Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 4, 2021, Pages. 12982 - 12996 Received 05 March 2021; Accepted 01 April 2021. Interfering with Nucleic Acid Synthesis: Recent Progress of Nucleoside and Nucleotide Analogues in Anti-viral Treatment Selina Huang 1 1The Baylor School ABSTRACT Nucleoside/nucleotide analogues are a group of drugs that interfere with the synthesis of DNA or RNA, and have been used for anti-viral treatment for decades. Their importance is self-evident due to their ubiquitous mechanism of action, especially as we today face the challenge of COVID-19 pandemic. Here we review recent studies regarding nucleoside/nucleotide analogues in HIV, HBV, HCV, herpes and influenza virus infection, as well as the emerging SARS-CoV-2 infection, so as to shed light its current status of usage, and also to project the anti-viral strategy in the future. Index Terms—Antiviral drugs, nucleoside/nucleotide analogue, viral infection Introduction prevalence of viral infections across the world have been gravely threatening the public health. With hepatitis infection as a notable example, 325 million people globally by 2020 are suffering from it1. Novel diseases like coronavirus disease 2019 (COVID-19), having infected nearly 90 million people since its advent to January 20212, is still causing disastrous outbreaks, which shows the inability of human to response adeptly to such novel challenge. One type of antiviral drug, being nucleoside/nucleotide analogues, is a synthetic, chemically modified compound that mimics the structure of natural nucleosides or nucleotides, both of which are the building blocks of DNA and RNA.3 Pharmacologically, nucleoside/nucleotide analogues can disrupt or terminate the synthesis of viral DNA or RNA (Figure 1) 4. Given that these processes are universal among viruses, many nucleoside/nucleotide analogues have relatively broad-spectrum efficacy5. Based on their drug targets, nucleoside/nucleotide analogues can be classified as reverse transcriptase inhibitors, DNA polymerase inhibitors, and RNA polymerase inhibitors. A typical reverse transcriptase inhibitor is zidovudine, which is mostly used against HIV6. It is a synthetic thymidine nucleoside analogue that has its 3’ hydroxy group replaced by an azido group7, and this modification allows it to inhibit viral reverse transcription and to induce cDNA chain termination8. One example of DNA polymerase inhibitors is acyclovir, which is commonly used against viral infections caused by viruses of herpesvirus family9. Acyclovir is a synthetic purine nucleoside analogue that inhibits viral DNA polymerase by interrupting the growing viral DNA chain and terminating further polymerization10. An RNA polymerase inhibitor, remdesivir, is a monophosphoramidateprodrug of 1'-cyano-substituted adenosine nucleoside analogue that terminates viral RNA synthesis by inhibiting viral RNA polymerase11. More drugs of each category are listed in Table 1. In this review we will discuss how nucleoside/nucleotide drugs have evolved, and especially highlight their recent research in antiviral treatment. Five different viral infection is used as examples, including HIV, hepatitis, herpes, influenza, and SARS-CoV-2. Nucleoside/Nucleotide Analogues in HIV Treatment Human immunodeficiency virus (HIV) is a retrovirus that infects the host T lymphocytes through CD4 receptors and a co-receptor that can be CC-chemokine receptor 5 (CCR5) or CXC- chemokine receptor 4 (CXCR4)13. By depleting CD4+ T cells, HIV is the cause of acquired 12982 http://annalsofrscb.ro Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 4, 2021, Pages. 12982 - 12996 Received 05 March 2021; Accepted 01 April 2021. immune deficiency syndrome (AIDS)14. The main feature of HIV that makes HIV infection difficult to be completely cured is that it is able to have its DNA integrated into the host genome, making an HIV reservoir13,15. On the other hand, since HIV undergoes reverse transcription for its replication, this process can be inhibited by reverse transcriptase inhibitors13. Examples of reverse transcriptase inhibitors for HIV treatment are emtricitabine, lamivudine, stavudine, and zidovudine5. Ganciclovir, a DNA polymerase inhibitor and is originally used for herpes simplex virus (HSV) treatment, is also a nucleoside analogue that can treat HIV infections5,16. Emtricitabine, an analogue of cytidine, was first discovered in 1996 when its metabolites were identified from human urine sample in a clinical trial of anti-HIV compound17. Emtricitabine can serve as HIV post-exposure prophylaxis (PEP) when combined with tenofovirdisoproxilfumarate and rilpivirine18. Contradicting to previous belief, a recent study showed that the combination of emtricitabine, tenofovir and ritonavir-boosted lopinavir