Topoisomerase- Definition, Types, Structure, Functions, Mechanism

DNA is a complex molecule that stores and transmits genetic information in all living cells. However, DNA also faces many topological challenges that can affect its structure and function. For instance, DNA can become overwound or underwound, tangled or knotted, or linked with other DNA molecules. These topological problems can interfere with vital processes such as DNA replication, transcription, recombination and chromosome segregation.

To solve these problems, cells rely on a group of enzymes called topoisomerases. Topoisomerases are able to change the topology of DNA by making transient breaks in one or both strands of the DNA backbone and allowing the DNA to pass through the gap. By doing so, they can relax or introduce supercoils, unlink or link DNA molecules, and unknot or knot DNA loops. Topoisomerases are essential for cell survival and gene activity .

Topoisomerases are classified into two major types based on their mechanism of action: type I and type II. Type I topoisomerases cut one strand of DNA and change the linking number by one unit. Type II topoisomerases cut both strands of DNA and change the linking number by two units. Type I topoisomerases do not require ATP (except for reverse gyrase), while type II topoisomerases are ATP-dependent. Both types of topoisomerases use a conserved tyrosine residue to form a covalent bond with the DNA phosphate during the cleavage and religation steps .

The first topoisomerase was discovered in bacteria by James Wang in 1971. It is now called Escherichia coli (E. coli) topoisomerase I and belongs to the type IA family of enzymes. Later, a similar enzyme was found in eukaryotic cells by James Champoux and Renato Dulbecco. It is called eukaryotic topoisomerase I and belongs to the type IB family of enzymes. The first type II topoisomerase to be discovered was DNA gyrase from bacteria by Martin Gellert and coworkers in 1976. DNA gyrase is unique among topoisomerases in that it introduces negative supercoils into DNA. Other type II topoisomerases were subsequently identified from bacterial viruses and eukaryotes .

In this article, we will explore the definition, structure, types, functions and mechanism of action of topoisomerases in more detail. We will also discuss the inhibition of topoisomerases by small molecules and their clinical significance.

Topoisomerase is an enzyme that can alter the topology of DNA, which means the shape and arrangement of the double helix. Topology is important for DNA functions such as replication, transcription, recombination and chromatin organization. Topoisomerase can change the topology of DNA by making temporary cuts in one or both strands of the DNA backbone, allowing the DNA to unwind, untangle, or pass through each other, and then rejoining the cut ends.

The first topoisomerase was discovered by James Wang in 1971 while working on Escherichia coli (E. coli). He named it omega (ω) protein because it could relax negatively supercoiled DNA into a circular form resembling the Greek letter omega . Later, it was renamed as E. coli topoisomerase I (topo I) and classified as a type IA topoisomerase. This type of topoisomerase cuts only one strand of DNA and does not require ATP (a source of energy) for its activity.

The second type of topoisomerase to be discovered was DNA gyrase, also from bacteria, by Martin Gellert and coworkers in 1976. DNA gyrase belongs to the type II family of topoisomerases, which cut both strands of DNA and use ATP for their activity. DNA gyrase can introduce negative supercoils into DNA, which helps to compact the bacterial chromosome and facilitate its replication.

Since then, more types and subtypes of topoisomerases have been identified from different organisms, including viruses, archaea, eukaryotes and plants. They have different structures, mechanisms and functions, but they all share the ability to manipulate the topology of DNA.

Before we dive into the types and functions of topoisomerase, let us first understand some key terms that are related to the enzyme and its action on DNA.

