The role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia.

Tauopathies are neurodegenerative diseases characterized by deposits of abnormal Tau protein in the brain. Conventional tauopathies are often defined by a limited number of Tau epitopes, notably neurofibrillary tangles, but emerging evidence suggests structural heterogeneity among tauopathies. The prolyl isomerase Pin1 isomerizes cis P-tau to inhibit the development of oligomers, tangles and neurodegeneration in multiple neurodegenerative diseases such as Alzheimer's disease, traumatic brain injury, vascular contribution to cognitive impairment and dementia (VCID) and preeclampsia (PE). Thus, cis P-tau has emerged as an early etiological driver, blood marker and therapeutic target for multiple neurodegenerative diseases, with clinical trials ongoing. The discovery of cis P-tau and other tau pathologies in VCID and PE calls attention for simplistic classification of tauopathy in neurodegenerative diseases. These recent advances have revealed the exciting novel role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia.

Mechanical scission of a knotted polymer.

Molecular knots and entanglements form randomly and spontaneously in both biological and synthetic polymer chains. It is known that macroscopic materials, such as ropes, are substantially weakened by the presence of knots, but until now it has been unclear whether similar behaviour occurs on a molecular level. Here we show that the presence of a well-defined overhand knot in a polymer chain substantially increases the rate of scission of the polymer under tension (≥2.6× faster) in solution, because deformation of the polymer backbone induced by the tightening knot activates otherwise unreactive covalent bonds. The fragments formed upon severing of the knotted chain differ from those that arise from cleavage of a similar, but unknotted, polymer. Our solution studies provide experimental evidence that knotting can contribute to higher mechanical scission rates of polymers. It also demonstrates that entanglement design can be used to generate mechanophores that are among the most reactive described to date, providing opportunities to increase the reactivity of otherwise inert functional groups.

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction.

Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.

Changing Liquid Crystal Helical Pitch with a Reversible Rotaxane Switch.

The transmission of chiral information between the molecular, meso and microscopic scales is a facet of biology that remains challenging to understand mechanistically and to mimic with artificial systems. Here we demonstrate that the dynamic change in the expression of the chirality of a rotaxane can be transduced into a change in pitch of a soft matter system. Shuttling the position of the macrocycle from far-away-from to close-to a point-chiral center on the rotaxane axle changes the expression of the chiral information that is transmitted across length scales; from nanometer scale constitutional chirality that affects the conformation of the macrocycle, to the centimeter scale chirality of the liquid crystal phase, significantly changing the pitch length of the chiral nematic structure.

Stepwise Operation of a Molecular Rotary Motor Driven by an Appel Reaction.

To date, only a small number of chemistries and chemical fueling strategies have been successfully used to operate artificial molecular motors. Here, we report the 360° directionally biased rotation of phenyl groups about a C-C bond, driven by a stepwise Appel reaction sequence. The motor molecule consists of a biaryl-embedded phosphine oxide and phenol, in which full rotation around the biaryl bond is blocked by the P-O oxygen atom on the rotor being too bulky to pass the oxygen atom on the stator. Treatment with SOCl2 forms a cyclic oxyphosphonium salt (removing the oxygen atom of the phosphine oxide), temporarily linking the rotor with the stator. Conformational exchange via ring flipping then allows the rotor and stator to twist back and forth past the previous limit of rotation. Subsequently, the ring opening of the tethered intermediate with a chiral alcohol occurs preferentially through a nucleophilic attack on one face. Thus, the original phosphine oxide is reformed with net directional rotation about the biaryl bond over the course of the two-step reaction sequence. Each repetition of SOCl2-chiral alcohol additions generates another directionally biased rotation. Using the same reaction sequence on a derivative of the motor molecule that forms atropisomers rather than fully rotating 360° results in enantioenrichment, suggesting that, on average, the motor molecule rotates in the "wrong" direction once every three fueling cycles. The interconversion of phosphine oxides and cyclic oxyphosphonium groups to form temporary tethers that enable a rotational barrier to be overcome directionally adds to the strategies available for generating chemically fueled kinetic asymmetry in molecular systems.

Ratcheting synthesis.

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.

Switched "On" Transient Fluorescence Output from a Pulsed-Fuel Molecular Ratchet.

