QSAR studies in substituted 1,2,3,4,6,7,12,12a-octa-hydropyrazino[2',1':6,1]pyrido[3,4-b]indoles--a potent class of neuroleptics

Efficiency of Homology Modeling Assisted Molecular Docking in G-protein Coupled Receptors

BACKGROUND

Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In the absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery.

OBJECTIVE

The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane-bound proteins with the complex constitution, and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade, there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures; however, the majority of the GPCR structures remain unsolved. In this context, HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs.

METHODS

The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in the absence of GPCR crystal structures and (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor subtype selectivity and receptor behaviour in comparison with GPCR crystal structures.

RESULTS

The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario, it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases, HM proteins were found to outscore crystal structures.

CONCLUSION

The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at the molecular level. Thus, HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.

Alumina-supported Cu(II), a versatile and recyclable catalyst for regioselective ring opening of aziridines and epoxides and subsequent cyclization to functionalized 1,4-benzoxazines and 1,4-benzodioxanes

An easily accessible catalyst, alumina-supported copper(II), efficiently catalyzes the ring opening of aziridines and epoxides followed by cyclization of the corresponding intermediate to produce a variety of functionalized 1,4-benzoxazines and 1,4-benzodioxanes, respectively, in one pot without any ligand in high yields. The ring cleavages of aziridines and epoxides are highly regioselective. The catalyst is inexpensive, non-air-sensitive, environmentally friendly, and recyclable. The function of the catalyst and the reaction pathway are postulated. This protocol is successfully utilized for the formation of three carbon-heteroatom bonds, namely, C-O, C-N, and C-S, in one pot.

Rational design, synthesis and evaluation of (6aR∗,11bS∗)-1-(4-fluorophenyl)-4-{7-[4-(4-fluorophenyl)-4-oxobutyl]1,2,3,4,6,6a,7,11b,12,12a(RS)-decahydropyrazino[2′,1′:6,1]pyrido[3,4-b]indol-2-yl}-butan-1-one as a potential neuroleptic agent

In our pursuit to prepare a potent antipsychotic compound, a novel 1,2,3,4,6,6a,7,11b,12,12a-decahydropyrazino[2',1':6,1]pyrido[3,4-b]indole derivative was synthesized which incorporates the butyrophenone substructure twice. This molecule has shown D(1), D(2) and 5-HT(2A) receptor blocking activity where the ratio pK(i) (5-HT(2A)) to pK(i) (D(2)) is 1.42 better than risperidone (1.15). It blocks amphetamine induced hyperactivity/stereotypy and secondary conditioned avoidance responses in rodents at lower doses than those required for the neuroleptic drugs haloperidol and centbutindole (biriperone).

CoMFA and Docking Studies on Glycogen Phosphorylase a Inhibitors as Antidiabetic Agents

Glycogen phosphorylase (GP(a)) is a specific target for the design of inhibitors and may prevent glycogenolysis under high glucose conditions in type II diabetes. The carboxamides first reported by Hoover D. J. et al. (J. Med. Chem. 1998, 41, 2934-2938) are one of the major classes of GP(a) inhibitors other than glucose derivatives. The recent, X-ray crystallographic analyses (Oikonomakos et al. Biochim. Biophys. Acta 2003, 1647, 325-332) have revealed a distinct mechanism of action for these inhibitors, which bind at a new allosteric site away from the inhibitory and catalytic sites. To elucidate the essential structural and physicochemical requirements responsible for binding to the GP(a) enzyme and to develop predictive models, CoMFA and docking studies have been carried out on a series of indole-2-carboxamide derivates. The CoMFA model developed using pharmacophoric alignments and hydrogen-bonding fields demonstrated high predictive ability against the training (r2 = 0.98, q2 = 0.68) and the test set (r2pred = 0.85). Further the superimposition of PLS coefficient contour maps from CoMFA with the GP(a) active site (PDB: 1lwo) has shown a high level of compatibility.

Quantitative structure–activity relationship analysis of a series of 2,3-diaryl benzopyran analogues as novel selective cyclooxygenase-2 inhibitors

A series of recently synthesized 2,3-diaryl benzopyrans reported as novel selective cycloxygenase-2 inhibitors was subjected to quantitative structure-activity relationship (QSAR) analysis. Our attempt in correlating the derived physicochemical properties with the COX-2 inhibitory activity resulted in some statistically significant QSAR models with good predictive ability. The QSAR results and the probable pharmacophore features investigated through our study explored some interesting findings for the design of potent new class of selective COX-2 inhibitors.

Development and Use of Hydrophobic Surface Area (HSA) Descriptors for Computer-Assisted Quantitative Structure−Activity and Structure−Property Relationship Studies

A new series of 25 whole-molecule molecular structure descriptors are proposed. The new descriptors are termed Hydrophobic Surface Area, or HSA descriptors, and are designed to capture information regarding the structural features responsible for hydrophobic and hydrophilic intermolecular interactions. The utility of the HSAs in capturing this type of information is demonstrated using two properties that have a known hydrophobic component. The first study involves the modeling of the inhibition of Gram-positive bacteria cell growth of a series of biarylamides. The second application involves the study of the blood-brain barrier penetration of a diverse series of drug molecules. In both cases, the HSAs are shown to effectively capture information related to the hydrophobic components of these two properties. Additional evaluation of the new class of descriptors shows them to be unique in their ability to measure hydrophobic features among a diverse set of conventional structural descriptors. The HSAs are evaluated regarding their sensitivity to conformational changes and are found to be similar in that regard to other widely used molecular descriptors.