An Approach to the De Novo Synthesis of Life

Abstract

As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.

Figure 1

Emergence of life requires the integration of functional subsystems that are responsible for self-replication, compartmentalization, and metabolism under conditions that keep the system far from equilibrium and enable its open-ended Darwinian evolution. Adapted with permission from ref (11). Copyright 2020, Springer Nature.

Figure 2

(a) Simplified mechanism by which self-assembly can drive self-replication. (b) Kinetics of formation of different oligomers of 1a showing a distinct lag phase in the formation of replicator (1a)₆. (c) Assembly of precursors on the sides of the fibers promotes self-replication as evident from (d) high-speed AFM images of a fiber growing from a bound precursor aggregate at t = 0, 2, and 5 min (data taken from ref (64)). (e) Building blocks with which self-assembly driven self-replication has been observed include peptide derivatives 1a–f, but also amino-acid nucleic-acid chimeras 2 and 3 as well as molecules 1g and 4 lacking any of life’s current building blocks.

Figure 3

(a) Diversification of self-replicating molecules. Oxidizing a mixture of building blocks 1a and 1b leads to two separate sets of replicators that emerge at different times. The first set of hexamers rich in 1a induces the formation of a second set of hexamers that specialize on 1b. (b) Sample history dictates replicator composition. Whether building block 1d gives rise to hexamer or octamer replicator depends on whether the sample was exposed to independently prepared hexameric or octameric replicators, which cross-catalyze the formation of the replicator of 1d with the corresponding ring size. (c) Parasitic/predatory behavior in which replicator (1b)₈ cross-catalyzes the formation of (1f)_n(1b)_6–n which subsequently consumes the original replicator (1b)₈. Adapted with permission from ref (87). Copyright 2018, John Wiley & Sons, Inc.

Figure 4

(a) Replicator (1a)₆ catalyzes the retro-aldol reaction of methodol 5 involving imine formation between the nonprotonated lysine residues and 5. (b) The close proximity of many lysine side groups in the assemblies of replicator (1a)₆ perturbs the pK_A of the lysine groups resulting in the presence of nonprotonated lysines at neutral pH. (c) Proto-metabolism arising from replicator (1a)₆ catalyzing the cleavage of FMOC-glycine (6) to yield dibenzofulvene (7) which accelerates the oxidation of building block 1a into the small-ring precursors from which the replicator grows. (d) Postulated mechanism through which (1a)₆ catalyzes the cleavage of FMOC-glycine, relying on the simultaneous presence of protonated and nonprotonated lysine amine groups. (e) In an agitated sample prepared from dithiol building block 1a (200 μM) and FMOC-glycine 6 (100 μM) the emergence of (1a)₆ (dark blue circles) coincides with the onset of FMOC cleavage (red circles). Upon repeating the experiment in the absence of FMOC-glycine, replicator (1a)₆ emerges at the same time, but grew significantly slower (light blue circles). Adapted with permission from ref (3). Copyright 2020, Springer Nature. (f) Proto-metabolism arising through binding of dyes to replicator (1a)₆ which enhances the conversion of triplet to singlet oxygen, accelerating the production of replicator precursor. (g) Dyes used as cofactors for photomediated singlet-oxygen production.

Figure 5

(a) Continuous supply of NaBO₃ as oxidant and TCEP as reductant results in a chemically fueled replication-destruction regime in which the slow replicator (1a)₆ is able to outcompete the faster, more stable replicator (1a)₃ by virtue of being more resilient to chemical destruction. The thickness of the lines represent the magnitude of the flux of material through the different reaction paths (based on a kinetic model parametrized with mostly experimentally determined rate constants). (b) Qualitative Gibbs energy landscape showing the activation barriers (ΔG^⧧) for the interconversion between dithiol building block 1a and disulfide replicators (1a)₃ and (1a)₆ with disulfide formation in black and disulfide cleavage in blue. Abbreviations: rd = reductant; ox = oxidant; w = waste product.

Figure 6

Open-ended Darwinian evolution requires a huge structure space to be available to allow for continuous evolutionary inventions to be made. At any given time, an evolving system must only occupy a tiny subset of this space, putting demands on replication fidelity. In the process of evolution, the location of the occupied subset changes gradually. Note that the occupied and available structure spaces are not drawn to scale; the former is so much smaller than the latter that it would not be visible otherwise.