Periodic Reporting for period 2 - PROTEAS (Programming Terpene Cyclization Through Iterative Precursor Assembly)
Período documentado: 2021-05-01 hasta 2022-04-30
Small organic molecules represent invaluable tools for improving the quality of human life: they constitute a large fraction of the medicines currently in use, and can serve as biological probes, components of organic materials, fragrances, dyes etc. The synthesis of organic molecules however has traditionally required custom synthetic approaches that need to be carried out by trained experts, and which are often long and laborious. As already demonstrated by the rapid advances brought about by the development of automated peptide and oligonucleotide syntheses, the development of methods for the automated synthesis of custom small organic molecules from readily available building blocks would enable transformative innovation in a wide number of fields.
A number of exciting advances have already been made towards this goal; the Burke group recently reported an automated platform that allows the generalized building block-based synthesis of small molecules through the use of a palladium-catalyzed coupling reaction and a special N-methyl iminodiacetic acid (MIDA) protecting group for the boronate functionality. While such an approach can be readily applied to the synthesis of many linear structures, the major challenge now lies in the assembly of complex molecular frameworks, not easily reducible to individual building blocks. Importantly, Nature solves this problem by constructing modular linear structures that are then cyclized to form complex cyclic frameworks. One such reaction is the Tail-to-Head Terpene (THT) cyclization, which features in the biosynthesis of most terpenes and accounts for a large portion of the remarkable structural diversity this class of natural products displays. Despite the synthetic potential of this reaction, it has proven difficult to carry out using artificial, non-enzymatic means; recently, however, the Tiefenbacher group reported the capability of a hexameric supramolecular assembly (a supramolecular “capsule”) to catalyze this reaction and form terpene natural products difficult to obtain via other methods.
In this context, this project aims to combine these advances to provide a platform for the building block-based synthesis of complex terpene frameworks. A modular approach to linear THT cyclization precursors will allow for the investigation of the effects of specific changes in molecular structure on the outcome of the capsule-catalyzed cyclization reaction. The resulting understanding of the factors that govern the capsule-mediated THT cyclization reaction is expected to provide a method for the modular synthesis of complex molecular frameworks starting from a linear precursor, a result with profound implications for the future of automation in organic synthesis.
A number of exciting advances have already been made towards this goal; the Burke group recently reported an automated platform that allows the generalized building block-based synthesis of small molecules through the use of a palladium-catalyzed coupling reaction and a special N-methyl iminodiacetic acid (MIDA) protecting group for the boronate functionality. While such an approach can be readily applied to the synthesis of many linear structures, the major challenge now lies in the assembly of complex molecular frameworks, not easily reducible to individual building blocks. Importantly, Nature solves this problem by constructing modular linear structures that are then cyclized to form complex cyclic frameworks. One such reaction is the Tail-to-Head Terpene (THT) cyclization, which features in the biosynthesis of most terpenes and accounts for a large portion of the remarkable structural diversity this class of natural products displays. Despite the synthetic potential of this reaction, it has proven difficult to carry out using artificial, non-enzymatic means; recently, however, the Tiefenbacher group reported the capability of a hexameric supramolecular assembly (a supramolecular “capsule”) to catalyze this reaction and form terpene natural products difficult to obtain via other methods.
In this context, this project aims to combine these advances to provide a platform for the building block-based synthesis of complex terpene frameworks. A modular approach to linear THT cyclization precursors will allow for the investigation of the effects of specific changes in molecular structure on the outcome of the capsule-catalyzed cyclization reaction. The resulting understanding of the factors that govern the capsule-mediated THT cyclization reaction is expected to provide a method for the modular synthesis of complex molecular frameworks starting from a linear precursor, a result with profound implications for the future of automation in organic synthesis.
