PREPARED BY: MANOJ KUMAR YADAV ASSISTANT PROFESSOR (MEDICINAL CHEMISTRY) PIT, JAUNPUR manojniperrbl@gmail.com

1. COMPUTER AIDED DRUG DESIGNE BP807ET
PREPARED BY: MANOJ KUMAR YADAV
ASSISTANT PROFESSOR
(MEDICINAL CHEMISTRY)
PIT, JAUNPUR
manojniperrbl@gmail.com
01) Which of the following operations or calculations would generally be carried out using
quantum mechanics?
a. Energy minimisation
b. Identifying stable conformations
c. Partial atomic charges
d. Energy calculations for specific conformations
02) Which of the following software programs is not used for drawing 2D chemical structures?
a. ChemDraw
b. ChemWindow
c. Chem3D
d. Isis/Draw
03) Which of the following software programs is not dedicated to the creation of 3D chemical
models?
a. DOCK
b. Alchemy
c. Hyperchem
d. Discovery Studio Pro
4. Which of the following is associated with conformational searching?
a. LUDI
b. DOCK
c. Monte Carlo method
d. CoMFA
5. Molecular dynamics can be used to search for different conformations of a molecule. Which
of the following statements is false?
a. A variety of different conformations are generated by 'heating' the molecule to
900K.
b. The position and velocity of each atom is measured after each nanosecond of
movement

2. COMPUTER AIDED DRUG DESIGNE BP807ET
c. The programme treats each atom as a moving sphere
d. Each atom is only allowed to move a fraction of a bond length between each cycle
of calculations
6. Which of the following statements regarding molecular mechanics is untrue?
a. It treats atoms as spheres.
b. It treats bonds as rigid features.
c. It is a molecular modelling computational method.
d. It uses equations that obey the laws of classical physics.
7. Which of the following statements regarding quantum mechanics is untrue?
a. It uses quantum physics to calculate molecular properties.
b. It makes the assumption that nuclei are moving independently of each other
c. It makes the assumption that electrons move independently of each other.
d. There are two broad categories - ab initio and semi-empirical
8. Which of the following statements is true?
a. energy minimisation is carried out using molecular mechanics
b. energy minimisation is used to find the most stable conformation for a molecule
c. energy minimisation is carried out by varying only bond angles and bond lengths
d. energy minimisation stops when a structure is formed with a much greater stability than the
previous one in the process
9. What is meant by a local energy minimum in conformational analysis?
a. it is a localised region of a molecule which is free of steric strain
b. it is the most stable conformation of a structure
c. it is the initial structure that is formed when a 3D model is created, prior to energy
minimisation
d. it is the closest stable conformation to the starting structure
10. What is meant by a global energy minimum in conformational analysis?
a. It is a localised region of a molecule which is free of steric strain.
b. It is the most stable conformation of a structure.
c. It is the initial structure that is formed when a 3D model is created, prior to energy
minimisation.
d. It is the closest stable conformation to the starting structure.
.

3. COMPUTER AIDED DRUG DESIGNE BP807ET
11. The following diagram shows the energy of the starting structure prior to energy
minimisation. What is the likely result of energy minimisation?
a. Energy minimisation would have no effect and the structure would remain at
position Y.
b. The structure would be energy minimised and give the most stable structure
corresponding to position Z.
c. The structure would be energy minimised and give a final structure
corresponding to either position X or Z.
d. Energy minimisation would be carried out and the final structure would correspond
to position J.
12. Which of the following statements regarding structural overlays is false?
a. The two structures to be overlaid should both be in their active conformations.
b. Usually specific pairs of atoms are chosen (one from each molecule) to allow
the overlay to take place.
c. The fitting process normally involves both molecules being rigid and not changing
conformation during the overlay.
d. The overlay is carried out until a maximum value of the root mean square
distance between all the atom pairs is achieved.
13. Which of the following statements is true?
a. The most stable conformation of a drug is not necessarily the active conformation.
b. The active conformation is the most reactive conformation of a structure.
c. The active conformation is the conformation adopted by a target binding site when it binds
a drug.
d. The active conformation can be determined by conformational analysis.

