Organic & Biomolecular Chemistry Blog

Deoxyribonucleic acid (DNA) is one of the most famous molecules in the world. First isolated and identified by Freidrich Miescher in 1871,¹ DNA is responsible for coding ‘genetic instructions’ in all known living organisms and viruses. DNA molecules consist of two long helical biopolymer chains wrapped around a common axis and held tightly together by intermolecular forces called hydrogen bonds and base-stacking interactions. Each biopolymer chain is made up of small units called nucleotides, which themselves consist of a sugar, a phosphate group, and one of four different nucleobases (guanine, adenine, thymine or cytosine, abbreviated to G, A, T and C respectively). The specific orders in which the nucleotides appear in a DNA strand is what allows for the storage of genetic information.

Figure 1. Modified deoxycytosine and deoxyguanosine forming four hydrogen bonds

Shorter, single strands of nucleotide residues bonded together are called oligonucleotides. They are capable of binding to another oligonucleotide strand (via the same intermolecular forces as found in full length DNA helices) if the other strand has the ‘complimentary’ order of nucleotides (cytosine and guanine exclusively bind with each other; as do adenine and thymine). Due to this property, they are used in areas such as genetic testing, gene therapy, DNA probes and forensics.

The binding of one strand to its complimentary strand can be strengthened by modifying the nucleobase, as long as the  modifications do not disrupt duplex formation. In particular, the nucleobase cytosine has several reported modifications² which allow for additional hydrogen bonding (thus strengthening the binding of two strands). Unfortunately, a lot of the previously reported cytosine modifications have the drawback of long synthetic sequences necessary to make them.

In this paper, Sekine and co-workers report their modifications of cytosine nucleotides, and measure these new molecule’s binding affinities with guanine (the ‘complimentary’ base which cytosine hydrogen bonds with, Figure 1). As well as demonstrating an efficient synthetic route to their new cytosine derivatives, the authours prove that oligonucleotides which incorporate their modified cytosine residue show an increased binding affinity to the complimentary strands when compared with the unmodified, parent oligonucleotide. These promising results could lead to the design and synthesis of even better cytosine nucleotides inspired by the scaffold reported in this work, in turn leading to oligonucleotides which can perform better in DNA-recognition based tests.

To read more, see;

A new modified cytosine base capable of base pairing with guanidine using four hydrogen bonds
K. Yamada, Y. Masaki, H. Tsunoda, A. Ohkubo, K. Seio and M. Sekine,
Org. Biomol. Chem., 2014, DOI:10.1039/c3ob42420k. Download PDF

Free to access until 10th April

References

¹ R. Dahm, “Discovering DNA: Friedrich Miescher and the early years of nucleic acid research” Human Genetics, 2008, 122, 565–81.
² A. S. Wahba, A. Esmaeili, M. J. Damha, R. H. E. Hudson, Nucleic Acids Res., 2010, 38, 1048; S. Preus, K. Kilsa, L. M. Wilhelmsson, B. Albinsson, Phys. Chem. Chem. Phys., 2010, 12, 8881; A. Ohkubo, T. Sakaue, H. Tsunoda, K. Seio, M. Sekine, Chem. Lett., 2010, 39, 726.

Dr C. Liana Allen is currently a post-doctoral research associate in the group of Professor Scott Miller at Yale University, where she works on controlling the enantio- or regioselectivity of reactions using small peptide catalysts. Liana received her Ph.D. in organic chemistry at Bath University with Professor Jonathan Williams, where she worked on developing novel, efficient syntheses of amide bonds.

Posted on behalf of Steve Moore, web writer for Organic & Biomolecular Chemistry

The heat shock protein 90 (Hsp90) has a key role in some oncogenic pathways and is a widely studied target for anti-cancer therapeutics. The search for small molecule inhibitors of Hsp90 is ongoing. The most potent in vitro inhibitor of Hsp90 is radicicol, a resorcylic acid lactone; however radicicol lacks activity in vivo, possibly because of the presence of readily metabolised functional groups.

