Pseudopeptides and their design MCQs With Answer

Introduction: Pseudopeptides and their design is a critical topic for M.Pharm students aiming to understand modern peptide therapeutics and peptidomimetic strategies. This blog focuses on the structural modifications that convert natural peptides into pseudopeptides—molecules with enhanced metabolic stability, receptor selectivity, and improved pharmacokinetic profiles. You will learn design principles such as backbone and side‑chain modifications, cyclization, N‑methylation, peptoid and beta‑peptide approaches, and common synthetic and analytical techniques relevant to formulation and delivery. The MCQs that follow test conceptual understanding, synthetic strategy selection, stability factors, analytical evaluation, and formulation considerations important for translating pseudopeptides into drug candidates.

Q1. Which structural change most directly replaces the peptide backbone NH–CO linkage to create a typical “pseudopeptide” that resists proteolysis?

• Replacement of amide bond with an isosteric thioamide (C(S)–NH)
• Substitution of α‑carbon with a fluorine atom
• Glycosylation of side chains
• Terminal acetylation of N‑terminus

Correct Answer: Replacement of amide bond with an isosteric thioamide (C(S)–NH)

Q2. Which of the following best describes a retro‑inverso peptide modification?

• Replacing L‑amino acids with D‑amino acids while reversing the peptide sequence
• Cyclizing a linear peptide by connecting N‑ and C‑termini
• Incorporating β‑amino acids into the backbone
• Attaching a lipid chain to the N‑terminus to increase membrane affinity

Correct Answer: Replacing L‑amino acids with D‑amino acids while reversing the peptide sequence

Q3. Peptoids differ from peptides primarily because:

• Side chains are attached to the backbone nitrogen instead of the α‑carbon
• They contain only D‑amino acids
• They form disulfide bonds more readily
• They always adopt stable α‑helical structures

Correct Answer: Side chains are attached to the backbone nitrogen instead of the α‑carbon

Q4. Which backbone modification is most commonly introduced to increase cell permeability and reduce backbone hydrogen bonding?

• N‑methylation of backbone amide nitrogens
• Replacement of side chains with glycine
• Phosphorylation of serine residues
• Introduction of proline residues at termini

Correct Answer: N‑methylation of backbone amide nitrogens

Q5. Beta‑peptides are useful in pseudopeptide design because:

• They form noncanonical secondary structures and resist proteases
• They are always more soluble in water than α‑peptides
• They can be synthesized only by solution methods
• They cannot be cyclized

Correct Answer: They form noncanonical secondary structures and resist proteases

Q6. Which synthetic strategy commonly used in pseudopeptide production allows rapid assembly with facile purification and automation?

• Solid‑phase peptide synthesis (SPPS)
• Enzymatic ligation without protecting groups
• Mitsunobu reaction in solution phase only
• Gas‑phase synthesis

Correct Answer: Solid‑phase peptide synthesis (SPPS)

Q7. “Stapled peptides” are designed primarily to:

• Stabilize α‑helical structure and improve cell uptake
• Increase protease recognition and cleavage
• Replace all amide bonds with ester bonds
• Reduce molecular weight below 300 Da

Correct Answer: Stabilize α‑helical structure and improve cell uptake

Q8. Which analytical method gives direct information about secondary structure conformation of pseudopeptides in solution?

• Circular dichroism (CD) spectroscopy
• Reverse‑phase HPLC retention time only
• Electrospray ionization mass spectrometry (ESI‑MS) without fragmentation
• Infrared imaging of solid samples

Correct Answer: Circular dichroism (CD) spectroscopy

Q9. When designing orally bioavailable pseudopeptides, which modification most improves resistance to gastrointestinal proteases and permeability?

• Combination of N‑methylation and cyclization
• Increasing net negative charge at physiological pH
• Replacing aromatic residues with serine residues
• Attachment of multiple polyethylene glycol (PEG) chains to every residue

Correct Answer: Combination of N‑methylation and cyclization

Q10. Which of the following is an advantage of converting a peptide into a pseudopeptide for formulation?

• Increased metabolic stability allowing simpler delivery strategies
• Guaranteed elimination of immunogenicity
• Automatic improvement of aqueous solubility to any desired level
• Ability to be formulated as a volatile inhalation agent

Correct Answer: Increased metabolic stability allowing simpler delivery strategies

Q11. “Azapeptides” are characterized by which backbone modification?

