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CRITICAL ASSESSMENT OF COMPUTATIONAL HIT-FINDING EXPERIMENTS

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Challenge #1

Hit Identification
Method Name
CReM
Description of your approach (min 200 and max 800 words)

The workflow will consist of a preliminary part and two production parts. On the preliminary stage MD simulation of the protein will be performed to study protein flexibility and choose representative conformations. On the first stage we will enumerate possible ligands for each of the representative protein conformations by the fragment-based de novo approach CReM guided by docking (Autodock Vina). To create the library of fragments used for compound enumeration we will use Enamine database of previously synthesized compounds that should increase synthetic accessibility of designed molecules. Hit lists obtained for every representative protein conformation will be combined in one and compounds will be filtered by physicochemical properties regarding the traffic-lights evaluation protocol, structural alerts, synthetic accessibility score and further by a retrosyntetic tool (AiZynthFinder). The remaining compounds will be redocked by other docking programs (smina, gnina, DeepDock, etc) and ranked independently by each scoring function. We will count the number of times each compound will get in top 1% in every ranking list and choose those compounds which occurred more frequently in top 1% of different lists (consensus docking). For selected compounds we will perform MM-PBSA calculation of binding free energy (rescoring) to remove less promising molecules. From the remaining compounds we will select 50 diverse molecules. On the second stage we will use these 50 de novo generated molecules as queries to perform similarity search among Enamine REAL space using FTrees or using similarity search among previously synthesized Enamine compounds. All selected compounds will be subjected to the same filtering, consensus docking and rescoring procedure as described above to select other 50 compounds, which should be easy to synthesize. Using such a two-stage pipeline we will be able to perform adaptive search in Enamine REAL space.

Commercial software packages used

FTrees

Free software packages used

CReM, Autodock Vina, Smina, gnina, DeepDock

Hit Optimization Methods
Method type (check all that applies)
De novo design
High-throughput docking
Physics-based
Description of your approach (min 200 and max 800 words)

For active compounds we will establish more probable binding poses by ranking docking poses according to calculated binding free energy using MM-PBSA. Further we will enumerate possible analogs using CReM structure generation approach and Enamine fragment libraries. The enumeration will be guided by docking. During enumeration process we will preserve important protein-ligand contacts identified for active parent molecules. Generated compounds will be filtered by synthetic accessibility estimated by retrosynthetic tool (e.g. AiZynthFinder) and physicochemical properties regarding the traffic lights evaluation protocol. If the number of kept compounds will be large we will perform consensus docking as described previously to reduce their number to reasonable amount. Finally compounds will be ranked by MM-PBSA. Compounds ranked on top and which have small changes relatively to the parent active molecule may be subjected to alchemical free energy perturbation to estimate their change in affinity more precisely.

Method Name
CReM
Commercial software packages used

Shrodinger Maestro

Free software packages used

CReM, Autodock Vina, smina, gnina, DeepDock, GROMACS

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