Chapter 20 MCQs

. What are the two main targets currently used in anti-HIV therapy?

. Which of the following enzymes is responsible for processing HIV proteins during the production of new viruses?

. Which of the following statements is true regarding the following structure (nevirapine)?

An illustration depicts the structure of nevirapine. It is a benzene ring with a nitrogen atom linked to a seven membered ring with an N H group, carbonyl group and a nitrogen atom linked to a three membered ring. This ring is further connected to a benzene ring with a nitrogen atom and the methyl group is present as a substituent.

. Which of the following statements is true for non-nucleoside reverse transcriptase inhibitors?

. The protease enzyme in HIV has two important, identical amino acids involved in the catalytic mechanism which leads to peptide bond hydrolysis. What are the two amino acids?

. The HIV protease enzyme is symmetrical, whereas mammalian proteases are not. What significance might this have?

. The following structure (saquinavir) is a protease inhibitor.

An illustration depicts the structure of saquinavir. It is a six membered ring with two double bonds linked to a benzene ring with a nitrogen atom connected to a carbonyl group, N H group and a C H 2 group linked to a wedged hydrogen atom and a dashed bond linked to C O N H 2 group. The C H 2 group is linked to a carbonyl group, N H group, a carbon atom linked to a dashed hydrogen atom, a wedged bond linked to a benzene ring and a C H 2 group linked to a wedged O H group and a dashed hydrogen atom. This is further linked to a C H 2 group connected to a nitrogen atom linked to a six membered ring. The top part of the ring has a wedged hydrogen atom and a dashed bond linked to a carbonyl group, N H group and a carbon atom linked to three methyl groups. The sis membered ring is also linked to another six membered ring with two hydrogen atoms linked via a wedged bond. This part of the ring is decahydroisoquinoline ring.

The region marked in blue is a hydroxyethylamine moiety. What does this moiety represent?

. The following structure (saquinavir) is a protease inhibitor.

An illustration depicts the structure of saquinavir. It is a six membered ring with two double bonds linked to a benzene ring with a nitrogen atom connected to a carbonyl group, N H group and a C H 2 group linked to a wedged hydrogen atom and a dashed bond linked to C O N H 2 group. The C H 2 group is linked to a carbonyl group, N H group, a carbon atom linked to a dashed hydrogen atom, a wedged bond linked to a benzene ring and a C H 2 group linked to a wedged O H group and a dashed hydrogen atom. This is further linked to a C H 2 group connected to a nitrogen atom linked to a six membered ring. The top part of the ring has a wedged hydrogen atom and a dashed bond linked to a carbonyl group, N H group and a carbon atom linked to three methyl groups. The sis membered ring is also linked to another six membered ring with two hydrogen atoms linked via a wedged bond. This part of the ring is decahydroisoquinoline ring.

The decahydroisoquinoline ring system in the protease inhibitor shown above was used to replace an amino acid residue that is present in the lead compound used in the development of saquinavir. Which amino acid was replaced?

. The following structure (saquinavir) is a protease inhibitor.

An illustration depicts the structure of saquinavir. It is a six membered ring with two double bonds linked to a benzene ring with a nitrogen atom connected to a carbonyl group, N H group and a C H 2 group linked to a wedged hydrogen atom and a dashed bond linked to C O N H 2 group. The C H 2 group is linked to a carbonyl group, N H group, a carbon atom linked to a dashed hydrogen atom, a wedged bond linked to a benzene ring and a C H 2 group linked to a wedged O H group and a dashed hydrogen atom. This is further linked to a C H 2 group connected to a nitrogen atom linked to a six membered ring. The top part of the ring has a wedged hydrogen atom and a dashed bond linked to a carbonyl group, N H group and a carbon atom linked to three methyl groups. The sis membered ring is also linked to another six membered ring with two hydrogen atoms linked via a wedged bond. This part of the ring is decahydroisoquinoline ring.

Into which binding subsite of the protease enzyme's active site does the quinoline ring system fit?

. The following structure (ritonavir) is a protease inhibitor.

An illustration depicts two C H 3 groups linked to a five-membered ring with two double bonds, nitrogen and a sulfur atom linked to a C H 2 group linked to nitrogen linked to a methyl group further connected to a carbonyl group, N H group linked to a C H linked to a dashed bond and two methyl groups further linked to a carbonyl group, N H group and a C H group linked to a wedged bond to a phenyl group. This is further linked to a C H 2 group, C H linked to a dashed O H group linked to a C H linked to a dashed bond, and a phenyl group. The C H group is further connected to an N H group to a carbonyl group, an oxygen atom, and C H 2 linked to a five membered ring with two double bonds, a nitrogen atom and a sulfur atom.

What feature of the protease enzyme was the inspiration for the design of this particular structure?

. Which of the following protease inhibitors was developed by a hybridisation strategy?

. The following protease inhibitor (palinavir) illustrates an extension strategy involving the group shown in blue.

An illustration depicts the structure of ritonavir. It is a benzene ring linked to another benzene ring with a nitrogen atom further connected to a carbonyl group, N H group, a C H 2 group linked to a wedged bond and two C H 3 groups. The C H 2 group is also linked to a carbonyl group, N H group, a C H 2 group linked to a wedged bond and a phenyl group. The C H 2 group is further linked to an O H group, C H 2 group and a six membered ring with a nitrogen atom. This ring is linked to a dashed bond connected to a carbonyl group, N H group and a carbon linked to three C H 3 groups. The ring is also linked to a dashed bond linked to an oxygen atom, C H 2 group and a benzene ring with a nitrogen atom.

