Major Classes of Natural Products 2

Question 1

What are the building blocks of natural product peptides?

Answer 1

proteinogenic and non-proteinogenic amino acids

Question 2

Where have they been isolated from?

Answer 2

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

Question 3

Biosynthetic routes to make peptide natural products?

Answer 3

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

Question 4

Building blocks of Non-ribosomal peptides, and examples?

Answer 4

building blocks: amino acids

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

Question 5

NRP - biosynthesis overview

Answer 5

synthase/synthase gene (backbone)

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

Question 6

what are NRP synthesised by?

Answer 6

non-ribosomal peptide synthetases (NRPS)

Question 7

what are NRPSs?

Answer 7

megasynthetases - they have catalytic domains

Question 8

independent or dependent of mRNA?

Answer 8

independent of mRNA

Question 9

NRP Biosynthesis
are they modular or iterative?

Answer 9

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

Question 10

What do they need to activate the building block?

Answer 10

ATP

Question 11

synthetase vs polyketide synthase?

Answer 11

synthetase uses ATP

polyketide synthase does not use ATP

Question 12

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

Answer 12

1. activation and loading
2. initiation
3. elongation
4. termination

Question 13

NRPS Biosynthesis
1. activation and loading

Answer 13

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

Question 14

NRPS Biosynthesis
2. initiation

Answer 14

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

Question 15

NRPS Biosynthesis
3. Elongation

Answer 15

the remaining of amino acids are joined together

depends on how many extra modules we have

by condensation domains

Question 16

NRPS Biosynthesis
4. Termination

Answer 16

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

Question 17

one module =

Answer 17

one amino acid

Question 18

what are the 4 core domains?

Answer 18

C, A, PCP, TE

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

Question 19

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

Answer 19

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

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

Question 20

if a domain = three =

Answer 20

tripeptide

Question 21

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

Answer 21

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

tailoring genes:
- e.g. Methyl transferase

Question 22

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?

Answer 22

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

Question 23

How to recognise a NRPS-derived SM?

Answer 23

• 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

Question 24

NPs - Terpenes
Examples?

Answer 24

• Menthol
• B-carotene
• Pleuromutilin
• Botrydial
• Artemisinin

Question 25

Terpene biosynthesis overview

Answer 25

Synthase/synthetase gene (backbone) -> Terpene synthase + IPP

Question 26

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

Answer 26

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

Question 27

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?

Answer 27

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

Question 28

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?

Answer 28

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

Question 29

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

Answer 29

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)

Question 30

How to recognise a terpene-derived SM?

Answer 30

- 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

Question 31

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

Answer 31

- Menthol = terpenoid - B-carotene = terpene - Pleuromutilin = terpenoid - Botrydial = terpenoid - Artemisinin = terpenoid

Question 32

Main classes - summary

Answer 32

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