl-tRNA synthetase inhibitors

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes involved in protein biosynthesis in all living organisms and are an unexploited antibacterial targets, as many strains of bacteria have become resistant to all established classes of antibiotics. Therefore, the main aim of this study is to discover new lead molecules which would be useful as anti-bacterial compounds. Pharmacophore models were developed by using CATALYST HypoGen with a training set of 29 diverse methionyl-tRNA synthetase (MetRS) inhibitors. The best quantitative pharmacophore hypothesis (Hypo1) obtained a correlation coefficient of 0.975, root mean square deviation (RMSD) of 0.55 and cost difference (null cost-total cost) of 70.32. This Hypo1 was validated by two methods, first by using 104 test set molecules which resulted a correlation of 0.926 between HypoGen estimated activities versus experimental activities and secondly by Cat-Scramble validation method. This validated pharmacophore model was further used for screening databases for discovery of new MetRS inhibitors. The new lead compounds were further analyzed for drug-like properties. Homology modeled structure of Staphylococcus aureus MetRS was built and molecular docking studies were performed with many inhibitors using the newly built protein structure. Finally, it was found that the new leads exhibited good estimated inhibitory activity, calculated binding properties similar to experimentally proven compounds and also favorable drug-like properties.

4-quinolone derivatives: high-affinity ligands at the benzodiazepine site of brain GABA A receptors. synthesis, pharmacology, and pharmacophore modeling

The 3-ethoxycarbonyl-4-quinolone compound 1 has previously been identified via a database search as an interesting lead compound for ligand binding at the benzodiazepine site of GABA(A) receptors (Kahnberg et al. J. Mol. Graphics Modelling 2004, 23, 253-261). Pharmacophore-guided optimization of this lead compound yielded a number of high-affinity ligands for the benzodiazepine site including compounds 20 and 23-25 displaying sub-nanomolar affinities. A few of the compounds have been tested on the alpha(1)beta(2)gamma(2S) and alpha(3)beta(2)gamma(2S) GABA(A) receptor subtypes, and two of the compounds (5 and 19) display selectivity for alpha(1)- versus alpha(3)-containing receptors by a factor of 22 and 27, respectively. This selectivity for alpha(1)beta(2)gamma(2S) is in the same range as that for the well-known alpha(1) subunit selective compound zolpidem.