Synthesis and inhibitory studies of phosphonic acid analogues of homophenylalanine and phenylalanine towards alanyl aminopeptidases

Article abstract of DOI:10.3390/biom10091319

A library of novel phosphonic acid analogues of homophenylalanine and phenylalanine, containing fluorine and bromine atoms in the phenyl ring, have been synthesized. Their inhibitory properties against two important alanine aminopeptidases, of human (hAPN, CD13) and porcine (pAPN) origin, were evaluated. Enzymatic studies and comparison with literature data indicated the higher inhibitory potential of the homophenylalanine over phenylalanine derivatives towards both enzymes. Their inhibition constants were in the submicromolar range for hAPN and the micromolar range for pAPN, with 1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound 15c) being one of the best low-molecular inhibitors of both enzymes. To the best of our knowledge, P1 homophenylalanine analogues are the most active inhibitors of the APN among phosphonic and phosphinic derivatives described in the literature. Therefore, they constitute interesting building blocks for the further design of chemically more complex inhibitors. Based on molecular modeling simulations and SAR (structure-activity relationship) analysis, the optimal architecture of enzyme-inhibitor complexes for hAPN and pAPN were determined.

Full text of DOI:10.3390/biom10091319

biomolecules
Article
Synthesis and Inhibitory Studies of Phosphonic Acid
Analogues of Homophenylalanine and Phenylalanine
towards Alanyl Aminopeptidases
Weronika Wanat 1,
*
, Michał Talma 1 , Błaz˙ej Dziuk 2,3 and Paweł Kafarski 1
1
Department of Bioorganic Chemistry, Wrocław University of Science and Technology,
Wybrzez˙e Wyspian´skiego 27, 50-370 Wrocław, Poland; michal.talma@pwr.edu.pl (M.T.);
pawel.kafarski@pwr.edu.pl (P.K.)
Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland; blazej.dziuk@pwr.edu.pl
Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzez˙e Wyspian´skiego 27,
50-370 Wrocław, Poland
2
3
*
Correspondence: weronika.wanat@pwr.edu.pl; Tel.: +48-71-320-37-17
ꢀꢁꢂꢀꢃꢄꢅꢆꢇ
ꢀꢁꢂꢃꢄꢅꢆ
Received: 19 August 2020; Accepted: 12 September 2020; Published: 14 September 2020
Abstract: A library of novel phosphonic acid analogues of homophenylalanine and phenylalanine,
containing fluorine and bromine atoms in the phenyl ring, have been synthesized. Their inhibitory
properties against two important alanine aminopeptidases, of human (hAPN, CD13) and porcine
(pAPN) origin, were evaluated. Enzymatic studies and comparison with literature data indicated
the higher inhibitory potential of the homophenylalanine over phenylalanine derivatives towards
both enzymes. Their inhibition constants were in the submicromolar range for hAPN and the
micromolar range for pAPN, with 1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound
15c) being one of the best low-molecular inhibitors of both enzymes. To the best of our knowledge,
P1 homophenylalanine analogues are the most active inhibitors of the APN among phosphonic and
phosphinic derivatives described in the literature. Therefore, they constitute interesting building blocks
for the further design of chemically more complex inhibitors. Based on molecular modeling simulations
and SAR (structure-activity relationship) analysis, the optimal architecture of enzyme-inhibitor
complexes for hAPN and pAPN were determined.
Keywords: human and porcine alanine aminopeptidase; phosphonic acid inhibitors; fluorine and
bromine substitution; computer-aided simulations
1. Introduction
Zinc-dependent mammalian neutral aminopeptidases (APN/CD13) are considered pivotal targets
for treatment diseases, characterized by their overexpression. Accordingly, APNs represent the most
widely scanning transmembrane proteases belonging to M1 aminopeptidases family, with capacity to
control physiological processes based on the cleavage of neutral amino acid residues from peptide
and protein substrates. Dysregulation of APNs expression is revealed as a disorder of metabolic
pathways leading to the development of the pathologies related mainly with tumor-cell angiogenesis
and metastasis, inflammatory diseases or neuropeptides dysfunctions [1–3]. It is worth to mention
about their well-known function as a viral receptor, including human coronaviruses, where the CD13
amino acid fragment has been defined as a key for HCoV-229E infection [4].
The potential to affect many metabolic pathways, leading to incurable diseases, prompted the
search for new-targeted therapies with the manipulation of APNs activities. Except for the commercially
applied natural inhibitor of APN-bestatin, numerous scientific reports describe compounds with
inhibitory properties towards aminopeptidases, based on the aminophosphonate scaffold [5–8].
Biomolecules 2020, 10, 1319; doi:10.3390/biom10091319
www.mdpi.com/journal/biomolecules

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However, none of them were introduced to clinical studies yet and thus the design of new potent and
selective molecules is desirable.
In this paper we describe series of phosphonic acid analogues of homophenylalanine and
phenylalanine fluorinated and brominated in aromatic ring. We evaluated their inhibitory activities
towards two aminopeptidases: human (hAPN, CD13) and porcine (pAPN). Since the sequence
identity of the two enzymes is 79.3% and sequence similarity 89.4%, the porcine enzyme is often
used as a model one in studies on aminopeptidase N inhibitors development. On the other hand,
our previous studies [9,10] indicated that low-molecular inhibitors of these enzymes could be bound
substantially differently. Therefore, we undertook studies, which are a continuation of previous works
and complements the library of the phosphonic acid analogues of phenylalanine, which phenyl group
is substituted with halogens. Development of the new targeted compounds is in-online with scanning
low-molecular sets of compounds of similar structure as the first step to rational search for new building
blocks for potential drugs. Furthermore, this method is enforced by computer-aided studies, by means
molecular docking simulations. The crystallographic structures of the pAPN and hAPN have been
characterized [3,11] and thus the molecular modeling was used for better understanding of structural
preferences for effective inhibition.
