Types of Modification

CHAPTER 5: CHAPTER 5: STUDIES ON THE AGGREGATION INDUCED FLUORESCENCE EMISSION PROPERTY OF PYRENYLAMIDO

1.3. Types of Modification

Modified nucleosides can be classified mainly into two categories: (i) Base-modified and (ii) Sugar-modified nucleosides.

(i) Base-modified nucleosides: -

In the synthetic oligonucleotide research area, the synthesis of nucleobase modified nucleosides is probably the most common and most explored topic among researchers. Natural pyrimidine nucleobases can be modified via substitutions generally in C2, C4 N3, C5 and C6 positions (1.023-1.027, Figure 1.7).^44-51Among these, C5- substituted products are the most explored for their applications in medicinal and biochemistry.⁴⁴ Similarly in natural purine nucleobases, substitutions can be done effectively at C2, C6 and C8 positions (1.028-1.031, Figure 1.7).^52-56 An example of naturally occurring biologically active purine analog is 7-deazapurine (pyrrolo[2,3-d]pyrimidine).⁵⁷ Due to its

applications in many currently available drugs, the synthesis of its substituted nucleoside analogs is a recent topic of interest. Several modified 7-deazapurine nucleoside analogs have been utilized in various investigations.^58-63 Some examples of such types of nucleoside analogs are shown in Figure 1.7 (1.032-1.035).

Figure 1.7. Selected examples of base-modified nucleosides.

Some simple examples of base-modified nucleosides are isosteres of the natural DNA bases.⁶⁴ Generally, in these modified bases, the exocyclic carbonyl groups are replaced with C- F groups and N-H groups are replaced with C-H groups (Figure 1.8). These modified nucleosides have been utilized in several investigations.^65-68 The compounds 1.038 to 1.043 represent a broad family of nucleosides known as C-nucleosides, where the sugar moiety is linked to a base through a C-C single bond. Several naturally occurring C-nucleosides and their synthetic analogs contributed significantly in the field of medicinal chemistry.⁶⁹ A direct advantage of C-nucleosides is their higher stability against enzymatic and acid-catalyzed hydrolysis when compared to corresponding N-nucleosides.

Figure 1.8. Selected examples of base isosteres and C-nucleosides.

As mentioned in the above section, natural nucleobases show weak photophysical properties. However, nucleosides can be modified to impart useful photophysical properties.

Fluorescent nucleoside analogs often developed by modification on the natural nucleobases or by utilizing fluorophores with remarkable photophysical properties as base surrogates. Such fluorescent nucleoside base analogs can be classified as chromophoric base, Pteridine, expanded nucleobase, extended nucleobase, and isomorphic base analogs. Chromophoric base analogs are obtained by replacing natural bases with polycyclic aromatic hydrocarbons (PAH) (1.044-1.047, Figure 1.9).^70-72 These nucleoside analogs display high emission quantum efficiencies but lack Watson-Crick (W-C) hydrogen bonding ability. Pteridines are highly emissive planar heterobicyclic aromatic compounds. These compounds are naturally occurring and have chemical structures similar to purines (1.048-1.051, Figure 1.9). The initiation and development of pteridine labeled nucleosides were mostly done by Hawkins and co-workers.^73,

74 Expanded nucleobase analogs are developed by either fusion or insertion of aromatic rings into purine and pyrimidine bases (1.052-1.055, Figure 1.9). In many cases, such modifications lead to the generation of highly emissive nucleobases with H-bonding complementarity similar to that of natural nucleobases. Extended nucleobase analogs are often developed by attaching fluorophores with known photophysical properties to the nucleobases either through rigid or flexible linkers (1.056-1.059, Figure 1.9).^{75, 76} The parent fluorophores normally retained their photophysical properties when attached to the nucleobases via electronically nonconjugated linkers. On the other hand, attachment via electronically conjugated linkers typically generate new fluorophores with unique photophysical properties. Isomorphic nucleobase analogs (1.060-1.063, Figure 1.9) are heterocycles which have a close resemblance to the

corresponding natural nucleobases in terms of structure and W-C base pairing property.^{75, 77, 78} When compared to other nucleobase analogs, a practical advantage of these analogs is their close resemblance to the natural nucleobases and minimal or non-perturbing nature. Because of the non-perturbing nature, isomorphic base labeled probes found numerous applications in the field of nucleic acid research.^{75, 77-79}

Figure 1.9. Selected examples of fluorescent base analogs.

(ii) Sugar-modified nucleosides: -

Research for the effective, selective and nontoxic antiviral agents initiated a variety of strategies for the development of modified nucleoside analogs. In many cases, these strategies involved the modification of the sugar moiety of natural nucleosides. For example, acyclic nucleosides like acyclovir and ganciclovir are clinically used for the treatment of herpes viruses. Dideoxynucleosides and their analogs such as didanosine (ddI), zalcitabine (ddC), stavudine (d4T) and avacavir are used for the treatment of AIDS (Figure 1.10).

Figure 1.10. Selected examples of clinically approved sugar modified nucleoside drugs.

Our research area is focused on the base modified pyrimidine nucleosides at C5-position, therefore we will not discuss the sugar modified nucleosides broadly. Some different types of biologically active sugar modified nucleosides are shown in Figure 1.11. Below sections will restrict the discussion about the C5 modification of 2′-deoxyuridine only. Therefore the examples will include the modified 2′-deoxyuridines wherein C5-position is modified.

Figure 1.11. Selected examples of sugar modified nucleosides.

1.4. 5-Substituted (C5) Modified Pyrimidine Nucleosides

5-substituted pyrimidine nucleosides consist of a special group of compounds highly recognized for their applications in pharmaceutical molecular genetics. Incorporation of diverse functionalities in the C5-position of pyrimidine nucleosides/nucleotides has been a continuous interest in order to improve their physicochemical properties such as metabolic

stability,oral bioavailability, and pharmacokinetics.^{80, 81} These molecules have shown potential antiviral activities against diverse classes of viruses and will be discussed later in this chapter.

The evolution of molecular techniques for the analysis of nucleic acids has a great impact on the development of molecular genetics. The molecular techniques used in this endeavor mostly related to the utilization of modified oligonucleotide probes. As a site for modification and attachment of molecular signaling components, the C5-position of pyrimidine nucleosides is possibly the ideal site as this site remains in the major groove of the B-DNA. As there is no significant steric hindrance at the major groove, even very large groups can be incorporated without destabilizing the DNA structure. Thus a wide selection of biologically active molecules is possible for incorporation at the C5-position of pyrimidine nucleosides/nucleotides for interpretation of molecular genetics. Moreover, C5-substituted pyrimidine derivatives are well- known for their high compatibility with the endogenous kinases and DNA polymerases needed for their incorporation into DNA.^82-84

1.5. Non-Fluorescent 5-Substituted Modified 2'-Deoxyuridines and

Dalam dokumen A Dissertation Submitted to the Indian Institute of Technology Guwahati As Partial Fulfillment for the Award of Degree of (Halaman 35-40)

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