Adenosine nucleoside and nucleoside phosphoramidite | Overview of important aspects

Adenosine nucleoside and nucleoside phosphoramidite | Overview of important aspects

Contents

Adenosine nucleoside

Adenosine nucleoside is found in nature in diversified forms. It consists of a nitrogenous base adenine linked to a five-carbon ribose sugar through a β-N9-glycosidic bond. Adenosine is present in nucleic acids such as DNA and RNA, considered the genetic material in every life form. Adenosine is also present in several essential biomolecules like adenosine monophosphate (AMP), adenosine diphosphate (ADP) and adenosine triphosphate (ATP). The AMP, ADP and ATP act as energy carriers in most biochemical processes. ATP is often regarded as the energy currency of the cell.

Another derivative of adenosine that is cyclic adenosine monophosphate (cAMP) is actively involved in the signal transduction pathways and other cell signalling events inside the body. 

Adenosine nucleoside
Figure: Adenosine nucleoside https://commons.wikimedia.org/wiki/File:Caffeine_and_adenosine.svg

Adenosine provides important framework structures in some vitamins like B12 and radical S-Adenosyl-l-Methionine (SAM) enzymes. 

Several adenosine derivatives are used in physiological abnormalities like supraventricular tachycardia (SVT) and in subjects with supraventricular tachycardia (SVT). Adenosine maintains the cardiac rhythm by modulating the ventricular response rate.

Adenosine also interacts with other purine derived molecules like methylxanthines. Methylxanthine acts as the antagonist of adenosine. Methylxanthine is used to nullify the pharmacological effects of adenosine. Methylxanthines are abundantly found in chocolate, tea, coffee etc., people consuming significant amounts of coffee or tea are given higher amount of adenosine for a proper pharmacological response.

Figure: Tea and coffee contains caffiene, it has structural similarity with adenosine https://commons.wikimedia.org/wiki/File:Caffeine_and_adenosine.svg

Adenosine metabolism

Adenosine is broken down by the enzyme called adenosine deaminase as soon as it enters into the blood circulation. The enzyme adenosine deaminase is present in the RBCs and the walls of blood vessels. For more details on adenosine (purine) metabolism click here

Dipyridamole causes an increase in coronary vasodilation by inhibiting adenosine nucleoside transporter, which results in the accumulation of adenosine in the bloodstream and causes vasodilation.

The deficiency of the adenosine deaminase enzyme causes severe immunodeficiency. 

Other important roles of adenosine nucleoside

– Various Adenosine nucleoside derivatives act as reverse transcriptase inhibitors and stalls the retroviral replication process.

– Adenosine acts as an anti-inflammatory agent. 

– Methotrexate triggers the release of adenosine; hence, it acts as an anti-inflammatory agent.

– Adenosine is known to exhibit inhibitory and suppressive effects on the central nervous system (CNS).

– Adenosine supress the effects of androgenetic alopecia. 

Increased adenosine levels cause drowsiness.

Nucleoside phosphoramidite

The nucleoside phosphoramidites are synthesized from nucleosides of natural and synthetic origin. They are used to synthesize nucleotide oligomers or oligonucleotides. The nucleotide oligomers are the short fragments of DNA/RNA. The reactive amino group (exocyclic) and hydroxyl present in the synthetic and naturally occurring nucleosides are appropriately protected to avoid unnecessary side reactions. The proper protection of the reactive hydroxyl group of the nucleoside analogue must convert it into respective phosphoramidite. The phosphoramidite is then incorporated into the synthetic DNA/RNA.

Figure: Nucleoside phosphoramidite, 5′ end is protected by DMT (4,4′-dimethoxytrityl) group and 3′ end is protected by cyanoethyl group https://commons.wikimedia.org/wiki/File:Phosphoramidite1.png

The phosphoramidite strategy allows the incorporation of nucleoside or nucleoside analogues in the middle of the oligonucleotide chain. The nucleoside must have two free hydroxyl groups or a nucleophilic group (mercapto or amino) and a free hydroxyl group for the desired incorporation. 