2. Materials and Methods
2.1. Chemistry
All chemicals were purchased from commercial suppliers (Sigma Aldrich, Poznan, Poland;
Trimen Chemicals, Lodz, Poland; POCh, Gliwice, Poland; ChemPur, Piekary Slaskie, Poland;
Archem, Kamieniec Wroclawski, Poland, Acros Organics, Geel, Belgium, Alfa Aesar, Lancashire,
United Kingdom), were of analytical grade and were used without further purification. Column
chromatography was performed using silica gel 60 (70–230 mesh). Analytical thin-layer chromatography
was carried out on Merck SilicaGel 60 F254 (Darmstadt, Germany) and for the visualization and detection
of the compounds’ UV light at 254 nm, 2,4-dinitrophenylhydrazine and potassium permanganate
were used. The 1H-, 13C-, 19F- and 31P-NMR spectra were recorded on 400YH (JEOL, Tokyo, Japan)
spectrometer at 295 K operating at 400MHz (1H), 101MHz (13C), 376MHz (19F) and 162MHz (31P).
Samples were diluted in chloroform-d, methanol-d4 and in the mixture of D2O + NaOD (99.8% at %D),
with all solvents being supplied by ARMAR AG (Dottingen, Switzerland). Chemical shifts are reported
relative to internal TMS (1H NMR), CFCl3 (19F NMR) and 85% H3PO4 (31P NMR) standards and are
given in parts per million (ppm), while coupling constant are reported in Hz. 19F NMR spectra were
measured without decoupling with protons. Mass spectra were recorded at the Faculty of Chemistry,
Wroclaw University of Science and Technology by using a Waters LCT Premier XE mass spectrometer
(electrospray ionization, ESI) (Waters, Milford, MA, USA). Melting points were determined on an
SRS Melting Point Apparatus OptiMelt MPA 100 (Stanford Research Systems, Sunnyvale, CA, USA)
and were reported uncorrected. All compounds were an equimolar mixture of R and S enantiomers.
Analytical quality control of the final compounds was performed by HPLC (Schimadzu, Mundelein,
IL, USA) and was at least above 95%. A reverse phase column (Kinetex 100A, C18, 5
µ
m, 150 mm
×
4.6 mm) was used as combination with the following separation conditions: 99.95% H2O, 0.05% TFA
(solvent A) and 99.95% CH3CN, 0.05% TFA (solvent B); 0.0–4.0 min, 0% B; 4.1–30.0 min 70% B. The
flow rate was 1 mL/min and the UV signal was recorded at 220 nm and 254 nm.
2.2. Synthesis of Substituted Methyl Phenylpropanoates/Methyl Phenylacetates (Compounds 2 and 8)
To the substituted phenylpropionic/phenylacetic acid (1 equiv, 0.01 mol) was added 50 mL of
MeOH and the mixture was cooled to 0 ◦C. Then, chlorotrimethylsilane (4 equiv, 0.04 mol) was added
dropwise with stirring. After the completion of addition, the reaction mixture was slowly heated to
room temperature and the resulting solution was stirred at room temperature for 6–12 h. Progress of
the reaction was monitored by TLC chromatography (cyclohexane/ethyl acetate 4:1, v/v). The resulting

Biomolecules 2020, 10, 1319
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mixture was concentrated on a rotary evaporator to give the respective acid methyl ester, which was
used without further purification. The structural analysis of the representative compound 2b is showed
below. The characterization data of the compounds 2c–2h and 8a–8e are given in Supplementary
Material (Section S1).
3-(2-Fluorophenyl)propionic Acid Methyl Ester (2b)
Yellow oil, yield 100%; 1H NMR (400 MHz, CDCl3),
= 18.6, 8.9, 4.8 Hz, 2H, 2xCHar), 3.66 (s, 3H, OCH3), 2.97 (t, J = 7.8 Hz, 2H, CH2), 2.63 (t, J = 7.8 Hz,
2H, CH2) ppm; 13C NMR (101 MHz, CDCl3),
= 173.22 (s, OOCH3), 161.24 (d, J = 245.3 Hz, Car-F),
130.67 (d, J = 4.8 Hz, Car), 128.19 (d, J = 8.1 Hz, Car), 127.38 (d, J = 15.6 Hz, Car), 124.14 (d, J = 3.6 Hz,
δ = 7.22–7.14 (m, 2H, 2xCHar), 7.02 (ddd, J
δ
C
Car), 115.37 (d, J = 21.9 Hz, Car), 51.72 (s, COOCH3), 34.27 (d, J = 1.5Hz, CH2), 24.67 (d, J = 2.8 Hz,
CH2) ppm; 19F NMR (376 MHz, CDCl3), δ = −118.45–−118.52 (m, 1F) ppm [12–14].
2.3. Synthesis of Substituted Phenylpropanols/Ethanols (Compounds 3 and 9)
Sodium borohydride (7 equiv, 0.07 mol) was suspended in THF (35 mL) and the respective
methyl ester in 5 mL THF was added (1 equiv, 0.01 mol). The resulting mixture was heated to reflux
temperature and stirred for 15 min. Then, methanol was slowly added (15 mL) and effervescence was
observed. After the completion of addition, the reaction was stirred in reflux for 20–30 min. Progress
of the reaction was monitored by TLC chromatography (cyclohexane/ethyl acetate 4:1, v/v). After the
reaction, solvent was removed by rotary evaporation and white paste left in the flask was dissolved in
50 mL of 1M HCl and the solution stirred overnight. The resulting liquid was neutralized by addition
of 2M NaOH and then extracted with CH2Cl2 and organic layer was dried over Na2SO4. Filtration and
concentration of organic residues gives the corresponding alcohol, which was used to the next step
without further purification. The structural analysis of the representative compound 3b is showed
below. The characterization data of the compounds 3c–3h and 9a–9e are given in Supplementary
Material (Section S2).
3-(2-Fluorophenyl)propanol (3b)
Colorless oil, yield 100%; 1H NMR (400 MHz, CDCl3),
CHar), 7.09–6.96 (m, 2H, 2xCHar), 3.66 (t, J = 6.4 Hz, 2H, CH2), 2.73 (t, 2H, J = 7.6 Hz, CH2), 1.87 (ddt, J
= 7.6, 6.4, 3.8 Hz, 2H, CH2), 1.53 (s, 1H, OH) ppm; 13C NMR (101 MHz, CDCl3),
= 161.29 (d, J = 244.4
Hz, Car-F), 130.77 (d, J = 5.1 Hz, Car), 128.62 (d, J = 16.0 Hz, Car), 127.71 (d, J = 8.1 Hz, Car), 124.08 (d, J
δ
= 7.17 (tdd, J = 7.4, 6.4, 1.6 Hz, 2H, 2
×
δ
= 3.5 Hz, Car), 115.30 (d, J = 22.3 Hz, Car), 62.22 (s, CH2OH), 33.02 (d, J = 1.1 Hz, CH2-Car), 25.34 (d, J =
