Introduction

In recent years, there have been significant developments made in the way new drugs are being discovered and developed. Such changes are driven by new technologies that have expanded the opportunities to prepare and screen large libraries of compounds in a rapid time frame by the use of high-throughput synthesis (HTS) and screening techniques. Investigations in medicinal chemistry are undertaken as an adventure of the human spirit, stimulated largely by curiosity and served by disciplined imagination.

In general, clinically used drugs are not discovered. What is more likely discovered is known as a lead compound. The lead is a prototypic compound that has the desired biological or pharmacological activity, but it may have many undesirable effects. The structure of the lead compound is then modified by synthesis to amplify the desired activity and to eliminate the unwanted properties. Most of the drugs have been investigated and developed based on results obtained from the screening of potential drugs. There are a variety of approaches used to identify a lead compound and these include random screening, non-random screening, drug metabolism studies, clinical observations and rational approaches.

A promising new approach to drug discovery concerns with synthesis and screening of combinational libraries in order to identify new compounds that express high affinity and specificity for a pharmacologically relevant, bimolecular target.

An essential aspect of screening large combinational libraries is the ability to identify the active components in these complex mixtures, which is usually based on the strength of binding to a selected target macromolecule.

Molecular modeling technique became popular to study the drug excipient interaction which helps to visualize the type and site of interaction on a computer monitor. These strategies are driven by the need to shorten time lines for bringing discovery to the market. As a result the role and needs of synthetic chemistry in the discovery and development of new therapeutic agents has been altered
Carbocyclic or heterocyclic ring systems comprise the core of chemical structures of the vast majority of therapeutic agents. This finding results in the majority of drugs exerting their effect by their actions at receptor or receptor-like sites on cells, enzymes, or related entities. These interactions depend on the receiving site being presented with a molecule that has a well-defined shape, distribution of electron density, and array of ionic or ionizable sites, which complement features on the receptor. These requirements are readily met by the relatively rigid carbocyclic or heterocyclic molecules. Similar groups/structures often exhibit similar biological activities. However, they usually exhibit different potency. The traditional structure activity relationship (SAR) investigations are a useful tool in the search for new drugs.

Free-standing benzene rings have provided the core for a very large number of biologically active compounds. Over the past few years, it has been established that several apparently quite unrelated drug classes owe their activity to effects on a shared biochemical system. A number of compounds have been found that treat elevated lipid levels by other diverse mechanisms

In that these semicarbazones have attained the special attention due to their structural relation activity towards the receptor therapy for Various diseases. These Semicarbazones have proved the efficiency and efficacy in combating various diseases9. Semicarbazone is a derivative of an aldehyde or ketone formed by a condensation reaction between a ketone or aldehyde and semicarbazide. It serves as important synthetic intermediates and can be preferably used for isolation, purification, characterization and protection of aldehydes and ketones. Several semicarbazones, as well as their sulfur analogs and its derivatives, have proved the efficiency and efficacy in combating various diseases In this we have made an attempt to synthesize the novel semicarbazone and has been employed for molecular docking to get the complete treatment for the various diseases.

MOLECULAR DOCKING STUDIES
The process of finding novel leads for a new target is the most important and undoubtedly one of the most crucial steps in identifying a drug and its development program. The study of the structure-activity relationships of a lead compound and its analogues can be used to determine the parts of the structure of the lead that are responsible for its biological activity Most drugs act at a specific site such as an enzyme or receptor. Compounds with similar structures often tend to have similar pharmacological activity. However, they usually exhibit differences in potency, unwanted side effects and in some cases different activities. The pharmacophore summarizes the important binding groups which are required for activity, and their relative positions in space with respect to each other. In order to identify the 3D pharmacophore, it is necessary to know the active confirmation of the molecule. There are various ways in which this might be done. Rigid analogues of the flexible compound could be synthesized and tested to see whether activity is retained. Alternatively, it may be possible to crystallize the target with the compound bound to the binding site. X-ray crystallography could be used to identify the structure of the complex as well as active confirmation of the bound ligand. Molecular-docking methodologies ultimately seek to predict (or often retrospectively reproduce) the best mode by which a given compound will fit into a binding site of a macromolecular target and it has caught the attention of many pharmaceutical and biotechnology companies eager to discover novel chemical entities.

EXPERIMENTAL DESIGN
Because the process of finding a novel compound showing bioactivity can be time-consuming and expensive, structure based drug design has been established as a vital first step to therapeutic development. Receptor-based design requires the availability of the receptor structure, which is used to examine the interactions that occur with any members of a large database of ligands. Docking procedures aim to identify correct poses of ligands in the binding pocket of a protein and to predict the affinity between the ligand and the protein.