Preparations of nucleoside phosphoramidite

The process of synthesis of nucleoside phosphoramidite is completed in three major steps:

Step 1: the free hydroxyl group of the protected nucleoside in the presence of weak acid undergoes phosphorodiamidite treatment. The 2-cyanoethyl N,N,N’,N’-tetraisopropylphosphorodiamidite is an amidite that is generally used for the commercial synthesis of stable nucleoside phosphoramidites. 

Step 2: introduction of organic base N-ethyl-N,N-diisopropylamine (Hunig’s base) in the medium to produce nucleoside diamidite.

Step 3: the solution is later treated with an alcohol corresponding to the phosphate protecting group, like using 2-cyanoethanol with a weak acid.

The formed nucleoside phosphoramidites are later purified using silica gel column chromatography. 

Purine nucleoside phosphorylase | Purine nucleoside phosphorylase function

The purine nucleotide phosphorylase (PNPase) catalyzes the reversible conversion of purine nucleoside and purine, as mentioned in the following reaction:

Purine nucleoside + phosphate –> Purine + α-D ribose-1-phosphate

PNPase is also known as inosine phosphorylase, and the systematic name is purine-nucleoside phosphate ribosyltransferase

The PNPase relates to the family of glycosyltransferases. PNPase acts on five-carbon sugar-containing nucleosides, and hence it is called pentosyltransferase.

Figure: Crystal structure of purine nucleoside phosphorylase https://commons.wikimedia.org/wiki/File:1rct.png

The PNPase is actively involved in the essential pathways such as nicotinate, nicotinamide, pyrimidine and purine metabolic pathways.

The essential enzymes of class glycosyltransferases are thymidine kinase, uridine kinase, cytidine kinase and deoxycytidine kinase, which catalyze the phosphorylation thymidine, uridine, cytidine and deoxycytidine, respectively.

Clinical importance: Along with adenosine deaminase, PNPase regulates the purine metabolism. Mutation in any of these enzymes results in the accumulation of deoxyadenosine triphosphates [(d)ATPs] which induce apoptosis (programmed cell death) in the lymphocytes. Such events in the lymphocytes result in SCID (severe combined immunodeficiency). 

Nucleoside therapy for mitochondrial depletion

Mitochondria are the cell organelle that contains their copy of circular DNA (it is known as mitochondrial DNA or mtDNA). It resembles the bacterial DNA or single circular chromosome hence called cell within a cell.  

Mitochondrial DNA contains genes that code for the enzyme required in the process of respiration to generate the energy needed to operate various cellular processes. Hence, mitochondria are known as the powerhouse. Therefore, mitochondrial DNA must be maintained for the proper functioning of the cell and other cellular activities. Changes in the mitochondrial DNA cause impairments in energy production and cellular processes, ultimately resulting in mitochondrial DNA depletion syndrome. 

The dNTPs required for the synthesis of mitochondrial DNA is the same as the cellular DNA but needs to be present in a balanced proportion inside the mitochondria. An imbalance in the proportion of the dNTPs inside mitochondria results in changes and mismatches in the mitochondrial DNA, which lead to mitochondrial DNA depletion syndrome.

Introducing dNTPs or other building blocks such as deoxynucleosides may help treat the mitochondrial DNA depletion syndrome by restoring the balance of dNTPs and repairing the mitochondrial DNA. This is known as nucleoside therapy.

Targeting nucleosides to the affected area of the body is quite challenging, making it challenging to balance the nucleoside levels at the target site. Researchers these days are modifying the nucleosides to make them more efficient to reach their target site. Targeting modified nucleoside in such way will prove to be a more efficient way to deal with mitochondrial DNA depletion syndrome with lesser after effects.

The researchers are trying to develop a novel, effective and efficient approach for producing mitochondrial DNA through modified nucleosides to combat mitochondrial DNA depletion syndrome. 

Researchers expect this study to pave the way for dealing with mitochondrial DNA depletion syndrome by the optimized choice of using nucleosides in combinations for effective results. 

Conclusions

In this article we have discussed about the important physiological aspects of adenosine nucleoside and nucleoside phorphoramidite in detail. we have also discussed about mitochondrial DNA depletion briefly in this article.

Interview Q & A

Q1 Is adenine a nucleotide?

Answer: Adenine is a purine (double-ringed) nitrogenous base that is present as a structural component in nucleosides as well as in nucleotides.