We report the synthesis and operation of a molecular energy ratchet that transports a crown ether from solution onto a thread, along the axle, over a fluorophore, and off the other end of the thread back into bulk solution, all in response to a single pulse of a chemical fuel (CCl3CO2H). The fluorophore is a pyrene residue whose fluorescence is normally prevented by photoinduced electron transfer (PET) to a nearby N-methyltriazolium group. However, crown ether binding to the N-methyltriazolium site inhibits the PET, switching on pyrene fluorescence under UV irradiation. Each pulse of fuel results in a single ratchet cycle of transient fluorescence (encompassing threading, transport to the N-methyltriazolium site, and then dethreading), with the onset of the fluorescent time period determined by the amount of fuel in each pulse and the end-point determined by the concentration of the reagents for the disulfide exchange reaction. The system provides a potential alternative signaling approach for artificial molecular machines that read symbols from sequence-encoded molecular tapes.

In Search of Wasserman's Catenane.

We repeat the earliest claimed [2]catenane synthesis, reported by Wasserman over 60 years ago, in order to ascertain whether or not a nontemplate, statistical synthesis by acyloin macrocyclization does indeed form mechanically interlocked rings. The lack of direct experimental evidence for Wasserman's catenane has led to it being described as a "prophetic compound", a technical term used in patents for claimed molecules that have not yet been synthesized. Contemporary synthetic methods were used to reconstruct Wasserman's deuterium-labeled macrocycle and other building blocks on the 10-100 g reaction scale necessary to generate, in principle, ∼1 mg of catenane. Modern spectrometric and spectroscopic tools and chemical techniques (including tandem mass spectrometry, deuterium nuclear magnetic resonance (NMR) spectroscopy, and fluorescent tag labeling) were brought to bear in an effort to detect, isolate, and prove the structure of a putative [2]catenane consisting of a 34-membered cyclic hydrocarbon mechanically linked with a 34-membered cyclic α-hydroxyketone.

Compact Rotaxane Superbases.

Challenges for the development of efficacious new superbases include their ease of synthesis, chemical stability, and high basicity, while minimizing nucleophilicity is important for reducing unwanted side reactions. Here, we introduce a new family of organic superbases, compact amine-crown ether rotaxanes, which show desirable characteristics in all these respects. Metal-free active template synthesis provides access to a range of rotaxanes with as little as three atoms between the stoppering groups, locking the location of a small crown ether (21C7 and 24C8 derivatives) over the amine group of the axle. The forced proximity of the interlocked protophilic components results in pKaH+ values as high as 32.2 in acetonitrile, which is up to 13 pKaH+ units greater than the pKaH+ values of the non-interlocked components, and brings the free base rotaxanes into the basicity realm of phosphazene superbases. The rotaxane superbases are generally chemically stable and, in a model reaction for superbases, eliminate HBr from a primary alkyl bromide with complete selectivity for deprotonation over alkylation. Their modest size, ease of synthesis, high basicity, low nucleophilicity, and, in the best cases, rapid substrate deprotonation kinetics and excellent hydrolytic stability make compact amine-crown ether rotaxane superbases intriguing candidates for potential applications in synthesis and supramolecular and materials chemistry.

Using Catalysis to Drive Chemistry Away from Equilibrium: Relating Kinetic Asymmetry, Power Strokes, and the Curtin-Hammett Principle in Brownian Ratchets.

Chemically fueled autonomous molecular machines are catalysis-driven systems governed by Brownian information ratchet mechanisms. One fundamental principle behind their operation is kinetic asymmetry, which quantifies the directionality of molecular motors. However, it is difficult for synthetic chemists to apply this concept to molecular design because kinetic asymmetry is usually introduced in abstract mathematical terms involving experimentally inaccessible parameters. Furthermore, two seemingly contradictory mechanisms have been proposed for chemically driven autonomous molecular machines: Brownian ratchet and power stroke mechanisms. This Perspective addresses both these issues, providing accessible and experimentally useful design principles for catalysis-driven molecular machinery. We relate kinetic asymmetry to the Curtin-Hammett principle using a synthetic rotary motor and a kinesin walker as illustrative examples. Our approach describes these molecular motors in terms of the Brownian ratchet mechanism but pinpoints both chemical gating and power strokes as tunable design elements that can affect kinetic asymmetry. We explain why this approach to kinetic asymmetry is consistent with previous ones and outline conditions where power strokes can be useful design elements. Finally, we discuss the role of information, a concept used with different meanings in the literature. We hope that this Perspective will be accessible to a broad range of chemists, clarifying the parameters that can be usefully controlled in the design and synthesis of molecular machines and related systems. It may also aid a more comprehensive and interdisciplinary understanding of biomolecular machinery.