2.6 Hz, CH2) ppm; 19F NMR (376 MHz, CDCl3), δ = −118.75–−118.88 (m, 1F) ppm [12,15,16].
2.4. Synthesis of Substituted Phenylpropionaldehydes/Phenylacetaldehydes by Using Pyridinium
Chlorochromate (PCC) (Compounds 4 and 10)
The substituted phenylpropanol or phenylethanol (1 equiv, 0.01 mol) was dissolved in 15 mL
of 99.8% CH2Cl2 and 1.5 g of SiO2 was added. After 10 min of stirring at room temperature
pyridinium chlorochromate-PCC (1.5 equiv, 0.015 mol) was added in one-portion. The mixture was
intensively stirred for 30–60 min and the progress of the reaction was monitored by TLC chromatography
(cyclohexane/ethyl acetate 4:1, v/v). Additionally, the aldehyde formation was observed by visualization
of the TLC plate with 2,4-dinitrophenylhydrazine (2,4-DNPH) indicator. After consumption of the
substrate 50 mL of diethyl ether was added and the supernatant was filtrated through a silica gel with
using diethyl ether as eluent. The solvents were removed under reduced pressure and the reaction
mixture (yellow oil) was purified on a silica column (cyclohexane/ethyl acetate 4:1, v/v) resulting
in the desired aldehyde as colorless or yellowish oil with a specific odor. The structural analysis
of the representative compound 4d and ester 5d (1H, 13C and 19F NMR spectra attached in Figure
S1) are showed below. The characterization data of the compounds 4e–4h, 10a and 10b are given in
Supplementary Material (Section S3).

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2.4.1. 3-(4-Fluorophenyl)propanal (4d)
Colorless oil, yield 63%; 1H NMR (400 MHz, CDCl3),
δ
= 9.80 (t, J = 1.3 Hz, 1H, CHO), 7.15 (ddd, J
= 8.3, 5.4, 0.5 Hz, 2H, 2xCHar), 6.97 (t, J = 8.8 Hz, 2H, 2xCHar), 2.92 (t, J = 7.7 Hz, 2H, CH2), 2.67–2.63
(m, 2H, CH2) ppm; 13C NMR (101 MHz, CDCl3),
= 178.90 (s, CHO), 161.63 (d, J = 244.2 Hz, Car-F),
135.82 (d, J = 3.3 Hz, Car), 129.80 (d, J = 7.9 Hz, 2
Hz,
H2-Car), 29.83 (d, J = 0.6 Hz, CH2) ppm; 19F NMR (376 MHz, CDCl3),
δ
×
Car), 115.42 (d, J = 21.2 Hz, 2
×
−
Car), 35.74 (d, J = 1.1
116.71 (tt, J = 8.7, 5.3
C
δ
=
Hz, 1F) ppm [17,18].
2.4.2. 3-(4-Fluorophenyl)propyl-3-(4-Fluorophenyl)propionate (5d)
Colorless oil, yield 25%; 1H NMR (400 MHz, CDCl3),
(m, 2H, 2xCHar), 6.99–6.92 (m, 4H, 4xCHar), 4.06 (t, J = 6.5 Hz, 2H, CH2), 2.91 (t, J = 7.7 Hz, 2H, CH2),
2.62–2.57 (m, 4H, 2xCH2), 1.92–1.84 (m, 2H, CH2) ppm; 13C NMR (101 MHz, CDCl3),
= 172.82 (s,
OOCH2), 161.50 (dd, J = 243.9, 14.7 Hz, 2 Car-F), 136.48 (dd, J = 59.9, 3.2 Hz, 2 Car), 129.79 (dd, J
Car), 63.75 (s, CH2), 36.01 (d, J = 0.9 Hz, CH2),
δ = 7.18–7.12 (m, 2H, 2xCHar), 7.11–7.05
δ
C
×
×
= 7.8, 2.7 Hz, 4
×
Car), 115.30 (dd, J = 21.1, 8.4 Hz, 4
×
31.39 (s, CH2), 30.34 (s, CH2), 30.23 (s, CH2) ppm; 19F NMR (376 MHz, CDCl3),
δ
= −116.88 (tt, J = 8.7,
5.3 Hz, 1F), -117.31 (dq, J = 8.9, 5.5 Hz, 1F) ppm.
2.5. Synthesis of Substituted Phenylacetaldehyde/Phenylpropionaldehyde by Using Dess-Martin Periodinane
(DMP) (Compounds 4 and 10)
The substituted phenylpropanal or phenylethanal (1 equiv, 0.01 mol) dissolved in 5 mL of dry
CH2Cl2 was added in one portion to the solution of Dess-Martin periodinane (1.2 equiv, 0.012 mol)
in dry CH2Cl2 (20 mL). The mixture was intensively stirred at room temperature and under argon
atmosphere for 10–15 min. Upon completion of the oxidation 20 mL of dichloromethane was added and
the reaction mixture was extracted with a solution of saturated sodium bicarbonate. The organic phase
was dried under sodium sulphate and evaporated under vacuum. The oily residue was purified by
column chromatography (cyclohexane/ethyl acetate 3:1, v/v) yielding the desired aldehyde as colorless
or yellowish oil with a characteristic odor. The characterization data of the compounds 4b, 4c, 10c–10e
have been presented attached in Supplementary Material (Section S4).
2.6. Diphenyl 1-{[(N-Benzyloxy)carbonyl]amino}alkylphosphonates (Compounds 6 and 13)
To the mixture of benzyl carbamate (1 equiv) and triphenyl phosphite (1 equiv) dissolved in
glacial acetic acid an aldehyde (1.1 equiv) was added slowly dropwise. Then mixture refluxed for
1-2h. The solvent was r◦emoved under reduced pressure and the oily residues were dissolved in
CH3OH and left at 20 C for crystallization or dissolved in acetone/hexane mixture and left at 4
−
◦C. White solid was filtered and washed with frozen methanol. When the ester did not crystallize
purification by column chromatography (cyclohexane/ethyl acetate 3:1, v/v) was indispensable. The
final ester was recrystallized from chloroform or dichloromethane and methanol (in ratio 1:4, v/v). The
structural analysis of the representative compound 6a is showed below. The characterization data of
the compounds 6b–6h and 13a–13e are presented in Supplementary Material (Section S5).
Compound 6a was prepared from commercially available aldehyde precursor.