Q2. List some derivatives of adenosine nucleoside?

Answer: Adenosine nucleoside derivatives or analogues have immense physiological implications and are often used to serve several purposes. For example, tecadenoson, soledenoson, N6 -tetrahydrofuranyl-5’-chloro-5’-deoxyadenosine, N-(1S,2S)- 2-hydroxy-cyclopentyl adenosine, regadenoson etc.

Q3. Important roles of adenosine nucleoside?

Answer: Researchers have reported adenosine nucleoside in diverse forms of nature. It is ubiquitously found in the genome of living organisms, essential biomolecules (ATP, ADP, AMP etc.,) and act as a secondary messenger in the cell signalling pathways.

Q4. An essential function of nucleoside phosphoramidite

Answer: The nucleoside phosphoramidites are used to produce oligonucleotides or oligomeric nucleotides. The oligomeric nucleotides are the short fragments of DNA or RNA.

Q5. Where is purine nucleoside phosphorylase found?

Answer: The purine nucleoside phosphorylase is an essential enzyme of the salvage pathway for nucleotide biosynthesis; thus, it is found in many tissues. A much higher amount of purine nucleoside phosphorylase is expressed in sinusoidal endothelial cells, kupffer cells and hepatocytes. The purine nucleoside phosphorylase also serves as a leakage marker for hepatocellular injury since its expression is more in hepatic cells and much lesser in muscles.

Q6. Clinical importance of purine nucleoside phosphorylase?

Answer: The purine nucleoside phosphorylase and adenosine deaminase play an important role in regulating the purine metabolic cycle. Purine nucleoside phosphorylase mutation results in the accumulation of dNTPs (deoxynucleoside triphosphates) which triggers the mechanism of apoptosis. Such events in the lymphocytes result in SCID (severe combined immunodeficiency).

Q7. What is mitochondrial DNA depletion?

Answer: The imbalance in the proportion of dNTPs in the mitochondrial matrix results in the impaired production of mitochondrial DNA. This affects the mitochondria’s proper functioning since there are several genes on the mitochondrial DNA that express to perform essential functions. Impaired mitochondrial DNA is unable to perform essential functions. This phenomenon is known as mitochondrial DNA depletion.

Q8. What is the best possible way to deal with mitochondrial DNA depletion?

Answer: Targeting nucleosides to the affected area of the body is quite challenging, making it challenging to balance the nucleoside levels at the target site. Researchers these days are modifying the nucleosides to make their targeted delivery easier. Targeting modified nucleoside in such way will prove to be a more efficient way to deal with mitochondrial DNA depletion syndrome with lesser after effects.

The researchers are trying to develop a novel, effective and efficient therapy for producing mitochondrial DNA through modified nucleosides to combat mitochondrial DNA depletion syndrome. Researchers expect this study to pave the way for dealing with mitochondrial DNA depletion syndrome by the optimized choice of using nucleosides in combinations for effective results. 

Q9. What is the clinical importance of purine nucleoside phosphorylase?

Answer: Along with adenosine deaminase, PNPase regulates the purine metabolism. Mutation in any of these enzymes results in the accumulation of deoxyadenosine triphosphates [(d)ATPs] which induce apoptosis in the lymphocytes. Such events in the lymphocytes result in SCID (severe combined immunodeficiency).  

Q10. What are the additional groups present in nucleoside phosphoramidite?

Answer: Nucleoside phosphoramidite additionally have a 5′ end is protected by DMT (4,4′-dimethoxytrityl) group and 3′ end is protected by cyanoethyl group

About Dr. Abdullah Arsalan

I am Abdullah Arsalan , Completed my PhD in Biotechnology. I have 7 years of research experience. I have published 6 papers so far in the journals of international repute with an average impact factor of 4.5 and few more are in consideration. I have presented research papers in various national and international conferences. My subject area of interest is biotechnology and biochemistry with special emphasis on Protein chemistry, enzymology, immunology, biophysical techniques and molecular biology.

Let's connect through LinkedIn(https://www.linkedin.com/in/abdullah-arsalan-a97a0a88/) or Google scholar(https://scholar.google.co.in/citations?user=AeZVWO4AAAAJ&hl=en).

Leave a Comment

Your email address will not be published. Required fields are marked *