Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm

Journal name:
Nature Chemistry
Volume:
8,
Pages:
138–143
Year published:
DOI:
doi:10.1038/nchem.2410
Received
Accepted
Published online

Abstract

Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79–85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

At a glance

Figures

  1. Multi-stage operation of a bidirectional small-molecule transporter system, 1, that uses a rotary switch to control a molecular robotic arm.
    Figure 1: Multi-stage operation of a bidirectional small-molecule transporter system, 1, that uses a rotary switch to control a molecular robotic arm.

    Stage one (attach): toggling the switch (orange) from its initial state, if necessary, steers the arm to be proximate to the cargo (red ball) enabling it to attach to the substrate by reversible covalent bond formation. Stage two (pick up, reposition, set down): conditions are changed so that the cargo can no longer detach from the arm and the switch mechanism causes bond rotation, resulting in transport of the substrate between the two platform sites (blue and green; the cargo–platform linkages need to be dynamic under these conditions). Stage three (release): cleavage of the cargo–arm bond releases the substrate at the new site and the switch (and robotic arm) can be reset to the original position(s).

  2. Synthesis of transporter–cargo conjugates Z-2-left and EZ-1-left.
    Figure 2: Synthesis of transporter–cargo conjugates Z-2-left and EZ-1-left.

    Reagents and conditions. Step a: (i) CF3CO2H, t-BuONO, CH2Cl2, −10 °C, 2 h; (ii) KOAc, CH2Cl2, −10 °C to RT, 2 h, 81%, E:Z ∼ 7:3. Step b: AcOH, CH2Cl2, 16 h, 80%. Step c: CF3CO2H (3 equiv.), CHCl3 (2.5 mM), 48 h, 57%. Step d: TCEP.HCl, Et3N, C2H2Cl4/DMSO (2:1), RT, 16 h, 80%. TCEP, tris(2-carboxyethyl)phosphine.

  3. Partial 1H NMR (600 MHz, 295 K, CD2Cl2) spectra of the transporter–cargo conjugates at distinctive stages of operation.
    Figure 3: Partial 1H NMR (600 MHz, 295 K, CD2Cl2) spectra of the transporter–cargo conjugates at distinctive stages of operation.

    a, EZ-1-left. b, Z-2-left. c, E-2-right. d, EZ-1-right. Each compound was prepared by an unambiguous synthetic route (Supplementary Section 3). Dashed lines connect resonances indicative of the configuration of the hydrazone switch (Hn and Hx), the position of the cargo (Ha) and the redox state of the thiol/disulfide groups (Hal and Ham). Proton assignments correspond to the lettering in Fig. 2. Signals from traces of residual solvent are shown in grey. Some small signals (for example, *) are due the minor acyl hydrazone rotamer (restricted rotation about the NH–CO bond) of the cargo.

  4. Operation of the molecular transporter to reposition a 3-mercaptopropanehydrazide cargo from blue to green or green to blue platform sites.
    Figure 4: Operation of the molecular transporter to reposition a 3-mercaptopropanehydrazide cargo from blue to green or green to blue platform sites.

    The structures shown are those present at each stage after work-up with base. Reagents and conditions for the isolation of intermediates at each stage. Forward transport (blue to green): step a, CF3CO2H (3 equiv.), C2D2Cl4/C6D5CD3 (1:2, 2.5 mM), then I2 (1.5 equiv.), RT, 2 min, 95%; step b, CF3CO2H (70 equiv.), C2D2Cl4/C6D5CD3 (1:2, 2.5 mM), RT, 6 h, then Et3N (140 equiv.), 83%; step c, TCEP.HCl (5 equiv.), Et3N (20 equiv.), C2D2Cl4/(CD3)2SO (2:1, 2.5 mM, 1% vol/vol H2O), RT, 1 h, 99%. Backward transport (green to blue): step d, Et3N (3 equiv.), C2D2Cl4 (5 mM), RT, then I2 (1.5 equiv.), 2 min, 95%; step e, CF3CO2H (5 equiv.), C2D2Cl4 (5 mM), RT, 6 d, then Et3N (10 equiv.), 91%; step f, TCEP.HCl (5 equiv.), Et3N (20 equiv.), C2D2Cl4/(CD3)2SO (2:1, 5 mM, 1% vol/vol H2O), RT, 16 h, 99%. Reagents and conditions for one-pot operation. Forward transport (blue to green): step a, EZ-1-left in C2D2Cl4/C6D5CD3 (1:2, 2.5 mM): CF3CO2H (3 equiv.), then I2 (1.5 equiv.), RT, 2 min; step b, CF3CO2H (70 equiv.), RT, 6 h, then Et3N (100 equiv.); step c, TCEP.HCl (5 equiv., in (CD3)2SO, 1% v/v H2O), RT, 90 min. EZ-1-right 72% (over three steps). Backward transport (green to blue): step d, EZ-1-right in C2D2Cl4/C6D5CD3 (1:2, 2.5 mM): Et3N (3 equiv.), then I2 (1.5 equiv.), RT, 2 min; step e, CF3CO2H (8 equiv.), RT, 11 d, then Et3N (30 equiv.); step f, TCEP.HCl (5 equiv., in (CD3)2SO, 1% vol/vol H2O), RT, 90 min. EZ-1-left 63% (over three steps).