Diphenyl 1-{[(N-benzyloxy)carbonyl]amino}-3-phenylpropylphosphonate (6a)
White solid, m. p. 115–116 ◦C; yield 60%; 1H NMR (400 MHz, CDCl3),
δ = 7.36–7.04 (m, 20H,
CHar), 5.17–5.09 (m, 3H, NH + CH2OC), 4.58–4.46 (m, 1H, CHP), 2.87 (ddd, J = 14.5, 9.7, 5.1 Hz, 1H,
CH2), 2.79–2.69 (br m, 1H, CH2), 2.43–2.30 (br m, 1H, CH2), 2.14–2.00 (br m, 1H, CH2) ppm; 13C NMR
(101 MHz, CDCl3),
Car), 136.13 (s, Car), 129.86 (d, J = 10.9 Hz, 4
128.41 (s, 2 Car), 128.29 (s, 2 Car), 126.36 (s, Car), 125.47 (d, J = 14.4 Hz, 2
Hz, 2 Car), 120.47 (d, J = 4.2 Hz, 2 Car), 67.53 (s, CH2Ph), 48.24 (d, J = 157.7 Hz, CHP), 32.06 (dd, J =
δ
= 155.95 (d, J = 6.0 Hz, CONH), 150.17 (dd, J = 23.0, 9.9 Hz, 2
Car), 128.66 (s, Car), 128.64 (s, 2 Car), 128.57 (s, 2
Car), 120.68 (d, J = 4.1
×
Car), 140.51 (s,
×
×
×
Car),
×
×
×
×
×

Biomolecules 2020, 10, 1319
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9.0, 4.7 Hz, CH2
C
H2CHP) ppm; 31P NMR (162 MHz, CDCl3),
δ
= 17.87 (s, 1P, trans), 17.57 (s, 1P, cis)
ppm; HRMS (ESI-MS) m/z [MH]+ calculated for C29H28NO5P: 502.1783, found: 502.1772; [M + Na]+
calculated for C29H28NO5PNa: 524.1603, found: 524.1619 [19,20].
2.7. Transesterification of Diphenyl 1-{[(N-Benzyloxy)carbonyl]amino}alkylphosphonates with Methanol
(Compounds 14 and 16)
To solution of the diphenyl 1-(N-benzyloxycarbonyloamino)alkylphosphonate (1 equiv, 0.002 mol)
dissolved in methanol (20–30 mL) anhydrous KF was added (10 equiv, 0.02 mol). To the stirred mixture
the 18-crown-6 was added in catalytic amount (~20 mg). Then, the mixture was refluxed 30 min. The
progress of the reaction was controlled by means of TLC (ethyl acetate/cyclohexane, 3:1, v/v). After
consumption of all the substrate the solvent was evaporated under reduced pressure and the resulting
solid was suspended in water and extracted with CH2Cl2 (3
under sodium sulphate and evaporated under vacuum. The obtained oil was purified by column
×
40 mL). The organic layer was dried
chromatography (ethyl acetate/cyclohexane, 3:1, v/v). The structural analysis of the representative
compound 14b is showed below. The characterization data of the compounds 14c, 14f, 14h
, 16d and
16e are given in Supplementary Material (Section S6).
Dimethyl 1-{[(N-benzyloxy)carbonyl]amino}-3-(2-fluorophenyl)propylphosphonate (14b)
1
White solid, m. p. 101–103 ◦C; yield 76%; H NMR (400 MHz, CDCl3),
δ
= 7.39–7.29 (m, 5H,
5xCHar), 7.16 (dd, J = 13.7, 6.9 Hz, 2H, 2xCHar), 7.06–6.94 (m, 2H, 2
CH2OC, trans), 5.13 (d, J = 28.9 Hz, 2H, CH2OC, cis), 4.19–4.07 (m, 1H, CHP, trans), 3.71 (dd, J = 12.3,
×
CHar), 5.13 (d, J = 4.3 Hz, 2H,
10.7 Hz, 6H, 2xCH3), 2.89–2.81 (m, 1H, CH2), 2.70–2.61 (m, 1H, CH2), 2.20–2.09 (m, 1H, CH2), 1.93–1.80
(m, 1H, CH2) ppm; 13C NMR (101 MHz, CDCl3),
δ
= 161.17 (d, J = 245.0 Hz, Car-F), 156.11 (d, J = 5.1
Hz, CONH), 136.29 (s, Car), 130.84 (d, J = 4.8 Hz, Car), 128.63 (s, 2 Car), 128.33 (s, 2 Car), 128.15
(d, J = 1.3 Hz, 2 Car), 124.17 (d, J = 3.6 Hz, Car), 115.38 (d, J = 21.9 Hz, Car), 113.18 (d, J = 21.0 Hz,
Car), 67.36 (s, H2Ph), 53.33 (d, J = 7.1 Hz, OCH3), 53.23 (d, J = 6.5 Hz, OCH3), 47.09 (d, J = 156.2 Hz,
HP), 30.28 (d, J = 2.5 Hz, H2CH2CHP), 25.70 (dd, J = 13.9, 2.4 Hz, CH2
H2CHP) ppm; 19F NMR
118.28–
118.37 (m, F-H, cis), -118.44—118.55 (m, F-H, trans) ppm; 31P NMR
×
×
×
C
C
C
C
(376 MHz, CDCl3),
(162 MHz, CDCl3),
δ
=
−
−
δ
= 27.43 (s, 1P, trans), 26.94 (s, 1P, cis) ppm; HRMS (ESI-MS) m/z [MH]+ calculated
for C19H23FNO5P: 396.1376, found: 396.1374; [M + Na]+ calculated for C19H23FNO5PNa: 418.1196,
found: 418.1154.
2.8. Hydrolysis of Diphenyl and Dimethyl 1-{[(N-Benzyloxy)carbonyl]amino}alkylphosphonates (Compounds
15 and 17)
Diphenyl or dimethyl Cbz-protected 1-aminoalkylphosphonate esters were refluxed in 10 M
hydrochloric acid in acetic acid by 12–24 h (F
) or in 12 M HCl by 6-8 h (F*), respectively. After
evaporation of the volatile products, the obtained white solids were dissolved in EtOH and left for
crystallization at room temperature. The solid products were collected by filtration and recrystallized
from the hot mixture of H2O/EtOH. The characterization data of the final compounds 15a–15h and
17a–17e are showed below. The 1H NMR, 1H-31P HMQC and 1H-13C HMQC NMR spectra of the
representative final compound 15d were attached to Supplementary Material (Figure S2).
