Oligonucleotide

OLIGONUCLEOTIDE
Himal Barakoti
Roll no: 171709
M.pharm, 2nd sem
Department of Pharmacy
Assam Down Town University

CONTENTS
 Oligonucleotides: Introduction
 DNA & RNA
 Nucleotides
 Oligonucleotide Drug Delivery
 Drug Delivery strategies
 Modes of Action
 Advantages and limitations
 Summary
 References
Department of Pharmacy, ADTU
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INTRODUCTION: OLIGONUCLEOTIDE
 Greek “oligo” – Few or small
 “Polynucleotide whose molecules contain relatively small number of
nucleotides.”
 “Short nucleic acid chain usually consisting of approximately 25
nucleotides.”
“Short nucleic acid polymers used in research, genetic testing and
forensics.”
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DNA & RNA
 In 1869, Friedrich Miescher, young Swiss physician discovered DNA. He
termed the name “nuclein” as it came from nuclei. Later it was found
to be strongly acidic, thus the name was changed to nucleic acid.
 In 1880, Emil Fisher identified purine and pyrimidine bases.
 Albrecht Kossel identified nitrogenous bases of nuclein as well as 5
carbon sugar and phosphoric acid group for which He was awarded
nobel prize in 1910.
 In 1950, inter nucleotide bond was identified.
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5

DIFFERENCES IN STRUCTURE
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3 COMPONENTS OF NUCLEIC ACID
1. Pentose Sugar: 5’ and 3’ carbon of pentose sugar participate in
phosphodiester bond and 1’ is occupied by organic base.
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2. Organic Base: Heterocyclic compounds containing nitrogen in their
rings; hence also called nitrogenous base.
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3. Phosphoric acid: H3PO4 has three reactive hydroxyl group in which two
are involved in forming sugar phosphate backbone of DNA. Phosphate
moiety joins 5’C of one & 3’C of neighbouring pentose molecule to
produce phosphodiester linkage. (5’C—O—P—O—C3’)
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NUCLEOSIDES AND NUCLEOTIDES
 Linkage between Ribose sugar and organic base
yields ribonucleosides and between deoxyribose and
organic base produce deoxyribosides. Both are
termed as nucleosides.
 Nucleotides are phosphorylated derivatives of
nucleosides. A nucleotide is formed when a
phosphate group is attached either 3’C or 5’C of
pentose residue of nucleoside.
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SINGLE NUCLEOTIDE STRUCTURE
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Nucleosides and Nucleotides
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Mainframe of DNA and RNA strands
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INTRODUCTION: OLIGONUCLEOTIDE
 Greek “oligo” – Few or small
 “Polynucleotide whose molecules contain relatively small number of
nucleotides.”
 “Short nucleic acid chain usually consisting of approximately 25
nucleotides.”
“Short nucleic acid polymers used in research, genetic testing and
forensics.”
14

 Oligonucleotides are characterized by the sequence of nucleotide
residues that make up the entire molecule. The length of the
oligonucleotide is usually denoted by "-mer" (from Greek meros,
"part").
 For example, an oligonucleotide of six nucleotides is a hexamer, while
one of 25 nucleotides would usually be called a "25-mer".
 In nature, oligonucleotides are usually found as small RNA molecules
that function in the regulation of gene expression (e.g. microRNA), or
are degradation intermediates derived from the breakdown of larger
nucleic acid molecules.
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 Oligonucleotides are commonly prepared in laboratory by solid-phase
chemical synthesis method.
 Large number of DNA probes, each one with different sequence are
immobilized at defined position on solid surface, made up of either
nylon or glass.
 Whereas enzymes synthesize DNA and RNA only in a 5’ to 3’
direction, chemical oligonucleotide synthesis does not have this
limitation, although it is, most often, carried out in the opposite, 3' to
5' direction.
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 Traditional small-molecule antiviral agents inhibit enzymes that are
important to viral replication or reverse transcription.
 The synthesis and design of nucleoside-based antiviral agents is well-
established and many clinically important drugs have been developed
(e.g. acyclovir).
 However, it has proved difficult to develop compounds with the ability
to eliminate viruses entirely or to prevent their integration into the
host genome.
 For this reason a number of oligonucleotide-based approaches are
now being developed.
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OLIGONUCLEOTIDE DRUG DELIVERY
 Strategy of therapeutic oligonucleotides is divided into
four categories, as follows:
A) Single piece of oligonucleotide
B) Oligonucleotide-ligand conjugate
C) Oligonucleotide-polymer conjugate
D) Nanoparticle
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Department of Pharmacy, ADTU 19

