What Is Genotoxicity and Mutagenicity: Learn In 7 Minutes

Genotoxicity and Mutagenicity behavior of chemicals is a challenging task in the development of pharmaceuticals. The genotoxic and mutagenic chemicals can damage the DNA and that is why these chemicals can be carcinogenic. The meaning of Genotoxicity is to damage the DNA or genetic material. The DNA can be damaged by various sources and one of them is genotoxic chemicals or mutagenic chemicals. In this article, I will discuss skill-based knowledge on chemistry behind genotoxicity and mutagenicity and structure alert concept. After reading the post, all your doubts related to genotoxicity and mutagenicity will be cleared.

What is the Chemistry Behind Genotoxic chemicals?

DNA can be damaged by various sources and one of them is Genotoxic chemicals. These chemicals can cause genetic mutations, chromosomal breakage, chromosomal rearrangements, cancer and other adverse effects at very low levels. hence, genotoxicity can be defined as ” Genotoxicity is the ability of any chemical to damage DNA”

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Chemistry behind Genotoxicity

To understand Genotoxicity, we must first understand the structure of DNA, its components and the possible ways in which DNA can be damaged. The following are the possible path in which DNA can be damaged:

• Cross linking
• Oxidative
• Adduct formation and
• Strand breaks

DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone. The following are the base pairs:

• Adenine (A) – Thiamine (T)
• Guanine (G) – Cytosine (C)

Hence, any chemicals or agent which can alter the identity of these bases can damage the DNA. Now the question is how the identity of these bases can be affected

Hence, any chemical/agent which can alter the identity of these bases can damage DNA. Now the question is how the identity of these bases can be affected. To understand the same let us discuss the structure of these bases. The following are the structures of these bases:

From the above structures, it is clear that these bases of DNA have multiple Nitrogen atoms. Since each Nitrogen atom contains one lone pair of electrons and hence these bases are electron rich compounds and hence can donate or share electrons with other chemicals in bond formation. It mean these bases act as nucleophiles’

Now the question is which type of chemicals can interact with the above base?

Electron-deficient molecules/cations / carbonium ions can accept the electron and make the bond with these bases. It means an Electrophile may attack on these bases and can affect the identity of DNA. Hence, Genotoxins can be defined as:

“Genotoxins are either electrophiles’ per se or can be activated to electrophilic reactive intermediates in vivo”

Structure Alerts Concept of SAs concept: How to identifying genotoxic chemicals?

Electrophiles or Electrophilic reactive intermediates can combine with nucleophilic part of DNA (base-pairs of DNA) and can damage the DNA. Substructure or functional groups of above characteristics are genotoxic in nature and call Structure Alerts concept or SAs concept. SAs concept is one of the most useful scheme to assess carcinogenic potential of an untested molecule and it is very helpful in pharmaceuticals development.

Difference Between Genotoxicity and Mutagenicity

Mutagenicity refers to the induction of permanent transmissible changes in the amount or structure of the genetic material of cells or organisms/DNA. It is associated with Mutation. The chemical/ agent causing the change is called Mutagen.

Genotoxicity is similar to Mutagenicity except the genotoxic effects are not necessary associated with mutations.

Note:

• All Mutagens are genotoxic, however, not all Genotoxins are mutagenic
• The mutagenicity effect is passed on to future generations whereas Genotoxicity is not

Genotoxic Chemicals in Pharmaceuticals

Genotoxic chemicals or Genotoxic impurities damage genetic material in the cells through interactions with DNA sequence/ structure. Therefore, these chemicals are highly toxic. It is impossible to avoid these chemicals in pharmaceutical development and hence, their control is required. But the biggest challenge is to identify and control these chemicals. In this post I will share skill-based knowledge to identify these chemicals. After reading this post you will be able to predict the genotoxic nature of any chemicals, having seen the structure. I will also explain the genotoxic nature of several chemicals like epoxides, aromatic amines, and aromatic nitro compounds.

Properties of Genotoxic Chemicals

One of the most characteristics features of Genotoxic chemicals is that these chemicals electrophiles’ or converted into electrophiles the body. Electrophiles having the following characteristics:

1. They may be carbonium ions e.g. CH³⁺
2. They may be cations e.g. Cd²⁺, Al³⁺
3. They may be electron deficient molecules e.g. BF₃, AlCl₃
4. Molecules which may convert into cations in the body e.g. Epoxides, Aromatic compounds

Hence any chemicals with above catachrestic may be genotoxic in nature.

Types of Genotoxicity

The Genotoxicity are categorised based on the type of genetic damage it causes. The following are the 7 main types of Genotoxicity:

1. Mutagenicity

• Definition: Mutagenic substances cause changes (mutations) in the DNA sequence of an organism, which can be passed down to offspring if they occur in germ cells (sperm or eggs).
• Mechanism: These mutations can be caused by:
  • Base substitutions (changing one base pair to another)
  • Frameshift mutations (insertion or deletion of base pairs that disrupt the reading frame of a gene)
  • Chromosomal rearrangements.
• Example: Chemicals like benzene or tobacco smoke have mutagenic effects.

2. Clastogenicity

• Definition: Clastogenic substances cause breaks in chromosomes, which can lead to chromosomal fragmentation, rearrangement, or loss of chromosome segments.
• Mechanism: Clastogenic effects often result in the formation of micronuclei, small chromosome fragments that remain outside the nucleus during cell division.
• Example: Radiation or certain chemotherapeutic agents are known clastogens.