During the Outgoing Phase of the Fellowship, a building block-based approach to the synthesis of linear THT cyclization precursors was developed, consisting of the palladium-mediated coupling of a “head” and a “tail” group. By providing a modular approach to precursor synthesis through the ability to swap out different head and tail groups, this allowed the convenient investigation of the effect of specific changes to the structure of the precursor on the outcome of the THT cyclization reaction. A library of different head and tail groups was therefore prepared, and the full array of cyclization precursors that derive from their combination was synthesized. By subjecting the library of linear precursors thus obtained to the capsule-catalyzed THT cyclization conditions, a number of diverse cyclic terpene scaffolds were obtained, comprising different natural and unnatural, fused and bridged ring structures. The study of the effects of substitution on the course of the cyclization, and the rationalization of the observed reactivity, are currently under further elaboration through computational studies in collaboration with the group of Prof. Dan Major (Bar-Ilan University). A manuscript on this part of the project is in preparation.
Additionally, during the Outgoing Phase efforts were directed towards constructing a modified version of the Burke group’s small molecule synthesizer capable of carrying out the entire coupling/cyclization sequence automatically. To this end, the coupling protocol was modified to incorporate the MIDA protecting group in order to allow for catch-and-release purification. A simplified prototype of the automated synthesizer was then constructed, based on the Burke group synthesizer but incorporating a new “cyclization” module. Development of this system is ongoing via a long-range collaboration with the Burke group.
During the Incoming Phase of the Fellowship, the broader applicability of the approach was investigated by applying the reactivity principles uncovered during the Outgoing Phase to the synthesis of a number of natural products. In the course of these studies the approach was extended to the synthesis of diterpene natural products; it was found that, as with the sesquiterpene case, control of the reaction cascade could be achieved by the variation of structural elements of the precursors, in this case leading to two different diterpene natural products.
Additionally, during the Outgoing Phase efforts were directed towards constructing a modified version of the Burke group’s small molecule synthesizer capable of carrying out the entire coupling/cyclization sequence automatically. To this end, the coupling protocol was modified to incorporate the MIDA protecting group in order to allow for catch-and-release purification. A simplified prototype of the automated synthesizer was then constructed, based on the Burke group synthesizer but incorporating a new “cyclization” module. Development of this system is ongoing via a long-range collaboration with the Burke group.
During the Incoming Phase of the Fellowship, the broader applicability of the approach was investigated by applying the reactivity principles uncovered during the Outgoing Phase to the synthesis of a number of natural products. In the course of these studies the approach was extended to the synthesis of diterpene natural products; it was found that, as with the sesquiterpene case, control of the reaction cascade could be achieved by the variation of structural elements of the precursors, in this case leading to two different diterpene natural products.
The state-of-the-art in automated synthesis protocols allows for the preparation of a wide variety of linear molecules, but topologically complex cyclic structures represent a crucial limitation. As stated, to overcome this limitation, methods that allow for the conversion of modular linear structures (amenable to automated synthesis) to complex molecules need to be developed, and the reactivity rules that guide this linear-to-cyclized conversion need to be understood. The process developed during the Outgoing Phase represents such a linear-to-cyclized approach that provides coverage of a wide subset of terpenoid chemical space. Importantly, the overall sequence represents the “encoding” of a specific topologically complex, three-dimensional terpenoid structure into a linear “code” consisting of two blocks; this is a novel approach that is sure to have a profound impact on the development of automation in organic synthesis. Further elaboration of the results described here, until the end of the project, will involve the extension of the scope of the methodology developed and its application to the synthesis of natural structures of high value.
More generally, the development of methods towards the convenient synthesis of small organic molecules by non-experts stands to revolutionize Chemical Biology and Medicinal Chemistry research, much like the development of automated peptide and oligonucleotide syntheses did. The wider socio-economic implications of such an advance thus reside in easier access to novel medicines and chemical probes to elucidate biological phenomena, as well as to novel organic materials, dyes and fragrances; in other words, in easier access to the immense potential that small organic molecules possess.
More generally, the development of methods towards the convenient synthesis of small organic molecules by non-experts stands to revolutionize Chemical Biology and Medicinal Chemistry research, much like the development of automated peptide and oligonucleotide syntheses did. The wider socio-economic implications of such an advance thus reside in easier access to novel medicines and chemical probes to elucidate biological phenomena, as well as to novel organic materials, dyes and fragrances; in other words, in easier access to the immense potential that small organic molecules possess.