Recognition of Hydrophilic
Molecules by Designed
Small Molecular Receptor
in Water
L I T E R AT U R E S E M I N A R # 2 1 9 / 0 7 / 1 9
Y. K A M I M U R A

J. Mol. Biol., 2009, 385, 1422

1. Introduction
2. Analysis on molecular recognition in water
3. Case examples
Recognition of lysine in water
Recognition of glucose in water

4. Appendix

Introduction
IMolecular recognition
Specific interaction between two or more
molecules by non-covalent bonding.

lIt is one of the most basic phenomenon inorganisms.
lUnderstanding of it is of great importancefor every fields.

Fig1

Fig1 : J. Am. Chem. Soc., 2018, 140, 13466

Introduction
I1967 : Crown ether (C. J. Pdersen)
ISince then, molecular recognition has been
intensively studied.
ICyclic host molecules can be divided into 2
groups; molecules with hydrophobic cavity
and molecules with polar binding site.

Fig1

Fig2

Fig1 : https://www.nobelprize.org/prizes/chemistry/1987/pedersen/biographical/
Fig2 : https://www.chem-station.com/

Introduction
IThere are some reports of molecular
recognition by hydrophobic host.

ISize and shape have more effect thanfunctional group.
IComparing hydrophilic hosts andhydrophobic hosts, the latter arepreferred.

DMSO

DMF

acetonepyrroleDBO cyclopentanone
F.Biedermann et al, J. Am. Chem. Soc., 2012, 134, 15318

Introduction
IMolecular recognition by a molecule with polar binding site is also
reported.

IHowever, affinity is significantly attenuated in water.
8 : 𝐾𝑎 = 1.0×106 M-1 (CHCl3)→

71±8 M-1 (H2O)

Guest molecule
Host molecule
C. Allott et al, Chem. Commun., 1998, 2449

1. Introduction
2. Analysis on molecular recognition in water
3. Case examples
Recognition of lysine in water
Recognition of glucose in water

4. Appendix

Molecular recognition in water
IBiomolecules can recognizehydrophilic molecules in water.
IThey have hydrophilic recognition site
in its hydrophobic cavity.
IArtificial mimic of it was conceived.

B. J. Shorthill et al., J. Am. Chem. Soc., 2004, 126, 12732

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Molecular recognition in water
IHow hydrophobic effect works inthe recognition of hydrophilicmolecules?
IIs CH-π interaction involved?

IHow can the host distinguishbetween these similar molecules?
In CHCl3
𝐾𝑎 = 102

In water
𝐾𝑎 = 104

Selective

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Molecular recognition in water
IAuthors analyzed the complexation process, using 44 hydrophilic
small molecules as hosts.

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

JACS, 2018, 140, 13466

AffinityPCA
IDipole moment has medium
degree of negative correlation withthe binding affinity.
ILogP, surface area, polarizability,
volume have weak positivecorrelation.
IHowever none of the parameters
is sufficient for the explanation of
the affinity.
G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

JACS, 2018, 140, 13466

Dipole moment

JACS, 2018, 140, 13466

Effect of hydrophobic group

JACS, 2018, 140, 13466

Difference of Ka between similar molecules

Effect of solvent
H2OCHCl3

IMDO

22000±730 M-1→

41±1 M-1

I1,4-dioxane

14000±1500 M-1→

62±1 M-1

IPyrazine

2200±38 M-1→

11±1 M-1

IEA

3400±24 M-1

→

ND

IDMC

2300±110 M-1→

ND

IBenzene

1300±190 M-1→

ND

H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Effect of solvent
INormally, great decrease in affinity is observed when the solvent ischanged from chloroform to water.

IWell-definedness of the cavity seems to be important.

Guest molecule
Host molecule
C. Allott et al, Chem. Commun., 1998, 2449

Hydrophobic effectIAverage number of H-Bonding of cavity
water is less then bulk water(3.6).

IExclusion of cavity water (High energywater) is favorable in terms of enthalpygain.

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Hydrogen bonding
IBlue: H-bonding x1
IYellow: NH-π

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Hydrogen bonding
IRed: H-bonding x2

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Hydrogen bonding
IMeasured if host-gest hydrogenbond compensate for desolvationenergy of the host.

NMR titration

IComplexation with Pyrazine, 1,4diozane, MDO is favorable.
IComplexation with DMC, EA,
benzene is disfavorable.
IComplexation with the latermolecules is mainly driven by theexclusion of the cavity water.
G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

Entropy and enthalpyIWeak entropy-enthalpy compensation
was observed.

IRoughly speaking, enthalpy but not
entropy is the major driving force forthe complexation.

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

The criteria for good guest molecules
1.Good guest should be able to form hydrogen bondwith the host.
2.Good guest should not have additional hydrogenbond acceptor.
3. Good guest should have large enoughhydrophobic group in order to expel the cavitywaters.