3. Aneugenicity

• Definition: Aneugenic substances cause changes in the number of chromosomes in a cell (aneuploidy) by disrupting the normal process of cell division.
• Mechanism: This typically occurs by interfering with the mitotic spindle, leading to improper segregation of chromosomes during cell division.
• Example: Certain heavy metals (e.g., cadmium, lead) and some anticancer drugs are known to be aneugenic.

4. Carcinogenicity

• Definition: Carcinogenic substances are capable of inducing cancer by causing genetic mutations or chromosomal alterations that promote uncontrolled cell growth.
• Mechanism: Carcinogens can be mutagenic or clastogenic and typically promote the activation of oncogenes or the inactivation of tumor suppressor genes.
• Example: Asbestos, tobacco smoke, and certain chemicals like benzene are known carcinogens.

5. Teratogenicity

• Definition: Teratogenic substances cause developmental malformations in an embryo or fetus, often by interfering with genetic material or the cell division process during pregnancy.
• Mechanism: Teratogens may affect the genetic material of cells in a developing embryo, leading to developmental abnormalities.
• Example: Thalidomide (which caused birth defects) and certain alcohol and drug exposures are teratogenic.

6. Chromosomal Aberrations

• Definition: Chromosomal aberrations involve the structure or number of chromosomes being altered. This can include deletions, duplications, inversions, and translocations.
• Mechanism: These changes may lead to the loss of genetic material or the gain of abnormal genetic material, which can disrupt normal cellular functions.
• Example: Some viruses, like the human papillomavirus (HPV), can induce chromosomal aberrations leading to cancer.

7. Genotoxicity Induced by Oxidative Stress

• Definition: Some genotoxic agents act by increasing the production of reactive oxygen species (ROS), which can damage DNA through oxidative processes.
• Mechanism: ROS can cause DNA base modifications, strand breaks, and even cross-linking of DNA.
• Example: Air pollutants like ozone and certain environmental toxins may induce oxidative stress, leading to genotoxicity.

Genotoxic nature of Epoxides, Aromatic nitro compounds and Aromatic amines

Epoxides have a strained ring structure. This strained ring system of Epoxides facilitates the generation of a carbonium ion by opening the ring in the body (by the mechanism given below). This carbonium ion reacts with base pairs of DNA and damage the DNA. That is why Epoxides are Genotoxic.

Aromatic nitro compounds and Aromatic amines

The aromatic nitro compound is converted into Aromatic amino compound in the intestine by metabolic activation. This aromatic amine compound is oxidised to the N-hydroxy aryl amine. These aromatic amino compound and N-hydroxy aryl amine act electrophile (due to utilisation of amino group/-HN: lone pair of electrons in the ring by resonance). Hence, N-hydroxy aryl amine can react directly with DNA and can block replication of DNA. That is why Aromatic nitro compounds and Aromatic amines are genotoxic.

Factors affecting Genotoxicity

The following factors may affect the Genotoxic nature of Genotoxins:

• Each positional isomer is equally Genotoxic
• Ortho Substation with positive inductive effect can enhance the Genotoxicity
• Ortho and meta substitution with bulky group can suppress the genotoxicity
• Bulky groups ortho to an aromatic amino or substituted amino or nitro groups abolish toxicity.
• Compounds with high molecular weight and big seize having very little chance to absorb
• Highly hydrophilic compounds are poorly absorbed and are easily excreted
• Compounds which are to reactive may not be carcinogenic because the hydrolyze or polarise before they can reach critical target in the cell.
• Planner molecules with electrophilic functional groups can intercalate properly ino DNA e.g. Polycyclic aromatic hydrocarbons, and Aflatoxin

Conclusion

Identifying the Genotoxicity and mutagenicity nature of any chemicals and controlling genotoxins are the challenging tasks for a pharmaceutical professional. It needs both knowledge and integrated skills. This approach is very helpful. Though this approach is not perfect but very useful in predicting the Genotoxic nature of untested molecules during drug development. I hope this article has cleared all your doubts related to the structural identification of Genotoxic chemicals and enhanced your knowledge to the next level.

FAQs

How Genotoxic chemicals/impurities can be predicted based on structure?

Based on structure genotoxic nature of any chemical can be predicted. All genotoxic chemicals are electrophiles or converted into electrophiles in the body

Why Epoxides, Aromatic amines and Aromatic nitro compounds are Genotoxins?

The aromatic nitro compound is converted into Aromatic amino compound in the intestine by metabolic activation. This aromatic amine compound is oxidised to the N-hydroxy aryl amine. These aromatic amino compound and N-hydroxy aryl amine act electrophile (due to utilisation of amino group/-HN: lone pair of electrons in the ring by resonance). Hence, N-hydroxy aryl amine can react directly with DNA and can block replication of DNA. That is why Aromatic nitro compounds and Aromatic amines are genotoxic.

What are the different factors affecting genotoxicity?

Several factors like substitution on the molecule, polarity of the molecule, size of the molecule, reactivity of the molecule and molecular weight affect the genotoxic nature of any chemicals

What are the Genotoxic material in the pharmaceutical industries?

Genotoxic materials are those chemicals which can damage the DNA like aromatic amino compounds, aromatic nitro compounds and epoxides

What is the example of genotoxic agent?

Genotoxic agents are those chemicals which can damage the DNA like aromatic amino compounds, aromatic nitro compounds and epoxides

What are Genotoxic and non-genotoxic chemicals?

Genotoxic chemicals damage the DNA whereas Non-genotoxic chemicals do not damage the DNA

What is the Genotoxic material?

Genotoxic materials are those chemicals which can damage the DNA like aromatic amino compounds, aromatic nitro compounds and epoxides

References

• ICH M7