  5. Presumed intermediates in the rotary switching  and cargo transport mechanism.
    Figure 5: Presumed intermediates in the rotary switching 26 and cargo transport mechanism.

    Forward transport (top pathway, blue to green): protonation of Z-2-left with 70 equiv. CF3CO2H affords Z-2-H33+-left, which undergoes rotation about the C–N rotor–stator single bond to give Z-2-H33+-right (the platform–substrate hydrazone C=N bond is dynamic under these conditions). Deprotonation of Z-2-H33+-right generates an intermediate that subsequently relaxes through imine bond isomerization and C–N bond rotation into the more stable E-2-right form. Backward transport (bottom pathway, green to blue): protonation of E-2-right with 5 equiv. CF3CO2H gives Z-2-H22+-right, which undergoes rotation about the C–N rotor–stator single bond to generate Z-2-H22+-left (the platform–substrate hydrazone C=N bond is dynamic under these conditions), affording Z-2-left after neutralization. Supplementary Figs 3 and 9 show 1H NMR spectra of these processes.

Compounds

11 compounds View all compounds
  1. Ethyl 2-(5-(3-(3-(pyridin-2-yldisulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
    Compound S5 Ethyl 2-(5-(3-(3-(pyridin-2-yldisulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
  2. (E)-3-mercapto-N'-(4-methoxybenzylidene)propanehydrazide
    Compound S7 (E)-3-mercapto-N'-(4-methoxybenzylidene)propanehydrazide
  3. 3-(3'-Formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-ammonium 2,2,2-trifluoroacetate
    Compound S21 3-(3'-Formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-ammonium 2,2,2-trifluoroacetate
  4. Ethyl (EZ)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-(pyridin-2-yldisulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
    Compound S22 Ethyl (EZ)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-(pyridin-2-yldisulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
  5. Ethyl (EZ)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-((3-(2-((E)-4-methoxybenzylidene)hydrazinyl)-3-oxopropyl)disulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
    Compound S23 Ethyl (EZ)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-((3-(2-((E)-4-methoxybenzylidene)hydrazinyl)-3-oxopropyl)disulfanyl)propoxy)phenyl)pyridin-2-yl)acetate
  6. Ethyl (5Z,19E)-33-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-23-methyl-17-oxo-9-oxa-13,14-dithia-4,5,18,19-tetraaza-3(6,8)-quinolina-7(2,5)-pyridina-1,8(1,3),2(1,4)-tribenzenacycloicosaphane-5,19-diene-6-carboxylate-20-d
    Compound Z-2-left Ethyl (5Z,19E)-33-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-23-methyl-17-oxo-9-oxa-13,14-dithia-4,5,18,19-tetraaza-3(6,8)-quinolina-7(2,5)-pyridina-1,8(1,3),2(1,4)-tribenzenacycloicosaphane-5,19-diene-6-carboxylate-20-d
  7. Ethyl (E)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
    Compound E-1-left Ethyl (E)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
  8. Ethyl (Z)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
    Compound Z-1-left Ethyl (Z)-2-(2-(3-(3'-formyl-3-methyl-[1,1'-biphenyl]-4-yl)-6-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
  9. Ethyl (5E,19E)-36-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-23-methyl-17-oxo-9-oxa-13,14-dithia-4,5,18,19-tetraaza-3(3,8)-quinolina-7(2,5)-pyridina-1,8(1,3),2(1,4)-tribenzenacycloicosaphane-5,19-diene-6-carboxylate
    Compound E-2-right Ethyl (5E,19E)-36-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-23-methyl-17-oxo-9-oxa-13,14-dithia-4,5,18,19-tetraaza-3(3,8)-quinolina-7(2,5)-pyridina-1,8(1,3),2(1,4)-tribenzenacycloicosaphane-5,19-diene-6-carboxylate
  10. Ethyl (E)-2-(2-(6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-3-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
    Compound E-1-right Ethyl (E)-2-(2-(6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-3-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
  11. Ethyl (Z)-2-(2-(6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-3-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate
    Compound Z-1-right Ethyl (Z)-2-(2-(6-(3'-(formyl-d)-3-methyl-[1,1'-biphenyl]-4-yl)-3-(3'-((E)-(2-(3-mercaptopropanoyl)hydrazono)methyl)-3-methyl-[1,1'-biphenyl]-4-yl)quinolin-8-yl)hydrazono)-2-(5-(3-(3-mercaptopropoxy)phenyl)pyridin-2-yl)acetate

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Author information

Affiliations

  1. School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK

    • Salma Kassem,
    • Alan T. L. Lee,
    • David A. Leigh,
    • Augustinas Markevicius &
    • Jordi Solà

Contributions

A.M. and D.A.L. planned the project. S.K., A.T.L.L., A.M. and J.S. carried out the experimental work. D.A.L. directed the research. All authors contributed to the analysis of the results and the writing of the manuscript.

Competing financial interests

The authors declare no competing financial interests.

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