4. COMPUTER AIDED DRUG DESIGNE BP807ET
14. Which of the following statements is not true of cyclic structures?
a. They are normally more rigid than acyclic structures
b. They have fewer possible conformations
c. They are useful in determining the active conformation of a series of related
compounds
d. . They are easierto synthesise than more flexible acyclic molecules
15. What term is used to describe the process by which drugs are fitted into their target binding
sites using molecular modelling
a. Energy minimisation
b. Conformational searching
c. Docking
d. Overlaying
16. What term is used for the design of a novel drug based on molecular modelling studies of a
binding site
a. Drug development
b. Structure-based drug design
c. De novo drug design
d. Drug optimisation
17. Which of the following statements is false in de novo drug design?
a. The design of flexible molecules is superior to rigid ones.
b. Molecules should be designed to fit as snugly as possible into the target binding
site.
c. Molecules that have to adopt an unstable conformation in order to bind should be
rejected.
d. Desolvation energies cannot be ignored.
18. What is the software LUDI used for?
a. Docking molecules into binding sites
b. Automated de novo drug design
c. Creating 3D models of molecules
d. Conformational analysis
19. Which of the following statements is untrue when using molecular modelling to design a
combinatorial library?

5. COMPUTER AIDED DRUG DESIGNE BP807ET
a. Pharmacophore triangles can be used to design a library.
b. The aim is to synthesise the maximum number of structures likely to produce
the minimum number of pharmacophores.
c. Rigid structures should be analysed before flexible ones.
d. Structures should only be included in the library if they represent at least 10%
additional new pharmacophores compared to the total represented by structures
already present in the library.
20. Which of the following operations or calculations would generally be carried out using
molecular mechanics?
a. Heat of formation for specific conformations
b. Generating different conformations
c. Partial atomic charges
d. Transition-state energies
21. Which of the following operations or calculations would generally be carried out using
quantum mechanics?
a. Studying molecular motion.
b. Generating different conformations.
c. Energy minimisation.
d. Transition-state energies.
22. Which of the following software programmes is not used for drawing 2D chemical
structures?
a. ChemDraw
b. LUDI
c. ChemWindow
d. Isis/Draw
23. Which of the following software programmes is not dedicated to the creation of 3D
chemical models?
a. CAChe
b. CoMFA
c. ChemX
d. Sybil

6. COMPUTER AIDED DRUG DESIGNE BP807ET
24. Which of the following statements is false regarding Monte Carlo methods of
conformational searching?
a. The Monte Carlo method introduces a bias towards stable conformations.
b. The method has the drawback that the structure becomes stuck in a local
energy minimum 'well' and fails to reach the global energy minimum.
c. Energies of randomly created conformations are compared, then further minor
modifications are carried out on the more stable conformations.
d. Random conformations are generated by carrying out bond rotations
25. Molecular dynamics can be used to search for different conformations of a molecule. Which
of the following statements is false?
a. A variety of different conformations are generated by 'heating' the molecule to 900K.
b. The position and velocity of each atom is measured after each femtosecond of movement.
c. The programme treats each atom as a moving sphere.
d. Each atom is only allowed to move a bond length between each cycle of calculations.
26. Two molecules or molecular fragments containing an identical number and arrangement
of electrons should have similar properties are:
a. Isosteres
b. Isomers
c. Isotopes
d. None of above
27. Tolbutamide, an oral hypoglycemics agent having extended half-lives and with reduced
toxicity has been designed by replacement of:
a. Chlorine
b. Methyl
c. Amino
d. Ethyl
28. In 5-fluorouracil, an antineoplastic agent, Fluorine exerts inductive effect and
responsible for inhibition of which enzyme:
a. Esterase
b. Thymidylate synthase
c. Folatereductase
d. Phosphorylase