2.8.1. 1-Amino-3-Phenylpropylphosphonic Acid (15a)
◦
1
White solid, m. p. 296–298 C; yield 72% from diphenyl ester; H NMR (400 MHz, D2O +
NaOD), = 7.21–7.14 (m, 4H, 4xCHar), 7.10–7.05 (m, 1H, CHar), 2.71 (ddd, J = 13.6, 10.6, 4.9 Hz, 1H,
CH2CH2CHP), 2.46 (ddd, J = 13.5, 10.2, 6.7 Hz, 1H, CH2CH2CHP), 2.36 (td, J = 10.6, 3.1 Hz, 1H, CHP),
1.93–1.81 (m, 1H, CH2CH2CHP), 1.43 (dtdd, J = 13.9, 10.3, 6.7, 4.9 Hz, 1H, CH2C
2CHP) ppm; 31
NMR (162 MHz, D2O + NaOD),
= 20.87 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for
C9H14NO3P: 216.0790, found: 216.0783; HPLC- retention time: 10.26 min [21,22].
δ
H
P
δ

Biomolecules 2020, 10, 1319
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2.8.2. 1-Amino-3-(2-Fluorophenyl)propylphosphonic Acid (15b)
White solid, m. p. 292–294 ◦C; yield 53% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
= 7.21 (td, J = 7.7, 1.3 Hz, 1H, CHar), 7.10 (ddd, J = 13.2, 7.4, 1.6 Hz, 1H, CHar), 6.97 (ddd, J = 18.7, 11.9,
δ
7.9 Hz, 2H, 2
2.40 (td, J = 10.9, 2.9 Hz, CHP), 1.96–1.82 (m, 1H, CH2CH2CHP), 1.52–1.39 (m, 1H, CH2CH2CHP) ppm;
13C NMR (101 MHz, D2O + NaOD),
= 160.93 (d, J = 242.5 Hz, Car-F), 130.89 (d, J = 5.3 Hz, Car),
×
CHar), 2.82–2.72 (m, 1H, CH2CH2CHP), 2.52 (ddd, J = 13.8, 10.2, 6.7 Hz, CH2CH2CHP),
δ
129.52 (d, J = 16.1 Hz, Car), 127.71 (d, J = 8.2 Hz, Car), 124.30 (d, J = 3.4 Hz, Car), 115.18 (d, J = 22.1
Hz, Car), 50.01 (d, J = 138.2 Hz, CHP), 32.58 (s, CH2), 26.21 (dd, J = 13.6, 2.2 Hz, CH2) ppm; 19F NMR
(376 MHz, D2O + NaOD),
δ
=
−
119.31– δ =
119.40 (m, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
−
21.61 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for C9H13FNO3P: 234.0695, found: 234.0687;
HPLC-retention time: 11.12 min.
2.8.3. 1-Amino-3-(3-Fluorophenyl)propylphosphonic Acid (15c)
White solid, m. p. 292–294 ◦C; yield 55% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.17 (td, J = 7.9, 6.4 Hz, 1H, CHar), 6.98–6.88 (m, 2H, 2xCHar), 6.80 (td, J = 8.8, 2.6 Hz, 1H, CHar),
2.73 (ddd, J = 14.1, 10.7, 4.9 Hz, 1H, CH2CH2CHP), 2.49 (ddd, J = 13.7, 10.2, 6.6 Hz, 1H, CH2CH2CHP),
2.37 (td, J = 10.7, 3.1 Hz, 1H, CHP), 1.95–1.82 (m, 1H, CH2CH2CHP), 1.52–1.39 (m, 1H, CH2CH2CHP)
ppm; 13C NMR (101 MHz, D2O + NaOD),
δ = 162.70 (d, J = 242.6 Hz, Car-F), 145.82 (d, J = 7.3 Hz,
Car), 130.05 (d, J = 8.5 Hz, Car), 124.37 (d, J = 2.5 Hz, Car), 115.18 (d, J = 20.7 Hz, Car), 112.45 (d, J =
21.1 Hz, Car), 49.79 (d, J = 138.1 Hz, CHP), 33.69 (s, CH2), 32.76 (d, J = 12.9 Hz, CH2) ppm; 19F NMR
(376 MHz, D2O + NaOD),
δ
=
−
114.38– δ =
114.47 (m, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
−
21.68 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for C9H13FNO3P: 234.0695, found: 234.0691;
HPLC-retention time: 12.00 min.
2.8.4. 1-Amino-3-(4-Fluorophenyl)propylphosphonic Acid (15d)
◦
1
White solid, m. p. 303–305 C; yield 86% from diphenyl ester; H NMR (400 MHz, D2O +
NaOD), = 7.21–7.14 (m, 2H, 2xCHar), 6.97–6.90 (m, 2H, 2xCHar), 2.78–2.69 (m, 1H, CH2CH2CHP),
2.49 (ddd, J = 13.7, 10.2, 6.7 Hz, 1H, CH2CH2CHP), 2.40 (td, J = 10.7, 3.1 Hz, 1H, CHP), 1.95–1.84 (m,
1H, CH2CH2CHP), 1.53–1.41 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
160.93 (d, J = 240.5 Hz, Car-F), 138.82 (d, J = 2.8 Hz, Car), 130.04 (d, J = 7.9 Hz, 2 Car), 115.01 (d, J =
21.0 Hz, 2
Car), 49.80 (d, J = 138.3 Hz, CHP), 34.06 (s, CH2), 32.17 (d, J = 12.9 Hz, CH2) ppm; 19F NMR
(376 MHz, D2O + NaOD),
δ
δ
=
×
×
δ
=
−
118.21– δ =
118.30 (m, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
21.77 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for C9H13FNO3P: 234.0695, found: 234.0689;
−
HPLC-retention time: 11.97 min.