• DNA topology: It is the study of the shape and configuration of DNA molecules. DNA topology can be affected by various factors such as temperature, pH, salt concentration, and the presence of enzymes like topoisomerase. DNA topology can be described by three parameters: twist, writhe, and linking number.
• Twist (Tw): It is the number of helical turns of the two strands of DNA around each other. Twist can be positive or negative depending on the direction of the turns. For example, in a right-handed double helix like B-DNA, each turn is a positive twist. Twist can be changed by breaking and rejoining one or both strands of DNA.
• Writhe (Wr): It is the number of times that the double helix of DNA crosses over itself in three-dimensional space. Writhe can also be positive or negative depending on the direction of the crossing. For example, in a circular DNA molecule, a clockwise crossing is a positive writhe and a counterclockwise crossing is a negative writhe. Writhe can be changed by bending or twisting the DNA molecule.
• Linking number (Lk): It is the sum of twist and writhe of a closed circular DNA molecule. Linking number is an invariant property of a closed circular DNA molecule, meaning that it cannot be changed without breaking one or both strands of DNA. Linking number can be used to measure the degree of supercoiling of a closed circular DNA molecule.
• Supercoiling: It is the phenomenon in which a closed circular DNA molecule coils upon itself due to changes in twist or writhe. Supercoiling can be positive or negative depending on whether the coiling is in the same or opposite direction as the helical turns. For example, in a right-handed double helix like B-DNA, if the twist is reduced by one turn, the writhe will increase by one turn in the same direction, resulting in positive supercoiling. Conversely, if the twist is increased by one turn, the writhe will decrease by one turn in the opposite direction, resulting in negative supercoiling. Supercoiling can affect the accessibility and function of DNA.
• Topoisomerase: It is an enzyme that can change the topology of DNA by breaking and rejoining one or both strands of DNA. Topoisomerase can alter the twist, writhe, and supercoiling of DNA by changing its linking number. Topoisomerase can also resolve knots and tangles in DNA that may arise during replication, transcription, recombination, or other processes. Topoisomerase can be classified into two major types: type I and type II.

In this article, we will explore more about these two types of topoisomerase and their roles in various biological processes.

Topoisomerases are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA.

Topoisomerases are divided into two classes: type I enzymes (EC 5.6.2.1) break single-strand DNA, and type II enzymes (EC 5.6.2.2) break double-strand DNA.

Type I Topoisomerase

Type I topoisomerase is a type of topoisomerase that cuts on a single strand of DNA. It is not an ATP-dependent enzyme (except for reverse gyrase). It mainly changes the linking number by plus one.

Type I topoisomerase can be further classified into three subtypes based on evolutionary, structural, and mechanistic considerations: type IA, type IB, and type IC.

• Type IA topoisomerases bind to the 5′ end of the DNA and show homology to topoisomerase I of E. coli. They include topo IA (found in eubacteria), topo III (found in eubacteria and eukaryotes), and reverse gyrase (found in archaebacteria and eubacteria). Reverse gyrase is the only type I topoisomerase that is ATP-dependent and can introduce positive supercoils into DNA.
• Type IB topoisomerases bind to the 3′ end of the DNA and show homology to topoisomerase I of humans. They form a nick in one strand and pass the other strand through the break. They include topo IB (found in eukaryotes and some viruses), topo V (found in archaea), and topo VI (found in some plants).
• Type IC topoisomerases contain only one type of topoisomerase i.e. topoisomerase V. It binds to the 3′ end of the DNA and is found in archaebacteria. It shows a controlled mechanism of rotation.

Type II Topoisomerase

Type II topoisomerase is a type of topoisomerase that cuts on both strands of DNA at once. It is an ATP-dependent enzyme. It changes the linking number by two.

Type II topoisomerase can be further classified into two subtypes based on evolutionary, structural, and mechanistic considerations: type IIA and type IIB.

• Type IIA topoisomerases are found in viruses and all cellular organisms. They include topo II (found in eukaryotes), topo IV (found in bacteria), and gyrase (found in bacteria and some eukaryotes). Topo IV differs from gyrase in that it is not involved in DNA wrapping while gyrase is involved in DNA wrapping and promoting negative supercoils. Gyrase is the only type II enzyme that can introduce negative supercoils into DNA.
• Type IIB topoisomerases include topo VI which can be found in archaea and some plants. It forms a heterotetramer with two subunits A and B that are related to type IA enzymes. It can introduce positive or negative supercoils into DNA depending on the direction of rotation.

Type I topoisomerase is a type of topoisomerase that cuts one of the two strands of double-stranded DNA, relaxes the strand, and reanneals the strand. It is not an ATP-dependent enzyme (except for reverse gyrase). It mainly changes the linking number of a circular DNA strand by units of strictly 1 (type IA) or multiples of 1 (type IB).

Type I topoisomerase has several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis.

Type I topoisomerase can be subdivided according to its structure and reaction mechanisms into three subfamilies: type IA, type IB and type IC.

Type IA topoisomerase

Type IA topoisomerase binds to the 5′ end of the DNA and forms a 5′-phosphotyrosyl intermediate. It shows homology to topoisomerase I of E. coli. It can only relax negatively supercoiled DNA.