7. COMPUTER AIDED DRUG DESIGNE BP807ET
29. In cholinergic agonists replacement of quaternary ammonium group with the
phosphonium and arsonium analogues include which substitution:
a. Univalent substitution
b. Divalent substitution
c. Trivalent substitution
d. Tetravalent substitution
30. The substitution in which steric arrangement and electronic configuration are similar to
those of the parent compound
a. Isosterism
b. Bio-isosterism
c. Classical Isosterism
d. Non-classical isosterism
31. Pethidine and meperidine areester of a piperidyl carboxylic acid:
a. Methyl
b. Ethyl
c. Propyl
d. Butyl
32. By opening of the thiazole ring of the sulphathiazole to give a thioureaqunit, sulphur
ato is replaced by which atom
a. Oxygen
b. Nitrogen
c. Carbon
d. None of these
33. Which bond of diethyl stilbestrol was important for the orientation of the phenolic and
ethyl groups for binding to the estrogenic receptor:
a. Upper
b. Lower
c. Central
d. Front

8. COMPUTER AIDED DRUG DESIGNE BP807ET
34. In amide group bioisosteres, amide bond is required as:
a. Hydrogen donor
b. Hydrogen acceptor
c. Both (a) and (b)
d. None of above
35. Which bioisosteres have been successfully employed in the development of H2-
receptor antagonist:
a. Amide bioisosteres
b. Thioureabioisosteres
c. Halogen bioisosteres
d. Classical bioisosteres
36. Who is the father of cocept of QSAR
a. Corwin Hansch
b. Meyer-Overton
c. Ferguson
d. Richest
37. QSAR helps in drug design as it helps in... ..... ..
a) Prediction of biological activity of drug
b) Minimizing of side effect
c) Optimization of lead
d) All of the above
38. EIectric and steric property mainelly helps in
a) Absorbtion of drug
b) Penetration of drug
c) Drug-receptor interaction
d) None of the above
39. Organic solvent used in measuring partition-coefficient is... . . . . . . . . . . . .
a) Aceton
b) n-octanol
c) Benzene
d) Propranol
40. Ionization of benzoic acid is used in .....
a) Hydrophobic parameter

9. COMPUTER AIDED DRUG DESIGNE BP807ET
b) Steric parameter
c) Electronic parameter
d) None of the above
41. DYLOMMS (Dynamic Lattice-Oriented Molecular modelling system) is related to:
a) SAR
b) 2D-QSAR
c) 3D-QSAR
d) None
42. Colchicineis a lead compound for agents which act as inhibitor of:
a) tubulin polymerization
b) Cell wall synthesis
c) Protein synthesis
d) Metabolites
43. The biological activity of most drugs is related to a combination of physicochemical
properties. This statement is relevant to:
a) Hammett’s substituent constant
b) Tafts steric constant
c) Hansch analysis
d) Free Wilson analysis
44. Partial Least Square (PLS) is used in:
a. SAR
b. 2D-QSAR
c. 3D-QSAR
d. None
45. Xn, an indicator variable is related to:
a. Hammett’s substituent constant
b. Tafts steric constant
c. Hansch analysis

10. COMPUTER AIDED DRUG DESIGNE BP807ET
d. Free Wilson analysis
46. The measure value of the electron withdrawing or electron donating ability of a substituent
is known as:
a. Hammett’s substituent constant
b. b. Tafts steric constant
c. Hansch analysis
d. d. Free Wilson analysis
47. The numerical range for the thermodynamic activity which showing that they are active
only at relative high concentration is:
a. 0.1-1.0
b. 0.01-1.0
c. 0.001-0.01
d. 1-10
48. The positive value of Tt indicates that substituents is:
a. More hydrophobic than halogen
b. less hydrophobic than halogen
c. More hydrophobic than hydrogen.
d. less hydrophobic than hydrogen
49. The negative value of It indicates that substituents is:
a. More hydrophobic than halogen
b. More hydrophobic than hydrogen.
c. Less hydrophobic than halogen
d. Less hydrophobic than hydrogen
50. An equilibrium is set up between the ionized and unionized forms where the relative
properties of these species are known as:
a. Equilibrium
b. Dissociation constant

11. COMPUTER AIDED DRUG DESIGNE BP807ET
c. All of above
d. None
51. QSAR is....
(a) Quantitative structure activity relationship
(b) Quantity structure action result
(c) Quality structure action report
(d) All of the above
52. Software used in verloop steric parameter is
(a) Chemdraw
(b) Marwin sketch
(c) Argus
(d) Sterimol
53. Which parameter is used to find steric property
(a) Freewilson
(b) Hansch analysis
(c) Tafts steric constant
(d) Hammett constant
54. In which synthesis Solid support used in combinatorial chemistry
a. Liqiud phase synthesis
b. Solid phase synthesis
c. Phase —I synthesis
d. Conventional synthesis
55. An innovative process oi finding new medication based on the knowledge of a biological
Target is
(a) Drug design
(b) New design
(c) Modelling
(d) New target
56. Hammett’s constant used to find which parameters
a. HydrHydrophili