• Substitution of an α‑carbon with a nitrogen (N‑replacement of Cα)
• Replacement of amide carbonyl with sulfonyl group
• Attachment of azide to side chains only
• Full inversion of stereochemistry at all centers

Correct Answer: Substitution of an α‑carbon with a nitrogen (N‑replacement of Cα)

Q12. Which technique is most suitable to quantify binding kinetics (on‑ and off‑rates) between a pseudopeptide and a protein target?

• Surface plasmon resonance (SPR)
• Size exclusion chromatography (SEC) alone
• End‑point enzyme assay without time course
• Thin‑layer chromatography (TLC)

Correct Answer: Surface plasmon resonance (SPR)

Q13. In SPPS of pseudopeptides containing N‑methylated residues, which synthetic challenge is most commonly encountered?

• Slower amide bond formation and need for stronger coupling reagents
• Spontaneous racemization of D‑residues exclusively
• Inability to cleave from resin with TFA
• Lack of solubility of protected Fmoc amino acids only

Correct Answer: Slower amide bond formation and need for stronger coupling reagents

Q14. Which modification is often used to reduce renal clearance and extend circulation half‑life of pseudopeptides?

• PEGylation or conjugation to albumin‑binding moieties
• Complete removal of all charged residues
• Shortening peptide length to <5 residues always
• Attachment of multiple sulfate groups

Correct Answer: PEGylation or conjugation to albumin‑binding moieties

Q15. Which chemical reaction is widely used in pseudopeptide chemistry for bioorthogonal ligation due to its reliability and specificity?

• Copper‑catalyzed azide–alkyne cycloaddition (CuAAC, “click” chemistry)
• Wittig olefination on unprotected peptides
• Radical polymerization in aqueous buffer
• Fischer esterification of free carboxyl groups in water

Correct Answer: Copper‑catalyzed azide–alkyne cycloaddition (CuAAC, “click” chemistry)

Q16. Which pseudopeptide design approach is most useful to mimic β‑turns and improve receptor recognition?

• Incorporation of turn mimetics such as dPro–lPro or constrained dipeptide isosteres
• Complete removal of proline residues
• Replacing all turns with flexible glycine linkers
• Extending chain length by polyalanine inserts

Correct Answer: Incorporation of turn mimetics such as dPro–lPro or constrained dipeptide isosteres

Q17. Which formulation concern is particularly critical for pseudopeptides prone to aggregation?

• Choice of buffer, pH, ionic strength and use of stabilizing excipients like sugars or surfactants
• Ensuring complete absence of any organic solvent traces only
• Mandatory lyophilization without any stabilizer
• Use of strong acids to maintain low pH permanently

Correct Answer: Choice of buffer, pH, ionic strength and use of stabilizing excipients like sugars or surfactants

Q18. Which property of pseudopeptides most directly reduces recognition by proteases?

• Alteration or replacement of the scissile amide bond or local backbone conformation
• Increasing hydrophobicity at the peptide termini only
• Adding extra lysine residues to increase basicity
• Labeling with fluorescent dyes alone

Correct Answer: Alteration or replacement of the scissile amide bond or local backbone conformation

Q19. Which analytical method provides high‑resolution structural information (atomic detail) for a pseudopeptide–protein complex?

• X‑ray crystallography or cryo‑EM when crystals or particles are obtainable
• Analytical ultracentrifugation in dilute buffer only
• UV absorbance at 280 nm without separation
• Basic SDS‑PAGE gel mobility shift

Correct Answer: X‑ray crystallography or cryo‑EM when crystals or particles are obtainable

Q20. Which design trade‑off is most commonly encountered when optimizing pseudopeptides for both potency and oral bioavailability?

• Increased lipophilicity may improve permeability but can reduce solubility and increase clearance risk
• Maximizing polarity always increases oral absorption without drawbacks
• Extensive PEGylation always improves both potency and oral uptake
• Adding multiple charged residues uniformly improves metabolic stability and taste

Correct Answer: Increased lipophilicity may improve permeability but can reduce solubility and increase clearance risk

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