The antagonist binding pocket identified from literature for alpha-1A-adrenergic receptor is shown in the figure below (Fig. 2). Outcome of molecular docking of five established (lead) molecules showing appreciable interactions in terms of re-rank scores are provided in Table 1.

Perusal of tables concludes that among five chosen lead compounds (Phenoxybenzamine, Phentolamine, Prazosin, Ergoloid Mesylate, and Labetalol), Prazosin binds strongly and efficiently to alpha-1A-adrenergicas an antagonist (Fig. 3). Surprisingly, when all similar compounds from library were analyzed based on re-rank score, two new chemical compounds (Table 2) were identified which are structurally similar

to Ergoloid Mesylate (pubchem CID 10289950) and Prazosin this website (pubchem CID 16191408). Hydrogen bond and electrostatic interactions are shown in diagrams separately (Fig. 3, Fig. 4 and Fig. 5). Best candidate obtained in present studies is a compound similar to Ergoloid Cyclopamine Mesylate (pubchem CID 10289950). Chemically this compound is N-(4,6-dimethoxy-2-[3-(piperidin-1-yl)propyl]aminopyrimidin-5-yl)-5-[(1,1,3,3,6-pentamethyl-1,3-dihydro-2-benzofuran-5-yl)methyl]furan-2-carboxamide with Molecular docking score −183.386 and re-rank score −113.571 ( Table 2). The next molecule with accepted antagonist effect is a compound similar to Prazosin with pubchem CID 16191408, which is chemically 3-[5-(2H-1,3-benzodioxol-5-yl)-1,3,4-oxadiazol-2-yl]-N-ethyl-N-[2-(1H-pyrazol-1-yl)ethyl]propanamide

with Molecular docking score −150.702 and re-rank score is −112.604 ( Table 2). Both the molecules mentioned above are newer and have never been tested for their alpha-1A-adrenergic receptor antagonist effects. Identification of the pharmacophores was achieved from the study of presence of amino acids around docked molecules with the best scores, as illustrated in Table 3. A comparative perusal of Table 3 proves that amino acids which play crucial role are Val 107, Val 157, Asp 106, Ile 157, Ser 158, Ala 189, and Ser 192, with most important and repetitive Phe 288 and Phe 289. Based on the chemical nature of amino acids, it was significantly concluded that the antagonist binding site Carnitine dehydrogenase of alpha-1A-adrenergic receptor is extensively and completely hydrophobic in nature. The above analysis is obtained from structure based pharmacophoric studies. Table 3 is a strong support of our statement and confirmation of hydrophobic nature of antagonist binding site. The conclusive framework achieved from structure based and ligand based studies confirms the hydrophobic nature of antagonist binding site of alpha-1A-adrenergic receptor. Structure based analysis confirms repetitive presence of amino acids Val 107, Val 157, Asp 106, Ile 157, Ser 158, Ala 189,Ser 192, Phe 288 and Phe 289 around antagonists.