12. COMPUTER AIDED DRUG DESIGNE BP807ET
b. Electronic
c. steric
d. Lipopliilie
57. Combinatorial synthesis is Used mainly for the synthesis of
a. Beta lacta
b. Monobactams
c. Tetracycline
d. Peptide Polymers
58. Relative distribution of drug in organic and aqueous mixture is Known
a. Hydrophilicity
b. Hydrophobicity
c. Partition coefficient
d. Lipophlicity
59. When both ligand and receptor are flexible. The ligand attach flexibly at the active site of
receptor to maximize attaching forces between them. This type of docking is known as:
a) Induced fit docking
b) Lock and key docking
c) Ensemble docking
d) Rigid docking
60. Multiple protein structures are utilized as an ensemble for docking with ligand in one of the
following technique:
a) Induced fit docking
b) Lock and key docking
c) Ensemble docking
d) Rigid docking
61. The docking combined with a scoring function can be used to quickly screen large
databases of potential drugs in silico to identify molecules that are likely to bind to protein
target of interest.This method is helpful for.
a) Hit identification
b) Lead optimization

13. COMPUTER AIDED DRUG DESIGNE BP807ET
c) Bioremediation
d) Drug-DNA interaction
62. The rotamer libraries of amino acid side chains are used for.
a) Ligand flexibility
b) Receptor flexibility
c) Scoring function
d) Search space
63. Force field energy estimation is most often used for:
a) Ligand flexibility
b) Receptor flexibility
c) Scoring function
d) Search space
64. Protein-ligand docking goftware congi8tN of two main components which works together
are:
a) Search Algorithm and Scoring function
b) Fragment based algorithm and Scoring function
c) Search algorithm and Genetic algorithm
d) Fragment based algorithm and Genetic algorithm
65. In molecular biology, there are two docking probletng arise are:
a) Protein- protein clocking and Rigid- body docking
b) Ligand- protein docking and Protein-Protein docking
c) Rigid-body docking and ligand-protein docking
d) None of these.
66. Rigid docking include:
a) Molecular shape representation
b) Surface patch matching
c) Filtering and scoring
d) All of above
67. E<1 implies for:
a) Positive enrichment
b) Negative enrichment

14. COMPUTER AIDED DRUG DESIGNE BP807ET
c) Positive and Negative enrichment
d) Constant enrichment
68. Challenges stand up during De novo design.
a) Structure generation
b) Scoring
c) Optimization
d) All of above
69. The non-bonded interaction which calculate the low energy conformation of a molecule also
known as:
a) London interaction
b) Van der Waals interaction
c) Coulomb interaction
d) ‘London-Van der Waal interaction
70. The electron wave function for all the electrons in a molecule tells us:
a. Electron rotation
b. Electron density
c. Electron affinity
d. All of above
71. The program which helps to join the templates, such ag five and six membered ring and
acyclic fragments to mimic pharmacophore model is:
a) SCROUT
b) UNITY
c) MACCS-3D
d) CAVEAT
72. Which program is using as shape based super position for identifying compound that have
similar shape:
a) CSD
b) DBS-3D
c) DOCK
d) ROCS

15. COMPUTER AIDED DRUG DESIGNE BP807ET
73. The model generated from MD deception trajectories show considerably better
representation of the flexibility of pharmacophore is:
a) Dynamic pharmacophore
b) Ligand pharmacophore
c) Structural pharmacophore
d) Pharmacophore filter
74. Interaction between a charged ion and a neutral molecule with a dipole moment is called:
a) Ion-dipole interaction
b) Dipole- dipole interaction
c) Bonded interaction
d) Non-bonded interaction
75. Virtual screening techniques are categorized on the basis of:
a) Structure based
b) Ligand based
c) Fragment based
d) Structure and ligand based
76. Quick searching of database of 3D structures programs includes:
a) Chem DBS-3D,
b) ALLADIN UNITY,
c) MACCS-3D
d) All of above
77. Name of the program in which fragments from bioactive conformation are joint with spacer
to generate a new structure to fit the model.
a) SCROUT
b) UNTY
c) NEWLEAD
d) QSAR
78. Virtual Screening is also called as:
a. Silico drug design
b. Rational drug design
c. Serendipity drug design
d. None of the above

