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Man-made atomic beads: manipulations with macrocycles



In attempts to explain the term “molecule” to a child, we can say that it is a bunch of grapes, and grapes are separate atoms. Exaggerated, but quite understandable. When it comes to macrocycles, then a comparison with beads is more likely to be suitable, because such molecules consist of rings consisting of atoms. The uniqueness of such structures lies in their form, which determines their properties. If the form can be controlled in a controlled manner, then the properties can also be changed. Scientists from the University of Montreal (Canada) have developed a new technique that allows you to gain control of macrocycles through a completely natural process called biocatalysis. How exactly does the new technique work, what results did it show during the tests, and what future awaits this discovery? We will look for answers to questions in the report of scientists. Go.

Study basis


Macrocycles are quite unique structures. They can act as ligands, i.e. be molecules that bind to other atoms through donor-acceptor interactions. This process means charge transfer between a donor (in this case, a macrocycle) and an acceptor (receiving side, i.e., another molecule or atom) without the formation of a chemical bond between them.

The result of such a bond most often becomes a coordination donor-acceptor bond, where the ligands are donors of the electron pair. It is important to note that during this transformation, the chemical properties of the bond participants also undergo changes.

The cyclic framework of a macrocycle is capable of imposing serious restrictions on the rotation of bonds *which can block functional groups or other molecular fragments in conformations * that would otherwise be unfavorable for an acyclic analogue (i.e., for a linear rather than a cyclic structure).
Rotation of bonds * - rotation around the line between two bound atoms (bond axis), where one end of the bond is stationary and the other rotates.
Conformation * is the spatial arrangement of atoms in a molecule of a certain configuration.
A similar situation is observed with planar (in the plane) chiral (exaggerated, specular) cyclophanes - a subset of macrocycles for which conformation or size limit the rotation of the aromatic * unit in the framework.
Aromaticity * is a property of some chemical compounds, due to which the conjugated ring of unsaturated bonds exhibits an abnormally high stability.


Image No. 1

According to scientists, planar chiralities in terpenes * of natural products, as well as in macrocyclic peptides, have already been studied quite well ( 1A ).
Terpenes * - a class of hydrocarbons with the composition C 5 H 8 n , are a product of isoprene polymerization. Terpenes in nature in large quantities are found in conifers.
Nevertheless, despite extensive knowledge, the synthetic methods used to create peptide cyclophanes pose a number of problems. The main one is the need to form a rigid and often intense macrocycle while maintaining high levels of enantioselection * .
Enantioselection * - selection of a specific enantiomer * of a compound as a reaction product.

Enantiomers are a pair of spatial isomers that have the same structure, but different (in this case, mirror) spatial position.
Therefore, the techniques of atroposelective macrocyclization can be divided into two main categories ( 1B ).

The most commonly used auxiliary compound is the conformation of the acyclic precursor via non-covalent interactions. Less commonly used is catalysis * for asymmetry during the formation of cyclophane.
Catalysis * - selective acceleration of one of the possible directions of a chemical reaction due to the action of the catalyst.
The biocatalysis considered in this work was previously used, however, in previous studies, the DKR (dynamic kinetic cleavage) method was more complex and consisted of additional steps preceding the desired result. This step is deacylation (removal of one or more acyl groups from the compound) to gain access to alcohol and amine ( 1C ).

If we compare the method proposed in this study with the DKR method, we can identify a number of differences ( 1D ).

First, in DKR, acylation is temporary, since a free alcohol or amine is usually required. In addition, the acylating agent may be added in excess to improve the reaction rate and the resulting product. In the process of macrocyclization, acylation is inherent in the final product, and stoichiometry (mass ratio) between the alcohol and the acylating agent is natural.

Secondly, in the absence of secondary alcohols, it is necessary to use a different racemization process. Despite the difficulties, scientists believe that the biocatalytic DKR variant of producing planar chiral cyclophanes has significant potential.

The bottom line is that commercially available lipases (water-soluble enzymes) have excellent thermal stability and high enantioselectivity, which makes them ideal reagents for macrocyclization processes through biocatalysis.

The researchers set themselves the task of creating a technique that allows the use of simple and affordable building blocks in the synthesis of plane-chiral macrocycles.

To accomplish this task, it was decided to use ordinary diacids (dibasic acids) or diesters (an organic compound containing two ester functional groups) as aliphatic linkers (marked with the letter A in image 1D ).

Chemoenzyme macrocyclization is also possible by sequential acylation using lipase on aromatic glycol (dihydric alcohol) (letter B in image 1D ).

In contrast to the classical DKR process, racemization * of intermediate C occurs via free rotation of the aromatic ring.
Racemization * is the conversion of a substance with one enantiomer to a substance with more than one enantiomer.
Despite the many positive characteristics of the method under consideration by chemoenzymatic macrocyclization, there are a number of problems. One of them is the fact that ring closure can lead to a “solid” macrocycle, and the enzyme must be able to contribute to such ring closure.

According to scientists, it was possible to increase the temperature to stimulate macrocyclization, but this could lead to decomposition of the enzyme or to a detrimental effect on the conformational stability of cyclophane.

To facilitate macrocyclization, longer diesters A could also be used , but the aromatic substituents R1 should be more bulky in order to limit the rotation of the ansa bridge (from the French anse - loop). Deputy sizeR1 is also critical because they must affect the selectivity of the enzyme, but should not adversely affect the reactivity.

In DKR secondary alcohols, CALB was previously used, i.e. lapase B hydrolases Candida antarctica (fungus), which showed excellent results. Therefore, it was decided to use it in this study ( 2A ).


