topoisomerase inhibitor topoisomerase inhibitor topoisomerase inhibitors are chemical compounds that block the action of topoisomerases, which are broken into two broad subtypes: type i topoisomerases (topi) and type ii topoisomerases (topii). topoisomerase plays important roles in cellular reproduction and dna organization, as they mediate the cleavage of single and double stranded dna to relax supercoils, untangle catenanes, and condense chromosomes in eukaryotic cells. topoisomerase inhibitors influence these essential cellular processes. some topoisomerase inhibitors prevent topoisomerases from performing dna strand breaks while others, deemed 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. history in the 1940s, great strides were made in the field of antibiotic discovery by researchers like albert schatz, selman a. waksman, and h. boyd woodruff that inspired significant effort to be allocated to the search for novel antibiotics. studies searching for antibiotic and anticancer agents in the mid to late 20th century have illuminated the existence of numerous unique families of both topi and topii inhibitors, with the 1960s alone resulting in the discovery of the camptothecin, anthracycline and epipodophyllotoxin classes. knowledge of the first topoisomerase inhibitors, and their medical potential as anticancer drugs and antibiotics, predates the discovery of the first topoisomerase (escherichia. coli omega protein, a topi) by jim wang in 1971. in 1976, gellert et al. detailed the discovery of the bacterial topii dna gyrase and discussed its inhibition when introduced to coumarin and quinolone class inhibitors, sparking greater interest in topoisomerase-targeting antibiotic and antitumor agents. topoisomerase inhibitors have been used as important experimental tools that have contributed to the discovery of some topoisomerases, as the quinolone nalidixic acid helped elucidate the bacterial topii proteins it binds to. topoisomerase inhibitor classes have been derived from a wide variety of disparate sources, with some being natural products first extracted from plants (camptothecin, etoposide) or bacterial samples (doxorubicin, indolocarbazole), while others possess purely synthetic, and often accidental, origins (quinolone, indenoisoquinoline). after their initial discoveries, the structures of these classes have been fine tuned through the creation of derivatives in order to make safer, more effective, and are more easily administered variants. currently, topoisomerase inhibitors hold a prominent place among antibiotics and anticancer drugs in active medical use, as inhibitors like doxorubicin (anthracycline, topii inhibitor), etoposide (topii inhibitor), ciprofloxaxin (fluoroquinolone, topii inhibitor), and irinotecan (camptothecin derivative, topi inhibitor) were all included in the 2019 who model list for essential medicines. topoisomerase i inhibitors mechanism topi relaxes dna supercoiling during replication and transcription. under normal circumstances, topi attacks the backbone of dna, forming a transient topi-dna intermediate that allows for the rotation of the cleaved strand around the helical axis. topi then re-ligates the cleaved strand to reestablish duplex dna. treatment with topi inhibitors stabilizes the intermediate cleavable complex, preventing dna re-ligation, and inducing lethal dna strand breaks. camptothecin-derived topi inhibitors function by forming a ternary complex with topi-dna and are able to stack between the base pairs that flank the cleavage site due to their planar structure. normal cells have multiple dna checkpoints that can initiate the removal of these stabilized complexes, preventing cell death. in cancer cells, however, these checkpoints are typically inactivated, making them selectively sensitive to topi inhibitors. non-camptothecins, such as indenoisoquinolines and indolocarbazoles, also associate with topi itself, forming hydrogen bonds with residues that typically confer resistance to camptothecin. indenosioquinolines and indolocarbazoles also lack the lactone ring present in camptothecin, making them more chemically stable and less prone to hydrolysis at biological ph. camptothecins camptothecin (cpt) was first derived from the tree camptotheca acuminata, native to southern china. it was isolated in a united states department of agriculture (usda) led search for cortisone precursors in the late 1950s and its anticancer activity explored in the early 1960s by dr. john hartwell and his team at the cancer chemotherapy national service center. clinical trials during the 1970s converted cpt into its sodium salt in order to increase its solubility, however, clinical