Type IA topoisomerase has a clamp-like structure with a large central cavity in which DNA binds. It has four domains: domain I contains the toprim domain; domain II is involved in DNA binding; domain III contains the active site tyrosine and a helix-turn-helix motif; and domain IV is involved in dimerization.

Type IA topoisomerase has three subtypes: topo IA, topo III and reverse gyrase.

• Topo IA is found in eubacteria and some archaea.
• Topo III is found in eubacteria and eukaryotes. It efficiently unknots and decatenates single-stranded or nicked DNA.
• Reverse gyrase is found in hyperthermophilic archaea and some bacteria. It is the only type I topoisomerase that is ATP-dependent and can introduce positive supercoils into DNA.

The mechanism of action of type IA topoisomerase involves three steps:

1. Cutting a single strand of DNA: The active site tyrosine attacks the phosphorus atom of the DNA backbone, breaking the phosphodiester bond and forming a covalent intermediate with the 5′ end of the DNA.
2. Passing of strand: The uncut DNA strand passes through the break, changing the linking number by one unit per cycle. The enzyme changes from a closed conformation to an open conformation, allowing the strand passage without ATP hydrolysis.
3. Religation: The 5′-OH of the ribose group of the cleaved strand attacks the phosphate group linked to the tyrosine, restoring the phosphodiester bond and releasing the enzyme.

Type IB topoisomerase

Type IB topoisomerase binds to the 3′ end of the DNA and forms a 3′-phosphotyrosyl intermediate. It shows homology to topoisomerase I of humans. It can relax both negative and positive supercoiled DNA.

Type IB topoisomerase has a C-shaped protein clamp that engages the DNA duplex. It has four domains: N-terminal domain contains the active site tyrosine; core domain contains two subdomains that form a hole for DNA passage; linker domain connects the core domain to the C-terminal domain; and C-terminal domain contains a zinc-binding motif and a winged-helix motif that cap the DNA entry and exit sites.

Type IB topoisomerase has two subtypes: topo IB and topo V.

• Topo IB is found in eukaryotes, poxviruses and some archaea.
• Topo V is found in some archaea and plants. It shows controlled rotation mechanism and can introduce negative supercoils into DNA under certain conditions.

The mechanism of action of type IB topoisomerase involves two steps:

1. Cleaving of DNA chain: The active site tyrosine attacks the phosphorus atom of the DNA backbone, breaking the phosphodiester bond and forming a covalent intermediate with the 3′ end of the DNA.
2. Swiveling of DNA strand: The torsional stress in the DNA causes the DNA strand to rotate around the intact strand, changing the linking number by multiples of one unit per cycle. The enzyme switches between a nicked and a religated state, with a preference for the religated state. The rotation of the DNA strand requires some opening of the flexible protein clamp, which may be facilitated by ATP hydrolysis.

Type I topoisomerases are enzymes that can alter the topology of DNA by introducing or removing supercoils. They do this by cleaving one strand of DNA, passing the other strand through the break, and rejoining the ends. They are generally ATP-independent, except for reverse gyrase, which can introduce positive supercoils with the aid of ATP hydrolysis.

Type I topoisomerases have several functions in different biological processes, such as:

• Relaxing DNA: Type I topoisomerases can relax both positively and negatively supercoiled DNA, depending on the type and orientation of the enzyme. For example, prokaryotic topoisomerase I (topo IA) can only relax negative supercoils, whereas eukaryotic topoisomerase I (topo IB) can relax both positive and negative supercoils . Relaxing DNA is important for reducing torsional stress and facilitating DNA replication and transcription.
• Breaking strands during recombination: Type I topoisomerases can also catalyze strand breaks during homologous recombination, which is a process of exchanging genetic information between two DNA molecules. For example, topoisomerase III (topo IA) is involved in resolving recombination intermediates such as Holliday junctions and double-strand breaks.
• Condensing chromosomes: Type I topoisomerases can also participate in the condensation of chromosomes, which is a process of compacting DNA into a more organized structure. For example, reverse gyrase (topo IA) can introduce positive supercoils into DNA, which can promote the formation of higher-order structures such as nucleoids in bacteria and archaea.
• Disentangling DNA during mitosis: Type I topoisomerases can also help in disentangling intertwined DNA during mitosis, which is a process of cell division. For example, eukaryotic topoisomerase I (topo IB) can introduce positive supercoils into DNA, which can separate the DNA of daughter chromosomes after DNA replication.

