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BIO343 - Natural Products Biotechnology > Major Classes of Natural Products 2 > Flashcards

Major Classes of Natural Products 2 Flashcards

1
Q

What are the building blocks of natural product peptides?

A

proteinogenic and non-proteinogenic amino acids

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2
Q

Where have they been isolated from?

A

from a range of organisms (fungi, bacteria, sponges, etc.)

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3
Q

Biosynthetic routes to make peptide natural products?

A

there are different type of biosynthetic routes to make peptide natural products

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4
Q

Building blocks of Non-ribosomal peptides, and examples?

A

building blocks: amino acids

penicillin G, tyrocidine A, cyclosporin A, cycloaspeptide A, cycloaspeptide E

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5
Q

NRP - biosynthesis overview

A

synthase/synthase gene (backbone)

  • non-ribosomal peptide synthetase (NRPS) + amino acids
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6
Q

what are NRP synthesised by?

A

non-ribosomal peptide synthetases (NRPS)

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7
Q

what are NRPSs?

A

megasynthetases - they have catalytic domains

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8
Q

independent or dependent of mRNA?

A

independent of mRNA

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9
Q

NRP Biosynthesis
are they modular or iterative?

A

modular (bacteria and fungi), there are some iterative examples (not covered here)

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10
Q

What do they need to activate the building block?

A

ATP

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11
Q

synthetase vs polyketide synthase?

A

synthetase uses ATP

polyketide synthase does not use ATP

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12
Q

NRPS Biosynthesis
Function of the domains (steps 1-4)

A
  1. activation and loading
  2. initiation
  3. elongation
  4. termination
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13
Q

NRPS Biosynthesis
1. activation and loading

A

Adenylation (A) domain will select and activate with ATP a specific amino acid

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14
Q

NRPS Biosynthesis
2. initiation

A

the first two amino acids will be joined together by the condensation (C) domain

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15
Q

NRPS Biosynthesis
3. Elongation

A

the remaining of amino acids are joined together

depends on how many extra modules we have

by condensation domains

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16
Q

NRPS Biosynthesis
4. Termination

A

peptide is released by the thioesterase (TE) domain or a terminal Condensation domain (CT) (small T at the bottom)

17
Q

one module =

A

one amino acid

18
Q

what are the 4 core domains?

A

C, A, PCP, TE

Condensation, Adenylation, PCP, TE/CT (small T, at the bottom)

19
Q

NRPS Biosynthesis - penicillin
Further modifications:
additional domains and tailoring genes?

A

additional domains:
- Epimerase (E)
- N-methyl transferase (NMeT)

tailoring genes
- e.g. oxidation for ring formation, Acyl transferase

20
Q

if a domain = three =

A

tripeptide

21
Q

NRPS Biosynthesis - Cyclosporin
further modifications:
additional domains and tailoring genes?

A

additional domains:
- Epimerase (E)
- N-methyl transferase (NMeT)

tailoring genes:
- e.g. Methyl transferase

22
Q

Yang et al. (2018)
NRPS Biosynthesis - Cyclosporin
1. produced by?
2. discovered in?
3. has what activities?
4. also used as an?
5. what does it prevent?
6. WHO?

A
  1. Tolypocladium inflatum
  2. 1971
  3. cyclosporin has antifungal activity
  4. used as an immunosuppressant drug
  5. prevent organ transplant rejection
  6. WHO - essential medicines
23
Q

How to recognise a NRPS-derived SM?

A
  • always have CHON as elements
  • can have halogen (Br, Cl, etc.)
  • similar number of nitrogen oxygens atoms
  • amides bonds are present
  • amino acid side chains
24
Q

NPs - Terpenes
Examples?

A
  • Menthol
  • B-carotene
  • Pleuromutilin
  • Botrydial
  • Artemisinin
25
Q

Terpene biosynthesis overview

A

Synthase/synthetase gene (backbone)

-> Terpene synthase + IPP

26
Q

Terpene Biosynthesis
1. what are the building blocks?
2. isolated from?
3. how many carbon units each do two building units have?
4. synthesised by?
5. what can be added?
6. what are the different classes based on?
7. difference between terpenoids and terpenes

A
  1. isopentyl pyrophosphates (IPP) and dimethylallyl pyrophosphate (DMAPP)
  2. from a range of organisms (fungi, bacteria, sponges, plants and animals)
  3. the two building units have 5 carbon units each (terpenes dividable by 5 carbons)
  4. synthesised by a terpene synthase that joins the two units together
  5. IPP can be added adding additional IPP units
  6. different classes based on the length
  7. terpenoids are terpenes with additional functional groups like (-OH)
    terpene = carbon, hydrogen in structure
    terpenoids = carbon, hydrogen, oxygen in structure
27
Q

Terpene Biosynthesis - pleuromutilin
1. produced by?
2. how many carbons does core structure have?
3. what activities?
4. what are its derivatives used in?
5. active against?

A
  1. Basidiomycota - Clitopilus passeckerianus
  2. 20 carbons
  3. antibiotic activity
  4. its derivatives are used in veterinary (used for swine (pigs) specifically) and human medicine
  5. active against Gram-negative bacteria
28
Q

Terpene Biosynthesis - artemisin
1. produced by?
2. how many carbons does the core structure have?
3. traditional medicine?
4. type of drug it is used for?
5. Nobel Prize in Medicine - who, what year, and what for?
6. market and lives saved?
7. how is the final step catalysed?

A
  1. Artemisia annua (sweet wormwood)
  2. core structure has 15 carbons
  3. Traditional Chinese medicine (317-420 AD)
  4. Antimalarial drug
  5. Tu Youyou, 2015, for the discovery
  6. Market $597.2M (2023) - over 200 M lives saved
  7. final step catalysed by UV light and oxygen
29
Q

Reed et al. (2023)
Terpene Biosynthesis - saponins
1. produced by?
2. extracted from?
3. used in?
4. also used for?

A
  1. plants terpenoids
  2. soapbark tree (Quillaja Saponaria)
  3. formulation of soaps, medicines, root beer foam, etc.
  4. adjuvants (substances that increase the effectiveness of drugs or vaccines) - immunostimulatory activity to vaccines (shingles, malaria, and COVID-19)
30
Q

How to recognise a terpene-derived SM?

A
  • the molecular formular has CH (terpenes) and CHO (terpenoids) as elements
  • main carbon skeleton should feature 5 or multiple of 5 carbons
  • common to alkenes and rings
31
Q

Examples of terpenes (including whether they are terpene or terpenoid)?

A
  • Menthol = terpenoid
  • B-carotene = terpene
  • Pleuromutilin = terpenoid
  • Botrydial = terpenoid
  • Artemisinin = terpenoid
32
Q

Main classes - summary

A

Synthase/synthetase gene (backbone)

-> Polyketide - Polyketide synthase (PKS) + Acyl CoA
-> Non-ribosomal peptides - Non-ribosomal peptide synthetase (NRPS) + amino acids
-> Terpenes/terpenoids - Terpene synthase + IPP

PKS and NRPS can be modular & iterative

BIO343 - Natural Products Biotechnology (4 decks)

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