trials were unsuccessful due to the compound's toxicity. it was not until 1985 that hsiang et al. deduced via topoisomerase relaxation assays that the anti-tumor activity of cpt was due to its topi inhibitory activity. cushman et al. (2000) mentions that due to a lack of observed dna unwinding in experiments involving cpt and the non-cpt topi inhibitor indenoisoquinoline, they believed that these inhibitors likely did not function through a mechanism involving dna intercalation. this hypothesis has been disproved, as x-ray crystallography based models have allowed for the visualization of topi inhibitor dna intercalation. one of important structural feature of cpt is its planar pentacyclic ring and lactone ring (the e-ring). the lactone ring is believed to create the active form of the drug, but it is often prone to hydrolysis, which causes a loss in function. the discovery of cpt led to the synthesis of three currently fda approved derivatives: topotecan (tpt), irinotecan, and belotecan. tpt is commonly used to treat ovarian and small cell lung cancer (sclc) while irinotecan is known to improve colon cancer. commonly, tpt is used in conjunction with a combination of drugs such as cyclophosphamide, doxorubicin, and vincristine. it was noted that iv treatment with tpt had similar response and survival rates to oral medication. furthermore, it has been shown that tpt treatment with radiotherapy can improve survival rates of patients with brain metastases. belotecan is a recent cpt derivative used to treat sclc. several clinical trials on cpt derivatives such as gimatecan and silatecan continue to progress. currently, silatecan is in a phase 2 study for the treatment of gliosarcoma in adults who have not had bevacizumab treatment. non-camptothecins despite the clinical success of the many cpt derivatives, they require long infusions, have low water solubility, and possess many side effects such as temporary liver dysfunction, severe diarrhea, and bone marrow damage. additionally, there has been an increase in observed single point mutations that have shown to prompt topi resistance to cpt. therefore, three clinically relevant non-cpt inhibitors, indenoisoquinoline, phenanthridines, and indolocarbazoles, are currently being considered by the fda as possible chemotherapies. among the non-cpt inhibitors, indolocarbazoles have shown the most promise. these inhibitors have unique advantages compared with the cpt. first, they are more chemically stable due to the absence of the lactone e-ring. second, indolocarbazoles attach to topi at different sections of the dna. third, this inhibitor expresses less reversibility than cpt. therefore, they require shorter infusion times because the topi inhibitor complex is less likely to dissociate. currently, several other indolocarbazoles are also undergoing clinical trials. other than indocarbazoles, topovale (arc-111) is considered one of the most clinically developed phenanthridine. they have been promising in fighting colon cancer, but have shown limited effectiveness against breast cancer. the first member of the indolocarbazole family of topoisomerase inhibitors, be-13793c, was discovered in 1991 by kojiri et al. it was produced by a streptomycete similar to streptoverticillium mobaraense, and dna relaxation assays revealed that be-13793c is capable of inhibiting both topi and topii. soon after, more indolocarbazole variants were found with topi specificity. cushman et al. (1978) details the discovery of the first indenoisoquinoline, indenoisoquinoline (nsc 314622), which was made accidentally in an attempt to synthesize nitidine chloride, an anticancer agent that does not inhibit topoisomerases. research on the anticancer activity of indenoisoquinoline ceased until the late 90s as interest grew for cpt class alternatives. since then, work on developing effective derivatives has been spearheaded by researchers like dr. mark cushman at purdue university and dr. yves pommier at the national cancer institute. as of 2015, indotecan (lmp-400) and indimitecan (lmp-776), derivatives of indenoisoquinoline, were in phase one clinical trials for the treatment of relapsed solid tumors and lymphomas. topoisomerase ii inhibitors mechanism topii forms a homodimer that functions by cleaving double stranded dna, winding a second dna duplex through the gap, and re-ligating the strands. topii is necessary for cell proliferation and is abundant in cancer cells, which make topoii inhibitors effective anti-cancer treatments. in addition, some inhibitors, such as quinolones, fluoroquinolones and coumarins, are specific only to bacterial type 2 topoisomerases (topoiv and gyrase), making