Optimization of Structure Based Virtual Screening Protocols Against Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents

Abstract

Thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKMtub ) is an established drug target against tuberculosis. The enzyme TMPKMtub is responsible for the survival of bacterium MTB and required to synthesize an essential building block of the bacterial DNA which is thymidine triphosphate (TTP). There are several potent inhibitors available against the target enzyme but the majority are substrate analogues. Recently, three dimensional structures of the enzyme TMPKMtub inhibitor complexes were resolved using X-ray crystallography. These available crystal structures were the basis of initiating a structure based lead identification campaign against TMPKMtub . The available information was utilized to perform structure-based virtual screening against TMPKMtub with the hope to diversify the structures of the current inhibitors. In order to setup the protocol, 10 000 out of 45 000 drug-like molecules were randomly selected from National Cancer Institute's (NCI) database. Additionally 105 known inhibitors along with 11 natural substrates were mixed with the 10 000 selected compounds. For the current study, a rigid based docking algorithm, i.e., FRED has been utilized to set up an efficient docking and scoring protocol. The methods including enrichment curves, consensus scoring and ROC curves are providing useful insights into the setting up of a suitable structure-based docking protocol against TMPKMtub . As a result, an optimum docking and scoring function has been identified for future large scale virtual screening. In the present work, we have demonstrated a rational choice of protocol for structure based virtual screening of chemical libraries and help to understand the influence of receptor flexibility by using multiple geometries.

Exploring Novel N-Myristoyltransferase Inhibitors: A Molecular Dynamics Simulation Approach

“…The prime objective behind using the decoy data set is to avoid the artificial enrichment . The decoys were prepared according to the protocol established earlier …”

“…37 The decoys were prepared according to the protocol established earlier. 38 For VS, Maybridge Screening Collection was downloaded from the Maybridge website (https://www.maybridge.com). As of December, 2018, Maybridge screening collection consisted of 52 066 compounds.…”

Protein kinases as antituberculosis targets The case of thymidylate kinases

“…Amidst several studies focusing on SAR studies Zaheer Ul Haq and his team optimized a structure based virtual screening protocol for TMPkmt inhibitors (56). To test the protocol they used a collection of 10,000 randomly selected molecules from the National Cancer Institute database along with 105 known substrates and inhibitors of TMPKmt.…”