ORIGINAL RESEARCH Structure modeling and hybrid virtual screening study of Alzheimer’s associated protease kallikrein 8 for the identification of novel inhibitors Syed Sikander Azam • Saad Raza Received: 12 November 2013 / Accepted: 27 January 2014 Ó Springer Science+Business Media New York 2014 Abstract Kallikrein 8 (KLK8) is an extra cellular serine protease which is responsible for nerve growth, and degen- eration and nervous plasticity have been associated with Alzheimer’s disease. In silico analysis of KLK8 has not been performed until now. This study is aimed at molecular mod- eling and lead identification for a potent inhibitor. The hybrid of ligand- and structure-based virtual screening was applied on commercially available compounds. Ligand similarity search was employed, followed by ligand docking protocol. Compound’s potential for their activity was deduced from docking scores and their interactions with the active site. For active permeation of compounds through blood brain barrier, their molecular properties were checked with previously reported compounds. The compound that showed the most potential according to criteria was 1-(3,5-difluorophenyl)-5- hydroxy-7-(4-hydroxy-3,5-dimethoxyphenyl)-6,7-dihydro- 1H-pyrrolo[3,2-b] pyridine-3-carboxylic acid (ZINC 61720639). Keywords Kallikrein 8  Alzheimer’s disease  Virtual screening  Molecular docking  In silico analysis Introduction Kallikrein (KLK) gene family is a subfamily of serine pro- teases. In humans, this gene family is located on chromo- some 9q13.3–q13.4, and fifteen members of KLK have been identified (Lawrence et al., 2010). Kallikrein 8 (KLK8) (also known as neuropsin/ovasin) was cloned from a human skin cDNA library as a homologue of mouse neuropsin (Yoshida et al., 1998). KLK8 is a chymotrypsin like serine protease; these proteases active site is called as ‘‘S1’’ which is mostly hydrophobic in nature, and the substrate polypeptide is composed of large hydrophobic amino acids like tyrosine, phenylalanine, or tryptophan near the cleaving site (Perona and Craik, 1995). KLK8 is found to be acting on numerous substrates including gelatin, collagen type 4, fibronectin, and it can also degrade single chain tissue plasminogen activator (Rajapakse et al., 2005). KLK8 mRNA is localized at high concentration in the skin and brain. Proteases have been shown to play essential roles in the nervous system, including neurite outgrowth, synaptic plasticity, and neuronal degen- eration (Shiosaka and Yoshida, 2000). Proteases are also implicated in etiology of Alzheimer’s disease (AD), which is characterized by neuronal damage and loss of brain function. Serine proteases are involved in the degradation of Blood Brain Barrier (BBB) during events of ischemia, head injury, and shock (Gingrich and Traynelis, 2000). They also have been shown to participate in the processing of physiologi- cally active macromolecules, digestion of extracellular matrix proteins, and cleavage of synapse-related proteins (Perona and Craik, 1995). KLK8 is found to be indirectly mediating a number of phenomena leading to brain damage, which include neurite outgrowth, edema, neuronal survival, apoptosis, hyperexcitability, seizure, ischemic, and excito- toxic brain damage (Gingrich and Traynelis, 2000). Inter- estingly, the KLK8 transcript level in the hippocampus of patients with AD was found to be elevated 11.5-fold com- pared to that in controls, suggesting that KLK8 may play a role in neurodegeneration (Shimizu-Okabe et al., 2001). This dramatic increase in KLK8 expression in AD could com- promise hippocampal plasticity by promoting excessive modification of the extracellular matrix (Shiosaka and Yos- hida, 2000). Furthermore, human KLK8 mRNA and its S. S. Azam (&)  S. Raza Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan e-mail: ssazam@qau.edu.pk; syedazam2008@gmail.com 123 Med Chem Res DOI 10.1007/s00044-014-0932-1 MEDICINAL CHEMISTR Y RESEARCH