them effective antibiotics. regardless of their clinical use, topoii inhibitors are classified as either catalytic inhibitors or poisons. topoii catalytic inhibitors bind the n-terminal atpase subunit of topoii, preventing the release of the separated dna strands from the topii dimer. the mechanisms of these inhibitors are diverse. for example, icrf-187 binds non-competitively to the n-terminal atpase of eukaryotic topoii, while coumarins bind competitively to the b subunit atpase of gyrase. alternatively, topoii poisons generate lethal dna strand breaks by either promoting the formation of covalent topii-dna cleavage complexes, or by inhibiting re-ligation of the cleaved strand. some poisons, such as doxorubicin, have been proposed to intercalate in the strand break between the base pairs that flank the topii-dna intermediate. others, such as etoposide, interact with specific amino acids in topii to from a stable ternary complex with the topii-dna intermediate. aminocoumarins aminocoumarins (coumarins and simocyclinones) and quinolones are the two main classes of topii inhibitors that function as antibiotics. the aminocoimarins can be further divided into two groups: traditional coumarin simocyclioners the coumarins group, which includes novobiocin and coumermycin, are natural products from the streptomyces species and target the bacterial enzyme dna gyrase (topii). mechanistically, the inhibitor binds in the b subunit of the gyrase (gyrb) and prevents atpase activity. this is attributed to the drug creating a stable conformation of the enzyme, which exhibits a low affinity for atp which is needed for dna supercoiling. it is proposed that the drug functions as a competitive inhibitor. thus, at high concentrations, atp outcompetes the drug. one limitation of traditional coumarins is gyrb ability to confer antibiotic resistance due to mutations and as a result decrease the inhibitor's ability to bind and induce cell death. simocyclinones are another class of topii antibiotics but differ from aminocoumarins in that they are composed of both aminocoumarins and a polyketide element. they also inhibit dna gyrase's ability to bind to dna instead of inhibiting atpase activity, and produces several antibiotic classes. these antibiotics are further divided into two group: actinomycin a and actinomycin b. it was shown that both actinomycin a and actinomycin b were highly effective in killing gram-positive bacteria. although simocyclinones are effective antibiotics, research has shown that one strain of aimocyclioners, s. antibioticus, cause streptomyces to produce antibiotics. quinolones quinolones are amongst the most commonly used antibiotics for bacterial infections in humans, and are used to treat illness such as urinary infections, skin infections, sexually transmitted diseases (std), tuberculosis and some anthrax infections. the effectiveness of quinolones is proposed to be from chromosome fragments, which initiate the accumulation of reactive oxygen species that leads to apoptosis. quinolones can be divided into four generations: first generation: nalidixic acid second generation: cinoxacin, norfloxacin, ciprofloxacin third generation: levofloxacin, sparfloxacin fourth generation: moxifloxacin the first quinolone was discovered in 1962 by george lesher and his co-workers at sterling drug (now owned by sanofi) as an impurity collected while manufacturing chloroquine, an antimalarial drug. this impurity was used to develop nalidixic acid, which was made clinically available in 1964. along with its novel structure and mechanism, nalidixic acid's gram negative activity, oral application, and relatively simple synthesis (qualities common among quinolones), showed promise. despite these features, it was relegated to solely treat urinary tract infections because of its small spectrum of activity. the newer generation of drugs are classified as fluoroquinolones due to the addition of a fluorine and a methyl-piperazine, which allows for improved gyrase targeting (topii). it is proposed that this added fluorine substituent aids in base stacking during fluoroquinolone intercalation into topii cleaved dna by altering the electron density of the quinolone ring. the first member of the fluoroquinolone subclass, norfloxacin, was discovered by koga and colleagues at the pharmaceutical company kyorin in 1978. it was found to possess higher anti-gram negative potency than standard quinolones, and showed some anti-gram positive effects. both its blood serum levels and tissue penetration abilities proved to be poor, and it was overshadowed by the development of ciprofloxacin, a fluoroquinolone with a superior spectrum of