In their search for new inhibitors of Hsp90, scientists from the University of Nottingham and the University of Sussex have synthesised a series of macrolactam radicicol analogues. A new synthetic route to N-methylated resorcylic acid macrolactams is described which permits convenient variation of ring size. Macrolactam binding to Hsp90 was demonstrated by isothermal calorimetry and conformational changes were observed in co-crystallization experiments with yeast Hsp90.

Synthesis of macrolactam analogues of radicicol and their binding to heat shock protein Hsp90
Bridie L. Dutton, Russell R. A. Kitson, Sarah Parry-Morris, S. Mark Roe, Chrisostomos Prodromou and Christopher J. Moody
Org. Biomol. Chem., 2014, DOI: 10.1039/C3OB42211A, Paper

Free to access until: 24th March Download PDF | Download HTML

Posted on behalf of Dr Liana Allen, guest web writer for Organic & Biomolecular Chemistry.

Antibiotics are drug compounds used to treat infections caused by bacteria, such as tuberculosis and some forms of meningitis. The processes involved in bacteria cell reproduction are highly complicated and many different targets along the biological pathway of bacterial cell replication have been identified as potential opportunities to disrupt bacterial growth. Antibacterial drugs can be described as ‘bactericidal’ if they kill the bacterial cells by inhibition of bacteria cell wall or cell membrane synthesis, or by interfering with an essential bacterial enzyme. Those which target bacterial protein synthesis can be described as ‘bacteriostatic’ as they stop bacteria from reproducing but otherwise do not harm them.

One specific mode of antibacterial action is interaction with DNA gyrase, which is an enzyme involved in the unwinding of double stranded DNA helices during DNA replication.¹ DNA gyrase is an enzyme which is not present in humans, making it an especially good target for antibiotics. One way in which antibacterial molecules interact with DNA gyrase is through stabilization of a DNA-gyrase covalent complex which is formed during the DNA replication process. The result of this interaction is the release of ‘broken DNA’, which kills the organism. For this reason, antibacterial agents which behave in this way are referred to as DNA gyrase poisons.

Microcin B17 (MccB17)

Microcin B17 (MccB17) is a peptide which displays antibacterial action and is thought to act as a DNA gyrase poison, but unfortunately, the full MccB17 peptide is not a suitable drug candidate due to its poor physiochemical properties. MccB17 is particularly interesting as the mature peptide contains some unusual hetrocyclic units.

In this paper, Katrina A. Jolliffe, Richard J. Payne and colleagues aimed to investigate the structure-activity relationship of MccB17 in order to determine exactly which parts of the peptide are needed for the antibacterial action and to develop a simplified DNA gyrase poison which would be a good lead candidate for antibacterial drug discovery. Using their own synthetic methodology,² they prepared a range of full length and truncated analogues of MccB17, then tested their abilities to act as DNA gyrase poisons. They then compared the results with a known, potent DNA gyrase poison, ciprofloxacin. Many of the prepared analogues showed activity very similar to the native peptide; however some of the truncated variants actually performed better in this test. These promising results now enable more detailed investigation into the mechanism of bactericidal action of MccB17. In a second series of experiments, the peptides were tested for their antibacterial activity against two strains of E. coli. In this test it was the full length native MccB17 which gave the best results, suggesting that, even though truncated analogues can still exhibit DNA gyrase poisoning activity, the full length sequence would still currently be needed for bactericidal activity in vivo.

To read more, see;

Synthesis of Full Length and Truncated Microcin B17 Analogues as DNA Gyrase Poisons
R. E. Thompson, F. Collin, A. Maxwell, K. A. Jolliffe and R. J. Payne,
Organic & Biomolecular Chemistry, 2014, DOI: 10.1039/C3OB42516A.

Free to access until 7th March

References
¹ Gore, J., Bryant, Z., Stone, M. D., Nöllmann, M., Cozzarelli, N.R., Bustamante, C. Nature, 2006, 439, 100.
² Thompson, R. E., Jolliffe, K. A., Payne, R. J., Org. Lett., 2011, 13, 680.