Which subsites are occupied by the extended residue?

. An enzyme carried by the flu virus catalyses the following reaction. Which enzyme is it?

An illustration depicts a catalysis reaction. An enzyme, neuraminidase carried by the flu virus catalyses the particular reaction. The molecule on the left is an O H group linked to a C H 2 group and another C H 2 group linked to a wedged O H group. This is further linked to a carbon atom linked to a dashed O H group further connected to a six membered chair form with an oxygen atom, an O H group, a C O 2 negative ion and an oxygen atom linked to a glycoprotein (lipid). This further forms sialic acid, which is n O H group linked to a C H 2 group and another C H 2 group linked to a wedged O H group. This is further linked to a carbon atom linked to a dashed O H group further connected to a six membered chair form with an oxygen atom, an O H group, a C O 2 negative ion and an OH group. The other product is glycoprotein or glycolipid.

. Which of the following statements is false regarding the characteristics of a good protein target for antiviral drugs?

. Which of the following antiviral drugs does not result in the eventual appearance of aciclovir triphosphate in virally infected cells?

An illustration depicts the structure of antiviral drugs A, B, C and D. Structure A is aciclovir and is a six membered ring with two double bonds, a nitrogen atom, N H group, a carbonyl group and an N H 2 group linked to a five membered ring with a double bond and two nitrogen atoms. One nitrogen atom is connected to a C H 2 group, an oxygen atom, two C H 2 groups further linked to an O H group. Structure B is valaciclovir, it comprises a six membered ring with two double bonds, a nitrogen atom, N H group, a carbonyl group and an N H 2 group linked to a five membered ring with a double bond and two nitrogen atoms. One nitrogen atom is connected to a C H 2 group, one oxygen atom, two C H 2 groups and an oxygen atom linked to a carbonyl group, a C H 2 group linked to a dashed hydrogen atom, wedged N H 2 group and a C H 2 group linked to two C H 3 groups. Structure C is desciclovir which is a six membered ring with two double bonds, a nitrogen atom, N H group, and an N H 2 group linked to a five membered ring with a double bond and two nitrogen atoms. One nitrogen atom is connected to a C H 2 group, oxygen atom, two C H 2 groups and an O H group. Structure D is Gangciclovir, which is a six membered ring with two double bonds, a nitrogen atom, N H group, a carbonyl group and an N H 2 group linked to a five membered ring with a double bond and two nitrogen atoms. One nitrogen atom is linked to a C H 2 group linked to an oxygen atom, two C H 2 groups and an O H group, and a C H 2 O H group.

. Podophyllotoxin is an antiviral agent that binds to tubulin and is used to treat warts.

An illustration depicts the structure of podophyllotoxin. It consists of a five membered ring with two oxygen atoms linked to a benzene ring further connected to a six membered ring having a wedged hydrogen atom and a dashed O H group connected at the top part and a wedged hydrogen atom and a dashed bond linked to a benzene ring and three O M e groups. The six membered ring is also linked to a five membered ring with a dashed hydrogen atom, wedged hydrogen atom, an oxygen atom and a carbonyl group.

How many HBAs are potentially present?

. Podophyllotoxin is an antiviral agent that binds to tubulin and is used to treat warts.

An illustration depicts the structure of podophyllotoxin. It consists of a five membered ring with two oxygen atoms linked to a benzene ring further connected to a six membered ring having a wedged hydrogen atom and a dashed O H group connected at the top part and a wedged hydrogen atom and a dashed bond linked to a benzene ring and three O M e groups. The six membered ring is also linked to a five membered ring with a dashed hydrogen atom, wedged hydrogen atom, an oxygen atom and a carbonyl group.

How many HBDs are potentially present?

. Podophyllotoxin is an antiviral agent that binds to tubulin and is used to treat warts.

An illustration depicts the structure of podophyllotoxin. It consists of a five membered ring with two oxygen atoms linked to a benzene ring further connected to a six membered ring having a wedged hydrogen atom and a dashed O H group connected at the top part and a wedged hydrogen atom and a dashed bond linked to a benzene ring and three O M e groups. The six membered ring is also linked to a five membered ring with a dashed hydrogen atom, wedged hydrogen atom, an oxygen atom and a carbonyl group.

Classify the labelled atoms below as one of the following

An illustration depicts the structure of podophyllotoxin. It consists of a five membered ring with two oxygen atoms linked to a benzene ring further connected to a six membered ring having a wedged hydrogen atom and a dashed O H group connected at the top part and a wedged hydrogen atom and a dashed bond linked to a benzene ring and three O M e groups. The six membered ring is also linked to a five membered ring with a dashed hydrogen atom, wedged hydrogen atom, an oxygen atom and a carbonyl group.

. A crystal structure (PDB 1SA1) has been obtained where podophyllotoxin is bound to tubulin.
From the Protein Data Bank, access the complex and reveal the binding mode for podophyllotoxin (Code [POD]700:B) using the NGL (WebGL) viewer.

Identify all the residues with which podophyllotoxin forms a hydrogen bond

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