2.8.5. 1-Amino-3-(2,4-Difluorophenyl)propylphosphonic Acid (15e)
White solid, m. p. 304–306 ◦C; yield 74% from diphenyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.19 (dd, J = 15.3, 8.4 Hz, 1H, CHar), 6.78 (t, J = 8.7 Hz, 2H, 2xCHar), 2.78–2.69 (m, 1H, CH2CH2CHP),
2.55–2.44 (m, 1H, CH2CH2CHP), 2.40 (td, J = 10.9, 3.0 Hz, 1H, CHP), 1.95–1.83 (m, 1H, CH2CH2CHP),
1.51–1.38 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
= 160.83 (ddd, J = 46.8,
33.8, 11.9 Hz, 2 Car-F), 131.34 (dd, J = 9.5, 6.9 Hz, Car), 125.30 (dd, J = 16.3, 3.6 Hz, Car), 110.94 (dd, J
δ
×
= 20.8, 3.6 Hz, Car), 103.63–103.07 (m, Car), 49.94 (d, J = 138.2 Hz, CHP), 32.52 (s, CH2), 25.69 (dd, J =
13.6, 1.4 Hz, CH2) ppm; 19F NMR (376 MHz, D2O + NaOD),
= 16.2, 8.7 Hz, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
δ
=
−
114.74– 114.84 (m, 1F), -115.23 (dd, J
−
δ
= 21.61 (s, 1P) ppm; HRMS (ESI-MS) m/z
[MH]+ calculated for C9H12F2NO3P: 252.0601, found: 252.0607; HPLC-retention time: 12.66 min.
2.8.6. 1-Amino-3-(3,4-Difluorophenyl)propylphosphonic Acid (15f)
White solid, m. p. 292–293 ◦C; yield 60% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.09–7.00 (m, 2H, 2
×
CHar), 6.95–6.91 (m, 2H, 2
×
CHar), 2.76–2.67 (m, 1H, CH2CH2CHP), 2.49

Biomolecules 2020, 10, 1319
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(ddd, J = 13.8, 10.2, 6.7 Hz, 1H, CH2CH2CHP), 2.40 (td, J = 10.5, 3.2 Hz, 1H, CHP), 1.97–1.84 (m, 1H,
CH2CH2CHP), 1.54–1.41 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
= 148.99
(ddd, J = 163.2, 151.6, 12.6 Hz, 2 Car-F), 140.12 (dd, J = 5.4, 3.9 Hz, Car), 124.58 (dd, J = 6.2, 3.3 Hz,
Car), 116.98 (dd, J = 21.1, 16.7 Hz, 2 Car), 49.74 (d, J = 138.0 Hz, CHP), 33.66 (s, CH2), 32.20 (d, J =
12.7 Hz, CH2) ppm; 19F NMR (376 MHz, D2O + NaOD),
139.66– 139.78 (m, 1F), -143.58—143.71
(m, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD), = 21.46 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+
δ
×
×
δ
=
−
−
δ
calculated for C9H12F2NO3P: 252.0601, found: 252.0595; HPLC-retention time: 13.58 min.
2.8.7. 1-Amino-3-(4-Trifluoromethylphenyl)propylphosphonic Acid (15g)
White solid, m. p. 295–296 ◦C; yield 68% from diphenyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.41 (dd, J = 67.8, 8.0 Hz, 4H, 4
10.1, 6.7 Hz, 1H, CH2CH2CHP), 2.40 (td, J = 10.5, 3.2 Hz, 1H, CHP), 1.99–1.87 (m, 1H, CH2CH2CHP),
1.57–1.44 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
= 147.56 (s, Car), 129.05 (s,
Car), 127.27 (q, J = 32.0 Hz, Car-CF3), 125.30 (q, J = 3.8 Hz, 2 Car), 124.53 (q, J = 271.0 Hz, CF3),
49.82 (d, J = 138.1 Hz, CHP), 33.70 (s, CH2), 32.89 (d, J = 12.8 Hz, CH2) ppm; 19F NMR (376 MHz, D2O
×
CHar), 2.85–2.77 (m, 1H, CH2CH2CHP), 2.58 (ddd, J = 13.6,
δ
2
×
×
+ NaOD),
δ
= δ = 21.65 (s, 1P) ppm; HRMS
62.32 (s, 3F) ppm; 31P NMR (162 MHz, D2O + NaOD),
−
(ESI-MS) m/z [MH]+ calculated for C10H13F3NO3P: 284.0663, found: 284.0668; HPLC-retention time:
16.84 min.
2.8.8. 1-Amino-3-(2-Trifluoromethylphenyl)propylphosphonic Acid (15h)
White solid, m. p. 244–246 ◦C; yield 35% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.45 (dd, J = 69.4, 7.7 Hz, 2H, 2
×
CHar), 7.31 (dt, J = 84.9, 7.6 Hz, 2H, 2
×
CHar), 2.95 (td, J = 13.0,
4.5 Hz, 1H, CH2CH2CHP), 2.59 (td, J = 12.6, 5.2 Hz, 1H, CH2CH2CHP), 2.45 (td, J = 10.9, 2.8 Hz, 1H,
CHP), 1.98–1.85 (m, 1H, CH2CH2CHP), 1.51–1.37 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz,
D2O + NaOD),
(s, Car), 125.88 (q, J = 5.8 Hz, Car), 124.74 (q, J = 273.0 Hz, CF3), 50.56 (d, J = 137.9 Hz, CHP), 34.27 (s,
CH2), 30.30 (d, J = 13.7 Hz, CH2) ppm; 19F NMR (376 MHz, D2O + NaOD),
59.28 (s, 3F) ppm;
31P NMR (162 MHz, D2O + NaOD), = 21.45 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for
δ = 141.63 (s, Car), 132.31 (s, Car), 131.36 (s, Car), 127.58 (q, J = 29.5 Hz, Car-CF3), 126.06
δ
=
−
δ
C10H13F3NO3P: 284.0663, found: 284.0659; HPLC-retention time: 15.19 min.
2.8.9. 1-Amino-3-(2-Bromo-4-Fluorophenyl)ethylphosphonic Acid (17a)
White solid, m. p. 285–287 ◦C; yield 56% from diphenyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.27 (dd, J = 8.8, 2.7 Hz, 1H, CHar), 7.23 (dd, J = 8.6, 6.3 Hz, 1H, CHar), 6.95 (td, J = 8.5, 2.7 Hz, 1H,
CHar), 3.12–3.06 (m, 1H, CH2CHP), 2.78 (ddd, J = 12.5, 10.6, 2.8 Hz, 1H, CHP), 2.62 (ddd, J = 14.0, 12.4,
6.5 Hz, 1H, CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
= 160.71 (d, J = 245.6 Hz, Car-F),
136.00 (dd, J = 15.7, 3.4 Hz, Car), 132.32 (d, J = 8.5 Hz, Car), 124.10 (d, J = 9.8 Hz, Car), 119.44 (d, J = 24.4
Hz, Car), 114.44 (d, J = 20.8 Hz, Car), 51.03 (d, J = 137.1 Hz, CHP), 37.04 (d, J = 1.6 Hz, CH2) ppm; 19
NMR (376 MHz, D2O+NaOD),
115.87 (td, J = 8.6, 6.3 Hz, 1F) ppm; 31P NMR (162 MHz, D2O +
NaOD),
= 20.81 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for C8H10BrFNO3P: 297.9644,
δ
F
δ
=
−
δ
found: 297.9486; HPLC-retention time: 12.25 min.
