Lead-Likeness and the Rule of Three

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Which of the following is the aim of virtual screening?

To analyze the results of an experiment

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

To purchase compounds from an external company

To synthesize compounds from libraries

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

To analyze the results of an experiment

To purchase compounds from an external company

To remove structures of no further interest (correct)

To synthesize compounds from libraries

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

An analysis of substructure filters

A sequence of methodologies used in virtual screening

A set of simple filters to assess the likelihood of poor absorption (correct)

An analysis of simple properties of drug molecules

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

SwissSimilarity Signup and view all the answers

What type of drug is Celecoxib?

COX-2 selective NSAID Signup and view all the answers

Which machine learning technique was used for the analysis?

Random Forest Signup and view all the answers

Which enzyme was used for docking the compounds?

PDB: 3LN1 Signup and view all the answers

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

Advancements in protein crystal structures Signup and view all the answers

What are the two components of the docking problem?

Exploring the space of possible protein–ligand geometries and scoring the poses Signup and view all the answers

What is the aim of a docking experiment?

To predict the 3D structure formed when molecules form an intermolecular complex Signup and view all the answers

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

Monte Carlo algorithm Signup and view all the answers

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 Signup and view all the answers

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

10 or fewer H-bond acceptors Signup and view all the answers

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

To classify compounds as drugs or non-drugs Signup and view all the answers

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

HVcpx, MDDD, NNRS, X2A, SRW05 Signup and view all the answers

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 Signup and view all the answers

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

DGsolvent Signup and view all the answers

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

DGrot Signup and view all the answers

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

DGint Signup and view all the answers