16. COMPUTER AIDED DRUG DESIGNE BP807ET
79. The techniques that hold a lot of prospective in target identification (generally
proteins/enzymes), target validation, understanding the protein is called as
a) Cheminformatics
b) Docking
c) Bioinformatics
d) None of the above
80. 3-D geometry of interaction features that a molecule must have in order to bind in a
protein’s active site is called as
a) Inactive compound
b) Pharmacophore
c) Active compound
d) Bioprecursor
81. Following is a type of docking.
a) Rigid
b) Flexible
c) Mannual /Semiflexible
d) All of the above
82. Based on the principle of conformation generation, the search methods are categorized
into.......
a) Stochastic
b) Systematic
c) Deterministic
d) All of the above
83. The field of science in which biology, computer science and information technology merges
to form a single discipline is called
a) Chemoinformatics
b) Bioinformatics
c) Rational drug design
d) None of the above
84. Representation of 2d molecular structures includes
a) Image file
b) Graph theory

17. COMPUTER AIDED DRUG DESIGNE BP807ET
c) Connection table
d) All of the above
85. The computerized method to understand and arrange the information associated with
biological macromolecules is:
a) Chemo-informatics
b) Bio-informatics
c) Chemical database
d) Biochemical database
86. Analysis under the bioinformatics to be done for a component having large dimensionality
and small sample size are:
a) Sequence analysis
b) Spectral analysis
c) Microarray analysis
d) Small sample domain analysis
87. NIH’s Molecular Libraries and Imaging initiative are the experimental project of:
a) Chemoinformatics
b) Bioinformatics
c) Chemical database
d) Biochemical database
88. The error in the Medicinal Chemistry publication can be indexed by the database:
a) FASTA
b) PSI-BLAST
c) WOMBAT
d) None of above
89. Which of the following is not the program of structural conversion and cleaning:
a) ChemAxon
b) MOE
c) 34 Sybyl
d) FASTA
90. From computational point of view which system is used for drug safety development:
a) DEREK
b) Topkat
c) MultiCASE

18. COMPUTER AIDED DRUG DESIGNE BP807ET
d) All of above
91. Transporter classification system consists of the database:
a) PubChem compound
b) PubChem substance
c) PubChem bioassay
d) All of above
92. ..........was the lead used for development of anti-inflammatory drug Indornethacin.
a. Histamine
b. Serotonin
c. Dopamine
d. Acetylcholine
93. Bupropion was discovered through:
a. Clinical observations
b. Metabolic studies
c. Serendipity
d. Random screening
94. Fexofenadine is a metabolite of
a. Diazepam
b. 5-Fluorouracil
c. Terfenadine
d. Fluoxetine
95. Librium was discovered through:
a. Clinical observations
b. Metabolic studies
c. Serendipity
d. Random screening
96. The active principle emetine is present in:
a. Ipecacuanha root
b. Coca leaf
c. Cinchona bark
d. Belladonna leaf

19. COMPUTER AIDED DRUG DESIGNE BP807ET
97. Sildenafil is used for the treatment of:
a. Erectile dysfunction
b. Colon cancer
c. Malaria
d. d. Dengue
98. A second messenger molecule that turns on the enzyme guanylatecyclase, which converts
guanosine triphosphate to cGMP:
a. Nitric oxide
b. Nitric acid
c. Nitrogen
d. Nitramine
99. Sildenafil inhibits which enzyme, preventing the hydrolysis of cGMP and prolonging the
vasodilation effect:
a. Protease
b. phosphodiesterase
c. DHFRase
d. d. Ligase
100. The accurate structure of penicillin was elucidated by Dorothy crowfoot
Hodgkin(oxford) in:
a. 1894
b. 1994
c. 1944
d. 1954