Dr C. Liana Allen is currently a post-doctoral research associate in the group of Professor Scott Miller at Yale University, where she works on controlling the enantio- or regioselectivity of reactions using small peptide catalysts. Liana received her Ph.D. in organic chemistry at Bath University with Professor Jonathan Williams, where she worked on developing novel, efficient syntheses of amide bonds.

Posted on behalf of Liana Allen, guest web writer for Organic & Biomolecular Chemistry  

All biological cells possess a cell membrane, which are lipid bilayers containing proteins embedded within them. One of the important properties of this membrane is its selective permeability to species such as small molecules and metal ions.¹ This characteristic allows cell membranes to separate compounds with different chemical properties and act as a barrier to certain substances. While selective permeability is an essential function of cell membranes, it also leads to low efficiency of drug molecules which have low permeability through the membrane, yet need to enter the cells to be of therapeutic value. This is one of the reasons that the use of anti-cancer therapeutic agents is currently limited.² 

One strategy to overcome this problem is to use a cell-penetrating peptide (CPP) as a ‘transporter’ of drug molecules across the cell membrane to deliver treatments into the target cells. Such transporter peptides are usually short, cationic sequences, allowing them to bind to the negatively charged head groups of lipids in the membrane and subsequent entry into the cell. This strategy offers an opportunity to increase the bioavailability of drugs and thus lower the dosage required to achieve a significant effect.³ While CPPs increase the amount of drug which enters the cell, one problem with this method is a lack of selectivity between diseased cells and normal, healthy cells. One approach which has been taken to further improve the selective delivery of drugs into target cells is conjugating the CPP to another ‘homing’ peptide, one which binds selectively to receptors in human tumor cells. This allows drug delivery to specific cells, decreasing the side effects and toxicity to normal, healthy cells. 

In this paper, the authours search for a cell-penetrating peptide to be used as a transporter of drugs through the membrane of cancerous cells. Their search was based on a library of peptides which all displayed the desired characteristics of CPPs.⁴ After establishing which the most efficient membrane-permeating peptide in the library was, a three-component conjugate of the CPP, a homing peptide and a known cytotoxic, anti-cancer agent (chlorambucil) was synthesized and tested to assess its cellular uptake and cytotoxicity. The authours identified a peptide named ‘BP16’ as a potential new CPP with high cellular uptake, yet no cytotoxicity towards cancerous or healthy cells. Conjugating the cytotoxic agent chlorambucil to BP16 led to an impressive 6- to 9-fold increase in the drugs activity. When combined with a homing peptide, the drug activity was increased a further 2- to 4.5 times. These promising results show that BP16 is a suitable non-toxic delivery vector for the transport of drugs through cellular membranes. 

To read more, see; 

Identification of BP16 as a non-toxic cell-penetrating peptide with highly efficient drug delivery properties
Soler, M. González, D. Soriano-Castell, X. Ribas, M. Costas, F. Tebar, A. Massaguer, L. Feliu, M. Plantas,
Organic & Biomolecular Chemistry, 2014, DOI: 10.1039/C3OB42422G

Free to access until 7th February 

Structure of BP16 and confocal microscopy image showing BP16 (green) and cell nucleus (blue) after 180 mins incubation at 37 oC

References 

¹ A. Lehninger, Principles of Biochemistry, 2nd Ed. 2003, (Worth Publishers ed.).
² E. Raschi, V. Vasina, M. G. Ursino, G. Boriani, A. Martoni, F. De Ponti, Pharmacol. Ther., 2010, 21, 389.
³ S. B. Fonseca, M. P. Pereira, S. O. Kelley, Adv. Drug. Deliv. Rev., 2009, 61, 953.
⁴ E. Badosa, R. Ferre, M. Planas, L. Feliu, E. Besalu, J. Cabrefiga, E. Bardaji, E. Montesinos, Peptides., 2007, 28, 2276. 

Dr C. Liana Allen is currently a post-doctoral research associate in the group of Professor Scott Miller at Yale University, where she works on controlling the enantio- or regioselectivity of reactions using small peptide catalysts. Liana received her Ph.D. in organic chemistry at Bath University with Professor Jonathan Williams, where she worked on developing novel, efficient syntheses of amide bonds.