A tape-reading molecular ratchet.

Cells process information in a manner reminiscent of a Turing machine1, autonomously reading data from molecular tapes and translating it into outputs2,3. Randomly processive macrocyclic catalysts that can derivatise threaded polymers have been described4,5, as have rotaxanes that transfer building blocks in sequence from a molecular strand to a growing oligomer6-10. However, synthetic small-molecule machines that can read and/or write information stored on artificial molecular tapes remain elusive11-13. Here we report on a molecular ratchet in which a crown ether (the 'reading head') is pumped from solution onto an encoded molecular strand (the 'tape') by a pulse14,15 of chemical fuel16. Further fuel pulses transport the macrocycle through a series of compartments of the tape via an energy ratchet14,17-22 mechanism, before releasing it back to bulk off the other end of the strand. During its directional transport, the crown ether changes conformation according to the stereochemistry of binding sites along the way. This allows the sequence of stereochemical information programmed into the tape to be read out as a string of digits in a non-destructive manner through a changing circular dichroism response. The concept is exemplified by the reading of molecular tapes with strings of balanced ternary digits ('trits'23), -1,0,+1 and -1,0,-1. The small-molecule ratchet is a finite-state automaton: a special case24 of a Turing machine that moves in one direction through a string-encoded state sequence, giving outputs dependent on the occupied machine state25,26. It opens the way for the reading-and ultimately writing-of information using the powered directional movement of artificial nanomachines along molecular tapes.

Social Self-Sorting Synthesis of Molecular Knots.

We report the synthesis of molecular prime and composite knots by social self-sorting of 2,6-pyridinedicarboxamide (pdc) ligands of differing topicity and stereochemistry. Upon mixing achiral monotopic and ditopic pdc-ligand strands in a 1:1:1 ratio with Lu(III), a well-defined heteromeric complex featuring one of each ligand strand and the metal ion is selectively formed. Introducing point-chiral centers into the ligands leads to single-sense helical stereochemistry of the resulting coordination complex. Covalent capture of the entangled structure by ring-closing olefin metathesis then gives a socially self-sorted trefoil knot of single topological handedness. In a related manner, a heteromeric molecular granny knot (a six-crossing composite knot featuring two trefoil tangles of the same handedness) was assembled from social self-sorting of ditopic and tetratopic multi-pdc strands. A molecular square knot (a six-crossing composite knot of two trefoil tangles of opposite handedness) was assembled by social self-sorting of a ditopic pdc strand with four (S)-centers and a tetratopic strand with two (S)- and six (R)-centers. Each of the entangled structures was characterized by 1H and 13C NMR spectroscopy, mass spectrometry, and circular dichroism spectroscopy. The precise control of composition and topological chirality through social self-sorting enables the rapid assembly of well-defined sequences of entanglements for molecular knots.

Tuning the Force, Speed, and Efficiency of an Autonomous Chemically Fueled Information Ratchet.

Autonomous chemically fueled molecular machines that function through information ratchet mechanisms underpin the nonequilibrium processes that sustain life. These biomolecular motors have evolved to be well-suited to the tasks they perform. Synthetic systems that function through similar mechanisms have recently been developed, and their minimalist structures enable the influence of structural changes on machine performance to be assessed. Here, we probe the effect of changes in the fuel and barrier-forming species on the nonequilibrium operation of a carbodiimide-fueled rotaxane-based information ratchet. We examine the machine's ability to catalyze the fuel-to-waste reaction and harness energy from it to drive directional displacement of the macrocycle. These characteristics are intrinsically linked to the speed, force, power, and efficiency of the ratchet output. We find that, just as for biomolecular motors and macroscopic machinery, optimization of one feature (such as speed) can compromise other features (such as the force that can be generated by the ratchet). Balancing speed, power, efficiency, and directionality will likely prove important when developing artificial molecular motors for particular applications.