Type II topoisomerase is a type of topoisomerase that cuts on both strands of DNA at once. It is an ATP-dependent enzyme. It changes the linking number by two.

Type II Topoisomerase Structure

Topoisomerase IIA in eukaryotes consists of two same monomers (A-A) whereas in prokaryotes they are formed heterotetramers (A2B2). Topoisomerase IIB is formed of heterotetramers only.

Topoisomerase II consists of four domains which include:

• ATPase domain at N-terminal
• A variable C-terminal domain
• Domain for binding of DNA located centrally
• A conserved domain of about a hundred amino acids i.e. toprim domain.

Type II Topoisomerase Types

It is of two basic types:

• Type IIA topoisomerases
• Type IIB topoisomerases

Type IIA topoisomerases

It is found in viruses and all cellular organisms. It is of three types:

• Topo II: It is found in eukaryotes.
• Topo IV: It is found in bacteria. It differs from Gyrase. It is not involved in DNA wrapping while Gyrase is involved in DNA wrapping and promoting negative supercoils.
• Gyrase: It is found in bacteria and some eukaryotes. It introduces negative supercoiling decreasing the linking number by two.

Type IIB topoisomerases

It includes Topo VI which can be found in archaea and some plants.

Type II Topoisomerase Mechanism of action

It occurs as follows with ATP hydrolysis.

1. Cleaving of DNA chain: The enzyme contains tyrosine residues. They form covalent bonds with the DNA strands and break the DNA chain. The lone pair of electrons of O-atom present in the tyrosine acts as a nucleophile and attacks on the Phosphorus in phosphate of DNA. It causes the shifting of a bond from phosphate to one of the O-atom attached to the ribose sugar forming a hydroxyl group. Hence the covalently bonded tyrosine attached with phosphorus breaks the phosphate-sugar backbone which cleaves the chain. This linking is termed 5′-phospho-tyrinosyl protein-DNA linkage. A duplex is broken by the action of the enzyme on both strands at once.
2. Crossing of the intact strand through the gap: In this case, another whole duplex strand passes through the gap over the broken duplex. In this step, the enzyme changes from closed conformation to open conformation favoring the passing of strand. ATP is utilized in this conformational change.

3. Religation: It is done by the attack of 3′-OH of the sugar of separated strand on phosphate group which has formed an intermediate linkage with tyrosine. It repels the bond with tyrosine and reforms the broken bond to join again. It occurs on both strands of duplex together ligating them. The enzymes regain their conformation and continue the cycle.

   Functions of Type II Topoisomerase

Type II topoisomerases are enzymes that cut both strands of the DNA helix simultaneously and change the linking number of DNA by two units. They use the hydrolysis of ATP to perform their functions, unlike type I topoisomerases.

Some of the functions of type II topoisomerases are:

• They promote the chromosome disentanglement by removing knots and tangles from the DNA molecules. This is especially important during DNA replication and segregation, when the daughter strands need to be separated from each other. Failure to do so can lead to cell death.
• They relax the supercoiled DNA by introducing positive or negative twists in the DNA helix. This can affect the accessibility and stability of the DNA for various processes such as transcription and recombination.
• They introduce negative supercoils in the DNA of prokaryotes by a specific type II enzyme called DNA gyrase. This helps to compact the bacterial chromosome and facilitate its unwinding for replication. DNA gyrase is also able to remove positive supercoils that may arise during transcription.
• They regulate gene expression by modulating the chromatin structure and interacting with transcription factors and co-factors. For example, type II topoisomerase β (TOP2β) is involved in the activation of neuronal genes by binding to their promoters and enhancers.
• They participate in DNA repair by resolving complex DNA structures that may arise from DNA damage or recombination events. For example, type II topoisomerase α (TOP2α) is involved in the repair of double-strand breaks by facilitating the formation of Holliday junctions and their resolution.

Topoisomerase Inhibition

Some chemical compounds can block the action of topoisomerases, which are enzymes that mediate the cleavage and re-ligation of DNA strands to relax supercoils, untangle catenanes, and condense chromosomes. These compounds are called topoisomerase inhibitors and they can interfere with the essential cellular processes of DNA replication, transcription, and recombination.

Topoisomerase inhibitors can be classified into two broad subtypes: type I topoisomerase inhibitors and type II topoisomerase inhibitors, depending on which type of topoisomerase they target. Type I topoisomerases (TopI) cut and rejoin one strand of DNA, while type II topoisomerases (TopII) cut and rejoin both strands of DNA .

