Lead-Likeness and the Rule of Three

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19 Questions

Which of the following is the aim of virtual screening?

To score, rank, and/or filter a set of structures

What is the purpose of using virtual screening methods of increasing complexity?

To remove structures of no further interest

What is the Rule of Five (ROF) in drug-likeness assessment?

A set of simple filters to assess the likelihood of poor absorption

Which software tool was used to generate the top 10 structures similar to Celecoxib?

SwissSimilarity

What type of drug is Celecoxib?

COX-2 selective NSAID

Which machine learning technique was used for the analysis?

Random Forest

Which enzyme was used for docking the compounds?

PDB: 3LN1

Which of the following is NOT a factor that contributed towards higher-throughput structure-based methods?

Advancements in protein crystal structures

What are the two components of the docking problem?

Exploring the space of possible protein–ligand geometries and scoring the poses

What is the aim of a docking experiment?

To predict the 3D structure formed when molecules form an intermolecular complex

Which of the following algorithms takes the ligand orientational and conformational degrees of freedom into account?

Monte Carlo algorithm

According to the 'rule of five', which of the following is more likely to result in poor absorption or permeation?

A molecular weight greater than 500

What are the criteria for a compound to be considered 'drug-like' according to the 'rule of five'?

10 or fewer H-bond acceptors

What is the main purpose of logistic regression and random forest techniques in drug discovery?

To classify compounds as drugs or non-drugs

Which molecular descriptors were identified as influential for druglikeness in the best logistic regression model?

HVcpx, MDDD, NNRS, X2A, SRW05

Which term in the scoring function accounts for the loss in translational and rotational degrees of freedom arising from the association of two bodies to give a single body?

DGt/r

Which term in the scoring function captures contributions to the free energy of binding from solvent effects?

DGsolvent

Which term in the scoring function represents the penalty associated with freezing internal rotations of the protein and the ligand?

DGrot

Which term in the scoring function accounts for the contribution from protein–ligand interactions, arising from electrostatic and van der Waals forces?

DGint

Test your knowledge on the theoretical developments and practical applications of lead-likeness in structure-based virtual screening. Explore the concept of the "rule of three" and its significance in compound acquisition and library design. Gain insights into the increasing interest in utilizing protein crystal structures for data analysis and higher-throughput screening.

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