Knotting matters: orderly molecular entanglements.

Entangling strands in a well-ordered manner can produce useful effects, from shoelaces and fishing nets to brown paper packages tied up with strings. At the nanoscale, non-crystalline polymer chains of sufficient length and flexibility randomly form tangled mixtures containing open knots of different sizes, shapes and complexity. However, discrete molecular knots of precise topology can also be obtained by controlling the number, sequence and stereochemistry of strand crossings: orderly molecular entanglements. During the last decade, substantial progress in the nascent field of molecular nanotopology has been made, with general synthetic strategies and new knotting motifs introduced, along with insights into the properties and functions of ordered tangle sequences. Conformational restrictions imparted by knotting can induce allostery, strong and selective anion binding, catalytic activity, lead to effective chiral expression across length scales, binding modes in conformations efficacious for drug delivery, and facilitate mechanical function at the molecular level. As complex molecular topologies become increasingly synthetically accessible they have the potential to play a significant role in molecular and materials design strategies. We highlight particular examples of molecular knots to illustrate why these are a few of our favourite things.

Transamidation-Driven Molecular Pumps.

We report a new class of synthetic molecular pumps that use a stepwise information ratchet mechanism to achieve the kinetic gating required to sequester their macrocyclic substrates from bulk solution. Threading occurs as a result of active template reactions between the pump terminus amine and an acyl electrophile, whereby the bond-forming reaction is accelerated through the cavity of a crown ether. Carboxylation of the resulting amide results in displacement of the ring to the collection region of the thread. Conversion of the carbamate to a phenolic ester provides an intermediate rotaxane suitable for further pumping cycles. In this way rings can be ratcheted onto a thread from one or both ends of appropriately designed molecular pumps. Each pumping cycle results in one additional ring being added to the thread per terminus acyl group. The absence of pseudorotaxane states ensures that no dethreading of intermediates occurs during the pump operation. This facilitates the loading of different macrocycles in any chosen sequence, illustrated by the pump-mediated synthesis of a [4]rotaxane containing three different macrocycles as a single sequence isomer. A [5]rotaxane synthesized using a dual-opening transamidation pump was structurally characterized by single-crystal X-ray diffraction, revealing a series of stabilizing CH···O interactions between the crown ethers and the polyethylene glycol catchment region of the thread.

Chemical fuels for molecular machinery.

Chemical reaction networks that transform out-of-equilibrium 'fuel' to 'waste' are the engines that power the biomolecular machinery of the cell. Inspired by such systems, autonomous artificial molecular machinery is being developed that functions by catalysing the decomposition of chemical fuels, exploiting kinetic asymmetry to harness energy released from the fuel-to-waste reaction to drive non-equilibrium structures and dynamics. Different aspects of chemical fuels profoundly influence their ability to power molecular machines. Here we consider the structure and properties of the fuels that biology has evolved and compare their features with those of the rudimentary synthetic chemical fuels that have so far been used to drive autonomous non-equilibrium molecular-level dynamics. We identify desirable, but context-specific, traits for chemical fuels together with challenges and opportunities for the design and invention of new chemical fuels to power synthetic molecular machinery and other dissipative nanoscale processes.

Pumping between phases with a pulsed-fuel molecular ratchet.

The sorption of species from a solution into and onto solids underpins the sequestering of waste and pollutants, precious metal recovery, heterogeneous catalysis, analysis and separation science, and other technologies1,2. The transfer between phases tends to proceed spontaneously in the direction of equilibrium. For example, alkyl ammonium groups mounted on silica nanoparticles are used to chemisorb cucurbituril macrocycles from solution through host-guest binding3,4. Molecular ratchet mechanisms5-7, in which kinetic gating8-12 inhibits or accelerates particular steps, makes it possible to progressively drive dynamic systems13-16 away from equilibrium17-21. Here we report on molecular pumps22 immobilized on polymer beads23-25 that use an energy ratchet mechanism5,9,19-21,26-30 to directionally transport substrates from solution onto the beads. On the addition of trichloroacetic acid (CCl3CO2H)19,31-33 fuel19,34-37, micrometre-diameter polystyrene beads functionalized38 with solvent-accessible molecular pumps sequester from the solution crown ethers appended with fluorescent tags. After fuel consumption, the rings are mechanically trapped in a higher-energy, out-of-equilibrium state on the beads and cannot be removed by dilution or exhaustive washing. This differs from dissipative assembled materials11,13-16, which require a continuous supply of energy to persist, and from conventional host-guest complexes. The addition of a second fuel pulse causes the uptake of more macrocycles, which drives the system further away from equilibrium. The second macrocycle can be labelled with a different fluorescent tag, which confers sequence information39 on the absorbed structure. The polymer-bound substrates can be released back to the bulk either one compartment at a time or all at once. Non-equilibrium40 sorption by immobilized artificial molecular machines41-45 enables the transduction of energy from chemical fuels for the use, storage and release of energy and information.

