Interact or not? That´s the question.
Hybrid organo-inorganic molecules are gaining lots of attention in medicinal chemistry lately. They can be applied in targeted cancer therapy or the treatment of other serious diseases. One of the inorganic pharmacophores (active parts of a therapeutic molecule) is metallacarborane COSAN, which is used to improve the function of many biologically active molecules targeting DNA. But how does COSAN itself interact with DNA? A new study conducted under the lead author Mariusz Uchman from the Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, now answers this question.
source: original paper
Metallacarboranes are 3D cage structures that can often be found useful in potentially therapeutic molecules thanks to their structure and ability to conveniently interact with biomolecules. Cobalt bis(dicarbolide) (COSAN) stands out indeed for its properties. It can self-organize in water solution and interacts with lipid membranes such as cell membranes, and with proteins. It can also pass through membranes and accumulate inside of cells, and in their nucleus. Its 3D structure lends COSAN an incredible stability in biological environments. It is thus often part of various derivatives used for diagnostic and therapeutic purposes such as conjugates with nucleosides or DNA intercalating molecules. However, the interaction between DNA and COSAN remains a mystery – some studies say they interact, and some don´t. So where is the truth?
The theory generally speaks against the possibility of interaction. The cage structure of COSAN is considerably big with 11 Å in length and 6 Å in width. Meanwhile, the space for intercalators in DNA is less than 4 Å wide, and the small grove, where molecules can also bind, measures just under 5 Å. Even though DNA is flexible to an extent, this interaction seems unlikely. The next option is an interaction via the so-called π-electron systems. These are present in DNA bases as well as in various aromatic organic compounds but not in COSAN, which makes this interaction impossible. Some molecules use hydrogen bonds to bind to DNA, and COSAN could too. However, the hydrogen bonds formed by COSAN are very weak. The group around boron atoms can also create so-called two-hydrogen bonds but these don´t have enough bonding partners on DNA. The last option is electrostatic interaction. This can however happen only for positively charged molecules which is not the case for COSAN.
The theory is not everything and it doesn´t always correspond to reality. So, what do experimental results tell us? The scientists used an array of methods to study the interaction from different points of view. UV-Vis spectral analysis as well as circular or linear dichroism should give us information about binding through change in the spectrum. Spectra of COSAN, however, stayed the same. To verify the influence of COSAN on the length and stability of DNA, researchers used the measurements of the viscosity of pure DNA versus DNA with COSAN. Had the interaction happened, the viscosity would have risen as the molecule of DNA would have lengthened. But nothing was observed. Intercalation of molecules into DNA can also be verified by “melting” DNA so that the strands disconnect. The “melting” temperature when this happens rises with the number of intercalated molecules as they stabilize the double helix. In this case, again, nothing happened. Further studies by NMR spectroscopy and equilibrium dialysis also agree that there is no interaction between DNA and COSAN.
Taking this into account, there must be another way for COSAN to mediate its toxicity. By studying the effect of this compound on red blood cells, which lack the nucleus, it turned out that the nucleus is not essential to COSAN´s function. Its function is probably more influencing the cellular membrane and scientists also proved COSAN´s ability to efficiently bind to proteins. The future of its use could thus lie in molecules targeted to various transcription factors and other proteins, that bind DNA. These proteins, contrary to enzymes or receptors, have large open active sites, which have been deemed “undruggable” so far. Derivatives of COSAN could, however, have a large affinity to these sites, and their indifference to DNA could even be an advantage.
The experiment thus agreed with the theory, and scientists managed to prove that even though DNA is flexible, it is not enough for COSAN to interact with it. The metallacarborane also doesn´t have any influence on the length and stability of DNA nor is DNA even needed for its function. COSAN influences proteins and the cell membrane, which could be used in its future applications. Further studies are still needed to confirm these conclusions.
Metallacarboranes are 3D cage structures that can often be found useful in potentially therapeutic molecules thanks to their structure and ability to conveniently interact with biomolecules. Cobalt bis(dicarbolide) (COSAN) stands out indeed for its properties. It can self-organize in water solution and interacts with lipid membranes such as cell membranes, and with proteins. It can also pass through membranes and accumulate inside of cells, and in their nucleus. Its 3D structure lends COSAN an incredible stability in biological environments. It is thus often part of various derivatives used for diagnostic and therapeutic purposes such as conjugates with nucleosides or DNA intercalating molecules. However, the interaction between DNA and COSAN remains a mystery – some studies say they interact, and some don´t. So where is the truth?
The theory generally speaks against the possibility of interaction. The cage structure of COSAN is considerably big with 11 Å in length and 6 Å in width. Meanwhile, the space for intercalators in DNA is less than 4 Å wide, and the small grove, where molecules can also bind, measures just under 5 Å. Even though DNA is flexible to an extent, this interaction seems unlikely. The next option is an interaction via the so-called π-electron systems. These are present in DNA bases as well as in various aromatic organic compounds but not in COSAN, which makes this interaction impossible. Some molecules use hydrogen bonds to bind to DNA, and COSAN could too. However, the hydrogen bonds formed by COSAN are very weak. The group around boron atoms can also create so-called two-hydrogen bonds but these don´t have enough bonding partners on DNA. The last option is electrostatic interaction. This can however happen only for positively charged molecules which is not the case for COSAN.
The theory is not everything and it doesn´t always correspond to reality. So, what do experimental results tell us? The scientists used an array of methods to study the interaction from different points of view. UV-Vis spectral analysis as well as circular or linear dichroism should give us information about binding through change in the spectrum. Spectra of COSAN, however, stayed the same. To verify the influence of COSAN on the length and stability of DNA, researchers used the measurements of the viscosity of pure DNA versus DNA with COSAN. Had the interaction happened, the viscosity would have risen as the molecule of DNA would have lengthened. But nothing was observed. Intercalation of molecules into DNA can also be verified by “melting” DNA so that the strands disconnect. The “melting” temperature when this happens rises with the number of intercalated molecules as they stabilize the double helix. In this case, again, nothing happened. Further studies by NMR spectroscopy and equilibrium dialysis also agree that there is no interaction between DNA and COSAN.
Taking this into account, there must be another way for COSAN to mediate its toxicity. By studying the effect of this compound on red blood cells, which lack the nucleus, it turned out that the nucleus is not essential to COSAN´s function. Its function is probably more influencing the cellular membrane and scientists also proved COSAN´s ability to efficiently bind to proteins. The future of its use could thus lie in molecules targeted to various transcription factors and other proteins, that bind DNA. These proteins, contrary to enzymes or receptors, have large open active sites, which have been deemed “undruggable” so far. Derivatives of COSAN could, however, have a large affinity to these sites, and their indifference to DNA could even be an advantage.
The experiment thus agreed with the theory, and scientists managed to prove that even though DNA is flexible, it is not enough for COSAN to interact with it. The metallacarborane also doesn´t have any influence on the length and stability of DNA nor is DNA even needed for its function. COSAN influences proteins and the cell membrane, which could be used in its future applications. Further studies are still needed to confirm these conclusions.
Magda Křelinová
Magda Křelinová
Published:
Sep 26, 2023 10:40 AM
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