Some topoisomerase inhibitors prevent topoisomerases from performing DNA strand breaks, while others, called topoisomerase poisons, associate with topoisomerase-DNA complexes and prevent the re-ligation step of the topoisomerase mechanism. These topoisomerase-DNA-inhibitor complexes are cytotoxic agents, as the un-repaired single- and double-stranded DNA breaks they cause can lead to apoptosis and cell death .

Because of this ability to induce apoptosis, topoisomerase inhibitors have gained interest as therapeutics against infectious and cancerous cells. Some examples of topoisomerase inhibitors are:

• Camptothecins: They are natural products derived from the bark of the Chinese tree Camptotheca acuminata. They inhibit TopI by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some semisynthetic derivatives of camptothecins are irinotecan and topotecan, which are used as adjunctive therapies for advanced colorectal, ovarian, and small cell lung cancer.
• Anthracyclines: They are natural products derived from bacteria of the genus Streptomyces. They inhibit TopII by intercalating between DNA base pairs and blocking the re-ligation step . Some examples of anthracyclines are doxorubicin, daunorubicin, epirubicin, and idarubicin, which are used for various types of leukemia and solid tumors.
• Epipodophyllotoxins: They are semisynthetic derivatives of podophyllotoxin, a natural product extracted from the roots of Podophyllum peltatum. They inhibit TopII by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some examples of epipodophyllotoxins are etoposide and teniposide, which are used for various types of leukemia and lymphoma.
• Quinolones: They are synthetic compounds that inhibit bacterial TopII (also called DNA gyrase) by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some examples of quinolones are nalidixic acid, ciprofloxacin, levofloxacin, and moxifloxacin, which are used as broad-spectrum antibiotics.
• Coumarins: They are natural products derived from plants of the genus Psoralea. They inhibit bacterial TopII (also called DNA gyrase) by interfering with ATP binding to the enzyme . Some examples of coumarins are novobiocin, coumermycin A1, and clorobiocin, which are used as antibiotics.

Topoisomerase inhibitors can have serious side effects due to their non-selective action on normal host cells. The major dose-limiting toxicities of topoisomerase inhibitors are hematologic (neutropenia, anemia, thrombocytopenia) and gastrointestinal (diarrhea, nausea). While serum enzyme elevations are not uncommon with chemotherapeutic regimens that include topoisomerase inhibitors, clinically apparent liver injury is uncommon.

Clinical Significance of Topoisomerase

Topoisomerases are important targets for many drugs that interfere with their catalytic activity and induce DNA damage in cells. Some of these drugs are used to treat bacterial infections and cancer.

• Antibacterial drugs: Some broad-spectrum antibiotics, such as fluoroquinolones, act by disrupting the function of bacterial type II topoisomerases, especially DNA gyrase and topoisomerase IV . These drugs prevent the religation of the cleaved DNA strands and cause double-strand breaks and cell death.
• Anticancer drugs: Some chemotherapy drugs work by interfering with topoisomerases in cancer cells, which are highly proliferative and depend on these enzymes for DNA replication and transcription . These drugs can be classified into two groups:
  • Topoisomerase I inhibitors: These drugs stabilize the covalent intermediate formed between topoisomerase I and the 3` end of the cleaved DNA strand, preventing religation and generating single-strand breaks . Examples of these drugs are camptothecin and its derivatives, such as irinotecan and topotecan .
  • Topoisomerase II inhibitors: These drugs stabilize the covalent intermediate formed between topoisomerase II and the 5` ends of the cleaved DNA strands, preventing religation and generating double-strand breaks . Examples of these drugs are etoposide, teniposide, doxorubicin and daunorubicin .

Topoisomerase inhibitors can induce apoptosis or senescence in cancer cells, but they can also cause adverse effects in normal cells, such as bone marrow suppression, cardiotoxicity and neurotoxicity . Therefore, the development of more selective and less toxic topoisomerase inhibitors is an active area of research.