as antiretroviral therapy (ART) to treat pregnant women with HIV do not lead to a higher risk of premature birth and death of infants than zidovudine, lamivudine, and ritonavir-boosted lopinavir (ZDV–3TC–LPV/r) did19. Moreover, it is worth noting that when virally suppressed HIV-positive patients switch from non-integrase inhibitor-based antiviral therapy to a co-formulated elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (E/C/F/TAF), they may experience moderate weight gain and significant increase in lipid levels20. Lamivudine is a cytidine nucleoside analogue that was the unnatural enantiomer derived from 2’-Deoxy-3’-thiacytidine (BCH 189), a potent anti-HIV agent21. Upon its advent, lamivudine continues to be able to partner with existing and novel therapies, and combination therapies with lamivudine had become more potent, safer, and more convenient in past years22. Lamivudine combined with Table 1.List of major nucleoside and nucleotide analogue drugs. Drug Name Types of Analogue Virus Target Reference Reverse Transcriptase Inhibitors Emitricitabine cytidine HIV, HBV [17-20] Lamivudine cytidine HIV, HBV [5], [21-26], [52] Stavudine thymidine HIV [27-30] Zidovudine thymidine HIV [31-34] Entecavir guanine HBV [42-44] Tenofovir adenine HIV, HBV [5], [39], [45-47] Adefovir adenine HBV [39], [48-52] Telbivudine thymidine HBV [53-56] DNA Polymerase inhibitors Ganciclovir guanine HIV, CMV [35-37], [80,81] Valganciclovir guanine CMV [35-37] Clevudine thymidine HBV [57-58] Acyclovir guanine HSV [68-70] Valaciclovir guanine HSV [68-70] Penciclovir guanine HSV [70-73] Famciclovir guanine HSV [70-73] Brivudine thymidine VZV [5], [74-76] Cidofovir cytidine CMV [77-79] 12983 http://annalsofrscb.ro Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 4, 2021, Pages. 12982 - 12996 Received 05 March 2021; Accepted 01 April 2021. RNA Polymerase inhibitors Favipiravir pyrazine Influenza B virus [93-98], [111] HCV, Influenza virus, SARS-CoV- Ribavirin guanine [11], [103-108] 2 [39], [59-60], [85- Sofosbuvir uridine HCV, SARS-CoV-2 89], [109] 2’FdG guanine Influenza A virus [39], [61-62], [110] Galidesivir adenine Ebola, SARS-CoV-2 [90-92] Figure 1.Mechanism of action of nucleoside/nucleotide analogues. Both nucleoside analogue and nucleotide analogue are phosphorylated upon cell entry to become active. The final triphosphate metabolites interact with viral enzymes and terminate the synthesis DNA or RNA.12 dolutegravir can be a promising maintenance therapy for virally controlled HIV-positive patients23 and a potential treatment for patients with HIV infection24,25. However, lamivudine monotherapy (LM) has led to immune decline when used on HIV-positive children who were previously receiving combination antiretroviral therapy (cART)26. Stavudine, an analogue of thymidine, was developed to treat HIV infection and was approved for medical use in 199627. Overall, the use of stavudine for HIV-positive patients is declining due to its side affects28,29.For example, using it is likely causing a higher risk of getting neuropathy28. Nevertheless, synthesized phosphoramidate derivatives of stavudine with different polyfluorinated variants to the aromatic ring (4-CF3 / 3-CF3 / 3-SF5) have shown potentials in exhibiting better anti-HIV activity and lower toxicity than unmodified stavudine30. Zidovudine is a thymidine analogue that was first found as potential agent against HIV infection in 198531 but had been limited in performance of viral resistance, efficacy, and safety and needed further studies32. The combination of zidovudine and lamivudine has the potential to treat HIV-associated neurocognitive disorder given its ability to localize the brain reigns in which HIV neurodegeneration occurs33. The use of zidovudine for pregnant women with HIV has a strong association with cardiac remodeling, which can lead to clinical heart failure and cardiovascular disease, and cardiac dysfunction of fetuses34. 12984 http://annalsofrscb.ro Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 4, 2021, Pages. 12982 - 12996 Received 05 March 2021; Accepted 01 April 2021. Ganciclovir is an analogue of guanine that inhibits DNA polymerase, initially developed to treat herpesvirus infection with or without HIV infection35,36. A recent study has shown that ganciclovir is able to directly reduce HIV viral load by inhibiting HIV reverse transcription37. Nucleoside/nucleotide Analogues in Hepatitis Treatment Hepatitis is the inflammation occurred in the liver that can be caused by bacteria, parasite, alcohol, auto-immune, etc., and it is mostly caused by virues38. The viruses causing hepatitis can be classified into hepatitis A, B, C, D, E, G viruses, in which hepatitis A, B, and C viruses are the most common38. Both hepatitis A virus (HAV) and hepatitis