2.8.10. 1-Amino-3-(2-Bromo-5-Fluorophenyl)ethylphosphonic Acid (17b)
White solid, m. p. 276–277 ◦C; yield 30% from diphenyl ester; 1H NMR (400 MHz, D2O+NaOD),
δ
= 7.51 (dd, J = 8.9, 5.4 Hz, 1H, CHar), 7.07 (dd, J = 9.5, 3.0 Hz, 1H, CHar), 6.87 (td, J = 8.6, 3.0 Hz, 1H,
CHar), 3.32–3.19 (m, 2H, CH2CHP), 2.84 (ddd, J = 15.5, 12.6, 6.1 Hz, 1H, CH2CHP) ppm; 13C NMR
(101 MHz, D2O + NaOD), 115.15 (td, J = 8.8, 5.5
ppm; 19F NMR (376 MHz, D2O + NaOD),
Hz, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD), = 20.77 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+
calculated for C8H10BrFNO3P: 297.9644, found: 297.9637; HPLC-retention time: 11.44 min.
δ
=
−
δ
=
−
δ

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2.8.11. 1-Amino-3-(3-Bromo-4-Fluorophenyl)ethylphosphonic Acid (17c)
White solid, m. p. 289–290 ◦C; yield 86% from diphenyl ester; 1H NMR (400 MHz, D2O+NaOD),
= 7.40 (dd, J = 6.8, 1.9 Hz, 1H, CHar), 7.12–7.07 (m, 1H, CHar), 6.98 (t, J = 8.7 Hz, 1H, CHar), 2.98 (d,
δ
J = 14.1 Hz, 1H, CH2CHP), 2.61 (td, J = 11.9, 2.5 Hz, 1H, CHP), 2.27 (ddd, J = 14.0, 12.3, 5.9 Hz, 1H,
CH2CHP) ppm; 13C NMR (101 MHz, D2O + NaOD),
δ
= 157.26 (d, J = 241.8 Hz, Car-F), 138.66 (dd, J =
15.8, 3.6 Hz, Car), 133.65 (s, Car), 129.91 (d, J = 7.2 Hz, Car), 116.07 (d, J = 22.0 Hz, Car), 107.75 (d, J =
20.7 Hz, Car), 52.05 (d, J = 137.9 Hz, CHP), 37.08 (s, J = 1.6 Hz, CH2) ppm; 19F NMR (376 MHz, D2O +
NaOD),
δ
=
−
112.99– δ = 20.55 (s, 1P) ppm;
113.06 (m, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
−
HRMS (ESI-MS) m/z [MH]+ calculated for C8H10BrFNO3P: 297.9644, found: 297.9634; HPLC-retention
time: 13.65 min.
2.8.12. 1-Amino-3-(4-Bromo-2-Fluorophenyl)ethylphosphonic Acid (17d)
White solid, m. p. 280–281 ◦C; yield 54% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.15 (dd, J = 9.8, 1.9 Hz, 2H, 2
CH2CHP), 2.66–2.58 (m, 1H, CHP), 2.48–2.39 (m, 1H, CH2CHP) ppm; 13C NMR (101 MHz, D2O +
NaOD), = 161.14 (d, J = 247.0 Hz, Car-F), 132.80 (d, J = 5.7 Hz, Car), 127.24 (d, J = 3.4 Hz, Car), 126.99
(t, J = 15.8 Hz, Car), 119.12 (d, J = 9.8 Hz, Car), 118.52 (d, J = 26.0 Hz, Car), 51.05 (d, J = 137.3 Hz,
CHP), 30.87 (s, CH2) ppm; 19F NMR (376 MHz, D2O + NaOD),
115.77 (t, J = 8.8 Hz, 1F) ppm;
31P NMR (162 MHz, D2O + NaOD), = 20.62 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for
×
CHar), 7.08 (t, J = 8.2 Hz, 1H, CHar), 2.91 (d, J = 14.0 Hz, 1H,
δ
δ
=
−
δ
C8H10BrFNO3P: 297.9644, found: 297.9644; HPLC-retention time: 13.45 min.
2.8.13. 1-Amino-3-(4-Bromo-3-Fluorophenyl)ethylphosphonic Acid (17e)
White solid, m. p. 291–292 ◦C; yield 52% from dimethyl ester; 1H NMR (400 MHz, D2O + NaOD),
δ
= 7.06 (dd, J = 10.1, 1.8 Hz, 1H, CHar), 7.06 (dd, J = 10.1, 1.8 Hz, 1H, CHar), 6.93 (dd, J = 8.2, 1.8 Hz,
1H, CHar), 3.05 (ddd, J = 14.2, 4.9, 2.7 Hz, 1H, CH2CHP), 2.72 (td, J = 12.0, 2.7 Hz,1H, CHP), 2.37 (ddd, J
= 14.1, 12.2, 5.9 Hz, 1H, CH2CHP) ppm; 13C NMR (101 MHz, D2O+NaOD),
= 158.61 (d, J = 243.8 Hz,
Car-F), 143.23 (s, Car), 133.10 (s, Car), 126.46 (d, J = 3.1 Hz, Car), 117.06 (d, J = 21.7 Hz, Car), 105.34 (d, J
= 20.8 Hz, Car), 51.95 (d, J = 137.3 Hz, CHP), 37.36 (s, CH2) ppm; 19F NMR (376 MHz, D2O + NaOD),
δ
δ
= δ = 19.82 (s, 1P) ppm;
109.36 (dd, J = 10.0, 7.5 Hz, 1F) ppm; 31P NMR (162 MHz, D2O + NaOD),
−
HRMS (ESI-MS) m/z [MH]+ calculated for C8H10BrFNO3P: 297.9644, found: 297.9637; HPLC-retention
time: 13.99 min.