Topoisomerases can also be involved in some autoimmune disorders and neurological diseases. For example, anti-topoisomerase I antibodies (also called anti-scl-70 antibodies) are found in some patients with scleroderma, a chronic inflammatory disease that affects the skin and other organs . These antibodies may recognize topoisomerase I as a foreign antigen and trigger an immune response that damages the tissues. Another example is spinocerebellar ataxia with axonal neuropathy (SCAN1), a rare inherited disorder that causes progressive neurological impairment . This disorder is caused by mutations in the gene encoding tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that repairs the covalent linkage between topoisomerase I and DNA. As a result, patients with SCAN1 accumulate unrepaired DNA damage and suffer from neuronal degeneration.

These examples illustrate the crucial role of topoisomerases in maintaining genomic stability and cellular function, as well as their potential as therapeutic targets or biomarkers for various diseases.

Comparison between Topoisomerase and Helicase

Topoisomerase and helicase are two enzymes that play important roles in DNA replication and other processes involving DNA topology. They have some similarities and differences in their structure, function and mechanism of action.

Similarities

• Both enzymes are involved in the unwinding of double-stranded DNA by changing its supercoiling state.
• Both enzymes require energy to perform their functions. Helicase uses ATP hydrolysis while topoisomerase uses the energy stored in the phosphodiester bonds of DNA.
• Both enzymes act on specific sites on DNA and can be regulated by various factors such as protein-protein interactions, DNA sequence and structure, and post-translational modifications.

Differences

• Helicase unwinds DNA by breaking the hydrogen bonds between the complementary base pairs, while topoisomerase unwinds DNA by breaking and rejoining the phosphodiester bonds in the backbone of one or both strands.
• Helicase acts on both DNA and RNA, while topoisomerase only acts on DNA.
• Helicase moves along the DNA strand in a 5` to 3` direction, while topoisomerase can act in any direction depending on the type and orientation of the enzyme.
• Helicase changes the linking number of DNA by one for each turn of the helix, while topoisomerase changes the linking number of DNA by two for type II and by one for type I.

• Helicase can only relax positive supercoils or introduce negative supercoils in DNA, while topoisomerase can relax both positive and negative supercoils or introduce either type of supercoils depending on the type and mechanism of the enzyme.

  
  

Some chemical compounds can block the action of topoisomerases, which are enzymes that mediate the cleavage and re-ligation of DNA strands to relax supercoils, untangle catenanes, and condense chromosomes. These compounds are called topoisomerase inhibitors and they can interfere with the essential cellular processes of DNA replication, transcription, and recombination.

Topoisomerase inhibitors can be classified into two broad subtypes: type I topoisomerase inhibitors and type II topoisomerase inhibitors, depending on which type of topoisomerase they target. Type I topoisomerases (TopI) cut and rejoin one strand of DNA, while type II topoisomerases (TopII) cut and rejoin both strands of DNA .

Some topoisomerase inhibitors prevent topoisomerases from performing DNA strand breaks, while others, called topoisomerase poisons, associate with topoisomerase-DNA complexes and prevent the re-ligation step of the topoisomerase mechanism. These topoisomerase-DNA-inhibitor complexes are cytotoxic agents, as the un-repaired single- and double-stranded DNA breaks they cause can lead to apoptosis and cell death .

Because of this ability to induce apoptosis, topoisomerase inhibitors have gained interest as therapeutics against infectious and cancerous cells. Some examples of topoisomerase inhibitors are:

• Camptothecins: They are natural products derived from the bark of the Chinese tree Camptotheca acuminata. They inhibit TopI by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some semisynthetic derivatives of camptothecins are irinotecan and topotecan, which are used as adjunctive therapies for advanced colorectal, ovarian, and small cell lung cancer.
• Anthracyclines: They are natural products derived from bacteria of the genus Streptomyces. They inhibit TopII by intercalating between DNA base pairs and blocking the re-ligation step . Some examples of anthracyclines are doxorubicin, daunorubicin, epirubicin, and idarubicin, which are used for various types of leukemia and solid tumors.
• Epipodophyllotoxins: They are semisynthetic derivatives of podophyllotoxin, a natural product extracted from the roots of Podophyllum peltatum. They inhibit TopII by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some examples of epipodophyllotoxins are etoposide and teniposide, which are used for various types of leukemia and lymphoma.
• Quinolones: They are synthetic compounds that inhibit bacterial TopII (also called DNA gyrase) by stabilizing the covalent intermediate between the enzyme and the cleaved DNA strand . Some examples of quinolones are nalidixic acid, ciprofloxacin, levofloxacin, and moxifloxacin, which are used as broad-spectrum antibiotics.
• Coumarins: They are natural products derived from plants of the genus Psoralea. They inhibit bacterial TopII (also called DNA gyrase) by interfering with ATP binding to the enzyme . Some examples of coumarins are novobiocin, coumermycin A1, and clorobiocin, which are used as antibiotics.