DOCKING SOFTWARE
Docking software programs such as protein preparation wizard (Maestro 8.5, Schrodinger, LLC), Marvin sketch-5.0.6.1 (Chemaxon), MGL Tools-1.4.6 and AutoDock4 (The Scripps Research Institute) have been used. Molecular docking studies were performed with X-ray crystal structure of human PPARa and PPARy using AutoDock4 (The Sripps Research Institute). X-ray crystallographic models 3G8I for hPPARa and 3 HOD for hPPARy were downloaded from Protein data bank (www.rcsb.org). Docking procedures were carried out by the method developed by Agnes et al.

Ligand preparation
Structures of ligands (Compound 01 to Compound 32) were sketched using Marvin Sketch-5.0.6.1 (Chemaxon), 3D-geometry optimized and saved in PDB format for AutoDock compatibility. MGLTools-1.4.6 (The Sripps Research Institute) was used to convert ligand.pdb files to ligand.pdbqt files.
Fig 1 Pharmacophore model of PPAR agonists

Protein preparation
For each protein target, the system expert selected a representative protein structure to be used for all docking calculations. The system expert therefore took special care to select a structure that both was a high-quality structure of good resolution. X-ray crystal structure of hPPARa (3G8I) and hPPARy (3 HOD) were downloaded from Protein data bank (www.rcsb.org). Protein preparation wizard (Maestro 8.5, Schrodinger, and LLC) was used to prepare protein. Through which hydrogens were added, water molecules were removed, side chains were optimized for hydrogen bonding and finally energy minimized using OPLS2001 force field. The energy minimized protein was then saved in PDB format. Using MGLTools-1.4.6 nonpolar hydrogens were merged,

AutoDock atom type AD4 and Gasteiger charges were assigned and finally saved in protein.pdbqt format.
Docking protocol
Grid parameter file (protein.gpf) and docking parameter files (ligand.dpf) were written using MGLTools-1.4.6. Receptor grids were generated using 60x60x60 grid points in xyz with grid spacing of 0.375 A. Grid box was centered cocrystallized ligand. Map types were generated using autogrid4. The 'Grid Parameter File' (protein.gpf) was used for generating map types of compound 13 with 3G8I (PPARa) and compound 31 with 3HOD (PPARy).

Docking was carried out with default parameters such as number of runs: 50, population size: 150, number of evaluations: 2500000 and number of generations: 27000, using autodock4. The 'Docking Parameter File' (ligand.dpf) was used for molecular docking of compound 13 with 3G8I (PPARa) and compound 31 with 3HOD (PPARy).

Fig. 4.2a. Interaction of Compound 13 with PPARy (PDB Code: 3HOD), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type Fig. 4.2b. Interaction of Compound 31 with PPARy (PDB Code: 3HOD), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type

Fig.4.3a. Interaction of Compound 13 with PPARa (PDB Code: 3G8I), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type

Fig.4.3b. Interaction of Compound 31 with PPARa (PDB Code: 3G8I), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type

Conclusion
Superimposition of docking structures of compound 13 and 31 with PPARa/y revealed that these analogues superimposed well with each other, whereas the linker and the tail parts adopt different conformations. The 4-substituted aromatic centre allows the best fit to the binding site by providing the optimum distance between the acidic head and oxygen at C-4 position of aromatic centre, thus moving the hydrophobic tail on aromatic centre close to the hydrophobic region of protein consisting of serine, tyrosine and histidine, resulting in strong hydrophobic interactions with these residues. From these findings, it can be suggested that the designing of new chemical analogues of vanillin semicarbazones and its structural modification with a very interesting pharmacological profile lead the necessity of further research.

Results:
Table 4.1. Compounds with their Docking scores Table 4.2. Interaction for PPARy
Table 4.3. Interaction for PPARa

Diagrams:
Fig. 4.2a. Interaction of Compound 13 with PPARy (PDB Code: 3HOD), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type
Fig. 4.2b. Interaction of Compound 31 with PPARy (PDB Code: 3HOD), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type
Fig.4.3a. Interaction of Compound 13 with PPARa (PDB Code: 3G8I), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type
Fig.4.3b. Interaction of Compound 31 with PPARa (PDB Code: 3G8I), H-bond interaction were shown in green dots and atoms establishing H-bonds were colored by atom type

Claims
By the molecular docking we have clearly claim that the Structure modifications of the lead compounds are designed to achieve specific goals over the prototypic molecule by the following improvements.
■S The development of more potent drugs
■S To eliminate or minimize toxic effects
S To discover the pharmacophore and to separate the molecular features responsible for the desired activity and the undesirable or toxic effects and
S Modification of the pharmacokinetic properties of the compound