Autonomous fuelled directional rotation about a covalent single bond.

Biology operates through autonomous chemically fuelled molecular machinery1, including rotary motors such as adenosine triphosphate synthase2 and the bacterial flagellar motor3. Chemists have long sought to create analogous molecular structures with chemically powered, directionally rotating, components4-17. However, synthetic motor molecules capable of autonomous 360° directional rotation about a single bond have proved elusive, with previous designs lacking either autonomous fuelling7,10,12 or directionality6. Here we show that 1-phenylpyrrole 2,2'-dicarboxylic acid18,19 (1a) is a catalysis-driven20,21 motor that can continuously transduce energy from a chemical fuel9,20-27 to induce repetitive 360° directional rotation of the two aromatic rings around the covalent N-C bond that connects them. On treatment of 1a with a carbodiimide21,25-27, intramolecular anhydride formation between the rings and the anhydride's hydrolysis both occur incessantly. Both reactions are kinetically gated28-30 causing directional bias. Accordingly, catalysis of carbodiimide hydration by the motor molecule continuously drives net directional rotation around the N-C bond. The directionality is determined by the handedness of both an additive that accelerates anhydride hydrolysis and that of the fuel, and is easily reversed additive31. More than 97% of fuel molecules are consumed through the chemical engine cycle24 with a directional bias of up to 71:29 with a chirality-matched fuel and additive. In other words, the motor makes a 'mistake' in direction every three to four turns. The 26-atom motor molecule's simplicity augurs well for its structural optimization and the development of derivatives that can be interfaced with other components for the performance of work and tasks32-36.

Insights from an information thermodynamics analysis of a synthetic molecular motor.

Information is physical, a realization that has transformed the physics of measurement and communication. However, the flow between information, energy and mechanics in chemical systems remains largely unexplored. Here we analyse a minimalist autonomous chemically driven molecular motor in terms of information thermodynamics, a framework that quantitatively relates information to other thermodynamic parameters. The treatment reveals how directional motion is generated by free energy transfer from chemical to mechanical (conformational and/or co-conformational) processes by 'energy flow' and 'information flow'. It provides a thermodynamic level of understanding of molecular motors that is general, complements previous analyses based on kinetics and has practical implications for machine design. In line with kinetic analysis, we find that power strokes do not affect the directionality of chemically driven machines. However, we find that power strokes can modulate motor velocity, the efficiency of free energy transfer and the number of fuel molecules consumed per cycle. This may help explain the role of such (co-)conformational changes in biomachines and illustrates the interplay between energy and information in chemical systems.

Vernier template synthesis of molecular knots.

Molecular knots are often prepared using metal helicates to cross the strands. We found that coordinatively mismatching oligodentate ligands and metal ions provides a more effective way to synthesize larger knots using Vernier templating. Strands composed of different numbers of tridentate 2,6-pyridinedicarboxamide groups fold around nine-coordinate lanthanide (III) ions to generate strand-entangled complexes with the lowest common multiple of coordination sites for the ligand strands and metal ions. Ring-closing olefin metathesis then completes the knots. A 3:2 (ditopic strand:metal) Vernier assembly produces +31#+31 and -31#-31 granny knots. Vernier complexes of 3:4 (tetratopic strand:metal) stoichiometry selectively form a 378-atom-long trefoil-of-trefoils triskelion knot with 12 alternating strand crossings or, by using opposing stereochemistry at the terminus of the strand, an inverted-core triskelion knot with six alternating and six nonalternating strand crossings.