OLIGONUCLEOTIDE DRUG DELIVERY
 Therapeutic oligonucleotides, on the basic of mechanism of action is
divided into 2 categories, as follows:
A) Antisense Oligonucleotides
B) Modulator of protein activity (Aptamers)
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A) ANTISENSE OLIGONUCLEOTIDES
 Many pharmacological approach involve creating compounds that
binds and disable protein.
Eg. Proponolol, Cimitidine
 A new way to block protein function is to prevent translation of
mRNA into protein.
 An Antisense oligonucleotide therapy is one such approach which
blocks protein formation by inhibiting translation step.
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 Antisense oligonucleotides are the molecules made
of synthetic genetic material, which interacts with
the natural genetic material that codes the
information for production of proteins.
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MOA : Antisense technology
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B) Modulator of protein activity (APTAMERS)
 Aptamers (Aptus- to fit, mer- smallest unit of repeating structures)
 Based on their 3-dimensional structure, Aptamers can well fittingly bind
to a wide variety of targets from single molecules to complex target
mixtures or whole organisms.
 Single stranded folded oligonucleotides and peptide that bind to
molecular (protein) targets with high affinity and specificity. Range in
size from 20 to 80 bases (6-26 kDa)
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25

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Aptamers Binding Mechanism

Advantages:
 Oligonucleotides can be manufactured quickly i.e. within a week
 Sensitivity of therapy can be easily measured.
 Potential of producing longer lasting responses.
Potential for enhanced binding affinity to target.
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Limitations:
 Antisense agents have to be protected against nucleolytic attack.
The pharmacokinetic characteristics of oligonucleotide drugs is similar to that of
naturally occurring nucleic acids, makes them poor therapeutic candidates, as
they are immediately degraded in vivo by nucleases and do not have adequate
pharmacokinetic properties.
 Larger dose are required for therapeutic response.
 The difficulty in directing to a particular cells.
The half-life in plasma is short.
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Applications:
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Antisense
oligonucleotide
therapy
As antiviral and antibacterial agents
CVS & CNS Therapeutics
Inflammation therapeutics
Oncology
Diabetes, Muscular Dystrophy, Asthma, Hair loss

Oligonucleotides also plays important role in:
 DNA sequencing: Determination of nucleotide sequence in DNA molecule.
 PCR: In-vitro technique of generating large quantity of specified target DNA.
 Artificial gene synthesis (DNA printing)
 Library construction of DNA
 Molecular Cloning: introducing recombinant DNA molecule and direct their
replication within host organism.
 Genetic testing, research and forensics.
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Examples:
 Fomiversin for the treatment of cytomegalovirus retinitis.
 Mipomersen for High cholesterol.
 Affnitak and Genasense against cancer.
 AV 1-6002 & AV 1-6003 in treatment of hemorrhagic fever.
 AP 1-2009 for the treatment of high grade gliomas.
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Some oligonucleotides therapeutics
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SUMMARY
 Oligonucleotides are characterized by the sequence of nucleotide residues
that make up the entire molecule.
 Oligonucleotide-based therapeutics on the mode of their action are
categorized as antisense oligonucleotides (ASOs), which are inhibitors of RNA
activity, or modulators of protein activity (aptamers).
 Numerous development programs for oligonucleotide therapeutics are
generating growing amount of data, contributing to better understanding of
the pharmaceutical characteristics of oligonucleotides.
 Advances on oligonucleotide delivery systems play a game-changing role in
turning the field of oligonucleotide therapeutics into a therapeutic reality…
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REFERENCES:
 U. Satyanarayana, U. Chakrapani, “Biochemistry” 5th Ed. (2017), Elsevier
 P.S. Verma, V.K. Agarwal, “Cell Biology: Cytology, Biomolecules and Molecular
Biology” 1st Ed. (2016), S. Chand and Company Pvt. Ltd
 B.D. Singh, “Genetics” 2nd revised Ed. (2009), Kalyani Publishers
 Yutaro Asami, Kotaro Yoshioka, Kazutaka Nishina, Tetsuya Nagata, Takanori
Yokota* “Drug delivery system of therapeutic oligonucleotides” Drug
Discoveries & Therapeutics. 2016; 10(5):256-262.
 Rudolph L. Juliano* “The delivery of therapeutic oligonucleotides” Nucleic
Acids Research, 2016, Vol. 44, No. 14
 Wissenschaftliche Prüfungsarbeit, “Oligonucleotide-based Therapeutics,
Development and Regulatory Challenges” 2016; 1-62
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Oligonucleotide

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