>

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

More strong affinity?
IIt is expected that if the guest
could expel more water, theaffinity will be stronger.
ICombining complexation
driven by hydrophobic effectand specific binding by Hbonding, interaction will bestronger and more selective.

G Huang et al, J. Am. Chem. Soc., 2016, 138, 14550.
H. Yao, et al., J. Am. Chem. Soc., 2018, 140, 13466

General tendency
IComplexation of a hydrophobic cavity and the guest moleculetends to be driven by a gain of enthalpy.

F.Biedermann., J. Am. Chem. Soc., 2012,134,15318

1. Introduction
2. Analysis on molecular recognition in water
3. Case examples
Recognition of glucose in water
Recognition of lysine in water

4. Appendix

Recognition of glucose
ISugar is a typical hydrophilic molecule.
ISugar is crucial element for organisms.

β-glucose

IRecognition of sugar is challenging not only
for synthetic hosts, but also for biomolecules.
IPeriplasmic GBP, which has the highest
affinity, bind to glucose in 5×106 M-1 affinity.
IOther typical lectins have weaker affinity.
glucose/galactose binding protein (E.coli)

PDB : 2HPH
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
IIn 1998, A.P.Davis and coworkers synthesized synthetic glucose
receptor, mimicking the binding site of E.coli periplasmic GBP.

A.P.Davis et al., Angew. Chem. Int. Ed., 1998,37, 2270
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
IH-bond between the N-H proton and the O atom of the glucose isresponsible for the recognition.

A.P.Davis et al., Angew. Chem. Int. Ed., 1998,37, 2270
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
IThe affinity was maintained evenin the presence of 8% of MeOH.
In CHCl3

In CHCl3(8% MeOH)

A.P.Davis et al., Angew. Chem. Int. Ed., 1998,37, 2270

Recognition of glucose
IIn H2O, glucose, binding constant was 9 M-1
IThe affinity was depleted by the addition oforganic solvents.
IThe effect was in order of

MeOH < DMSO < MeCN
IInvolvement of hydrophobic effect issuggested.

E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
INew host molecule for cellobiose wassynthesized by Davis’s group in 2007.

IThe new molecule maintained the binding
affinity even in the pure water.
IIn D2O: 600 M-1

Y.Ferrand et al., Science, 2007, 318, 619
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
IMethyl β-D-cellobioside had the strongest
affinity.
ID-Xylobiose which has very similar
structure had the affinity of 250.
IThe other substrate had very weak affinity.

Y.Ferrand et al., Science, 2007, 318, 619
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
IThe affinity was depleted by theaddition of organic solvents.

IThe effect was in order ofMeOH < DMSO < MeCN

IThe sensitivity for organic solvent
was stronger than the previous hostmolecule.
IInvolvement of hydrophobic effect issuggested.
Y.Ferrand et al., Science, 2007, 318, 619
E. Klein et al, Angew. Chem. Int. Ed., 2008, 47, 2693

Recognition of glucose
ILatest host molecule could bind glucose in a biomoleculecompatible affinity and selectivity. (In H2O : 1.8×104 M-1 )IComparing with the first molecule, the well-definedness of thecavity seems to be improved.

R.A.Tromans, Nat. Chem., 2019, 11, 52

Introduction
IMost other saccharides bound approximately 100 times weaker.
c.f. : lectin ConcanacalinA : 500 M-1 , also bind to mannose.

Nat. Chem., 2019, 11, 52

1. Introduction
2. Analysis on molecular recognition in water
3. Case examples
Recognition of glucose in water
Recognition of lysine in water

4. Appendix

Recognition of Lysine in water
I4-Sulfocalix[4]arene is used for the recognition ofLysine.

IThey form 1:1 complex in water.
IKD=600

IMethylated lysine binds stronger.

Sam van Dun et al., J. Am. Chem. Soc., 2017, 139, 13960
M. Selkti et al., Chem. Commun., 2000, 161

Recognition of Lysine in water
IAromatic AA and Acidic AA around the Lys binding site is conservedin Lysyl-tRNA synthetase.

Cryptosporidium parvam

E.coliHuman
PDB : 3BJU, 1BBU, 6HCW

Summery
IUnderstanding the molecular recognition of hydrophilic moleculesin water is important for many fields.

I Combining the complexation by the hydrophobic effect and therecognition by H-bonding is the basic strategy for the molecular
recognition in water.
IThis is also seen in biomolecules.

1. Introduction
2. Analysis on molecular recognition in water
3. Case examples
Recognition of glucose in water
Recognition of lysine in water

4. Appendix

Appendix : ITC

https://www.malvernpanalytical.com/jp/products/technology/microcalorimetry/isothermal-titration-calorimetry