Image No. 2

First, an molecule with an unsubstituted aromatic nucleus was evaluated ( 1a in image 2A ), after which the desired achiral (mirror-rotated) macrocycle ( 3a ) was isolated .

After ascertaining that CALB can stimulate macrocyclization, scientists examined subsequent cyclization with the replacement of the aromatic nucleus of OMe (methoxy) by groups ( 1b ). In this case, the output was only 10% of paracyclophan ( 3b ).

Performed variable temperature NMR spectroscopy of benzyl proton signals (highlighted in green at 2A ) showed signal fusion at 50 ° C.

Macrocyclization using larger bromo substituents (diol 1c ) was even less successful, most likely due to an unfavorable steric collision between the ortho-substituted benzyl diol and the active part of the enzyme.

In view of this, it was decided to redo the original diol by incorporating a methylene group near the aromatic nucleus ( 5 in Figure 2B ). With the expanded diol, it was possible to obtain the desired paracyclophan ( 6 in Figure 2B ) with good yield and high enantioselectivity.

Spectroscopy of signals of benzyl protons of paracyclophan showed the absence of signal fusion even at 100 ° C. If the temperature was lowered, then the yield of paracyclophan decreased. If it was increased, then there was no positive effect on the resulting paracyclophan.

Despite the fact that CALB favorably influenced the acylation of R-centered carbon chiral centers, it remained unclear how the active regions of CALB would adapt to the prochiral aromatic plane of the resulting macrocycle.

To better understand how CALB active sites work with different conformations of the cyclophane substrate, the molecular docking
procedure * ( 2C ) was performed .
Molecular docking * is a molecular modeling method that allows one to predict the most favorable orientation and conformation of one molecule (ligand) at the binding site of another (receptor) to obtain a stable structure.
The main product (-) - 6 (marked in green at 2C ) is oriented by its carboxyl groups to the nearby catalytic serine residue (Ser 105 ), and one of the bromine substituents is directed outside the active center.

The predicted translation (+) - 6 (marked in yellow at 2C ) is the result of a collision between the bromine atom and Leu 140 , which excludes the binding of the bromine atom in the hydrophobic region designated Leu 140 , Ala 141 and Leu 144 . When docking the initial dibromodiol (5), it enters the cavity, and its alcohol is distributed in the direction of the catalytically active serine.

The biocatalytic synthesis of paracyclophan can be easily reproduced on a gram scale, so it was decided to study the volume of the substrate taking into account the size of the ring.

Although dibromocyclophan 6 can be obtained using diacid with a 6-methylene spacer [- (CH 2 ) 6 -], reducing the spacer to four or five methylene units did not significantly increase ring deformation. As a result of this, [12] and [13] paracyclophanes with high enantioselectivity were obtained (image No. 3).


Image No. 3

This series of macrocycles can be obtained with chlorine or iodine atoms replacing bromine substituents. Changing the size of the halogen substituent did not have a significant effect on the yield and enantiological purity of the obtained [12] -, [13] - and [14] -paracyclophanes (10 → 12).

The expansion of the ansa bridge with an additional methylene spacer made it possible to obtain enough [15] paracyclophan (9). However, the resulting product was in the form of a racemic mixture, which indicates that the larger aliphatic ring no longer inhibits the rotation of planar cyclophane.

The larger size of iodine made it possible to synthesize enantio-enriched [15] -paracyclophan (17). To find out whether the active site of the enzyme can transfer more functionalized ansi-bridges, two functionalized ansi-bridges with phenyl-substituted (18) and alkynyl-substituted (19) nuclei in their framework, as well as [14] -paracyclophan 20, which has a disulfide bridge, were prepared .

A number of functionalized aromatic diols were also well tolerated during macrocyclization. Terphenyl-based macrocycle 21 can be formed by macrocyclization, as well as similarly substituted p-anisoyl and m-anisoyl cyclophanes (22 and 23, respectively) with high enantioselectivity. It was also possible to synthesize and [14] -paracyclophan 24 and 25, which have nuclei with phenylalkynyl or hexynyl substituents.

Finally, C1-symmetric derivatives with high enantioselectivity were obtained. Macrocycle 27 was isolated by one iodide substituent and one alkynyl unit, while macrocycle 28 was isolated by one bromide substituent and a Csp3-hybridized motif (benzyl).

It is noteworthy that halogen-containing planar chiral macrocycles can act as a platform for the synthesis of other derivatives using modern cross-linking methods. For example, bromosubstituted cyclophane 6 can be subjected to a Heck combination (Heck reaction) to form a macrocycle 30. The same, but with a lower yield (19%), can be achieved by a biocatalytic method with high selectivity.

For a more detailed acquaintance with the nuances of the study, I recommend that you look into the report of scientists andadditional materials to it.

Epilogue


This study cannot be called easy, because we are talking about modeling molecular structures. This work is reminiscent of the work of Hercule Poirot, when special attention is paid to the smallest details, because they have a huge impact on the overall picture.

Biocatalysis, as a method of obtaining planar chiral macrocycles, was studied for the first time in this work. The methods used earlier were much more expensive in terms of resources and time, or they used very toxic reagents. Biocatalysis, on the other hand, made it possible, using more than available materials, such as the CALB enzyme.

Biocatalysis is important for both chemists and physicians, as it allows you to give new compounds new functions due to the addition of additional structures.

The authors of the study plan to improve their methodology, since macrocycles have great potential in medicine (as antibiotics and anti-cancer agents) and even in electronics (for example, in laser technologies).

Thank you for your attention, remain curious and have a good working week, guys. :)

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