Topoisomerase inhibitors can have serious side effects due to their non-selective action on normal host cells. The major dose-limiting toxicities of topoisomerase inhibitors are hematologic (neutropenia, anemia, thrombocytopenia) and gastrointestinal (diarrhea, nausea). While serum enzyme elevations are not uncommon with chemotherapeutic regimens that include topoisomerase inhibitors, clinically apparent liver injury is uncommon.

Topoisomerases are important targets for many drugs that interfere with their catalytic activity and induce DNA damage in cells. Some of these drugs are used to treat bacterial infections and cancer.

• Antibacterial drugs: Some broad-spectrum antibiotics, such as fluoroquinolones, act by disrupting the function of bacterial type II topoisomerases, especially DNA gyrase and topoisomerase IV . These drugs prevent the religation of the cleaved DNA strands and cause double-strand breaks and cell death.
• Anticancer drugs: Some chemotherapy drugs work by interfering with topoisomerases in cancer cells, which are highly proliferative and depend on these enzymes for DNA replication and transcription . These drugs can be classified into two groups:
  • Topoisomerase I inhibitors: These drugs stabilize the covalent intermediate formed between topoisomerase I and the 3` end of the cleaved DNA strand, preventing religation and generating single-strand breaks . Examples of these drugs are camptothecin and its derivatives, such as irinotecan and topotecan .
  • Topoisomerase II inhibitors: These drugs stabilize the covalent intermediate formed between topoisomerase II and the 5` ends of the cleaved DNA strands, preventing religation and generating double-strand breaks . Examples of these drugs are etoposide, teniposide, doxorubicin and daunorubicin .

Topoisomerase inhibitors can induce apoptosis or senescence in cancer cells, but they can also cause adverse effects in normal cells, such as bone marrow suppression, cardiotoxicity and neurotoxicity . Therefore, the development of more selective and less toxic topoisomerase inhibitors is an active area of research.

Topoisomerases can also be involved in some autoimmune disorders and neurological diseases. For example, anti-topoisomerase I antibodies (also called anti-scl-70 antibodies) are found in some patients with scleroderma, a chronic inflammatory disease that affects the skin and other organs . These antibodies may recognize topoisomerase I as a foreign antigen and trigger an immune response that damages the tissues. Another example is spinocerebellar ataxia with axonal neuropathy (SCAN1), a rare inherited disorder that causes progressive neurological impairment . This disorder is caused by mutations in the gene encoding tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that repairs the covalent linkage between topoisomerase I and DNA. As a result, patients with SCAN1 accumulate unrepaired DNA damage and suffer from neuronal degeneration.

These examples illustrate the crucial role of topoisomerases in maintaining genomic stability and cellular function, as well as their potential as therapeutic targets or biomarkers for various diseases.

Topoisomerase and helicase are two enzymes that play important roles in DNA replication and other processes involving DNA topology. They have some similarities and differences in their structure, function and mechanism of action.

Similarities

• Both enzymes are involved in the unwinding of double-stranded DNA by changing its supercoiling state.
• Both enzymes require energy to perform their functions. Helicase uses ATP hydrolysis while topoisomerase uses the energy stored in the phosphodiester bonds of DNA.
• Both enzymes act on specific sites on DNA and can be regulated by various factors such as protein-protein interactions, DNA sequence and structure, and post-translational modifications.

Differences

• Helicase unwinds DNA by breaking the hydrogen bonds between the complementary base pairs, while topoisomerase unwinds DNA by breaking and rejoining the phosphodiester bonds in the backbone of one or both strands.
• Helicase acts on both DNA and RNA, while topoisomerase only acts on DNA.
• Helicase moves along the DNA strand in a 5` to 3` direction, while topoisomerase can act in any direction depending on the type and orientation of the enzyme.
• Helicase changes the linking number of DNA by one for each turn of the helix, while topoisomerase changes the linking number of DNA by two for type II and by one for type I.

• Helicase can only relax positive supercoils or introduce negative supercoils in DNA, while topoisomerase can relax both positive and negative supercoils or introduce either type of supercoils depending on the type and mechanism of the enzyme.

  
  

We are Compiling this Section. Thanks for your understanding.