2.9. Diphenyl α-Aminoalkilphosphonates (Representative Example)
Diphenyl 1-Amino-3-(2-Trifluoromethyl)phenylpropylphosphonate (18h)
White solid, m. p. 192–193 ◦C; yield 20%; 1H NMR (400 MHz, MeOD),
δ = 7.67 (d, J = 7.9 Hz, 1H,
CHar), 7.58 (t, J = 7.5 Hz, 1H, CHar), 7.47 (d, J = 7.7 Hz, 1H, CHar), 7.43–7.34 (m, 5H, CHar), 7.28–7.16
(m, 6H, CHar), 4.27 (dt, J = 14.1, 6.9 Hz, 1H, CHP), 3.17 (t, J = 8.4 Hz, 2H, CH2CH2CHP), 2.45 (tdt, J
= 14.0, 10.8, 6.9 Hz, 1H, CH2CH2CHP), 2.35–2.20 (m, 1H, CH2CH2CHP) ppm; 13C NMR (101 MHz,
MeOD),
= 6.0 Hz, 4
J = 5.6 Hz, 2
CHP), 30.75 (s, CH2), 28.74 (d, J = 7.7 Hz, CH2) ppm; 19F NMR (376 MHz, MeOD),
ppm; 31P NMR (162 MHz, MeOD), = 13.70 (s, 1P) ppm; HRMS (ESI-MS) m/z [MH]+ calculated for
C22H21F3NO3P: 436.1289, found: 436.1286.
δ
= 149.53 (dd, J = 9.8, 5.1 Hz, 2
Car), 128.06 (q, J = 29.7 Hz, Car), 126.96 (s, 2xCar), 126.05 (d, J = 5.9 Hz, 2
Car), 124.67 (q, J = 273.0 Hz, CF3), 120.32 (t, J = 3.7 Hz, 4 Car), 46.98 (d, J = 138.4 Hz,
60.60 (s, 3F)
×
Car), 138.54 (s, Car), 132.46 (s, Car), 131.25 (s, Car), 129.90 (d, J
×
×
Car), 125.85 (q,
×
×
δ
=
−
δ

Biomolecules 2020, 10, 1319
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2.10. Bioassay
2.10.1. Enzymatic Studies
Recombinant human alanine aminopeptidase (hAPN, EC 3.4.11.2) and porcine kidney
alanine aminopeptidase (pAPN, EC 3.4.11.2) were purchased as lyophilized powder from
R&D System (Minneapolis, MN, Canada) and Sigma Aldrich (Poznan, Poland), respectively.
Fluorogenic substrate-Ala-AMC (l-alanine-4-methylcoumaryl-7-amide) was supplied from PeptaNova
(Sandhausen, Germany). Each inhibitor, enzyme and substrate were dissolved in 50 mM Tris-HCl
buffer (pH = 7.00 and pH = 7.20 for hAPN and pAPN, respectively) and directly used in enzymatic
screening. Km values for the both enzymes towards Ala-AMC were determined analogously to the
literature [23] and were 73
17 were determined in 96-well plates with total volume of 100
µ
M for hAPN 90
µ
M for pAPN. Inhibitory constants for compounds 15 and
µ
L at 37 ◦C using a spectrofluorometer
(SpectraMax Gemini EM Fluorometer–Molecular Devices, San Jose, CA USA) operating at two
wavelengths: excitation355 nm and emission460 nm. Before screening both of the enzymes were
◦
preincubated 30 min at 37 C in the assay buffer before adding to the wells with appropriate
concentration of the substrate and inhibitor. The fluorogenic screening measurements included: (i)
eight concentrations of the respective inhibitor used in a range from 0.25 mM to 0.002 mM; (ii) 50 µM
concentration of the substrate for hAPN and 100 µM for pAPN; (iii) and enzyme concentration of 0.8
nM. The monitoring of the fluorogenic group release was continued for 15 min. The linear portion of
the progress curve was used to calculate velocity. For each inhibitor concentration the screening was
repeated three times. The types of the inhibition and inhibitory constants were calculated by using
the Lineweaver-Burk, Dixon plot and Cheng-Prusoff equation: Ki = IC50/[1 + (S/Km)] as described
earlier [24]. Kinetics parameters were calculated using GraphPad Prism (GraphPad 7.0, GraphPad
Software, San Diego, CA, USA, www.graphpad.com) and Microsoft Excel (Microsoft Corporation.
(2018). Microsoft Excel. Retrieved from https://office.microsoft.com/excel) computer programs.
2.10.2. Molecular Modelling
Crystal structures of enzymes were obtained from the Research Collaboratory for Structural
Bioinformatics Protein Data Bank (RCSB-PDB): for human (Homo sapiens) M1 aminopeptidase 4FYT [11
]
and porcine (Sus scrofa) M1 aminopeptidase 4FKE [ ]. The proteins were protonated at experimental pH.
3
Before docking, the structures of the inhibitors and their stereochemistry were considered, protonated
in experimental pH typical for each enzyme and optimized by LigPrep [25].
The binding modes of the inhibitors of both aminopeptidases were studied by molecular modeling.
All of the compounds (both enantiomers) were docked with the use of the induced fit docking algorithm
of the Maestro Schrodinger package [26]. This algorithm indicated which of the amino acids were well
scored and these were therefore considered in the next step. The VSGb (variable-dielectric generalized
Born) model was used, which incorporates residue-dependent effects. The solvent was water. Ligands
were docked with the sample ring conformations option with a 2.5 kcal/mol energy window and
standard glide, prime refinement and glide redocking (SP) procedures for the best pose for each
compound [27]. MM-GBSA (molecular mechanics-generalized Born surface area) was performed as a
rePrime refinement to calculate Gibbs free energies with protein flexibility, with the distances from
ligands also set as 0.0 Å and 5.0 Å. The first pose with the lowest binding energy in 5.0 Å was selected
as the best one.
2.10.3. Crystallography
The crystals of the compounds 13a
solution at room temperature. The single crystals were mounted on a CCD Xcalibur diffractometer,
with the graphite monochromatic, MoK radiation ( = 0.71073 Å) at room temperature for compounds
13a and 14c and at 100.0(1) K for compound 13c. The reciprocal space was explored by scans with
detector positions at 60 mm distance from the crystal. The diffraction data processing of studied
, 13c and 14c were grown by slow evaporation of the chloroform
α
λ
ω

Biomolecules 2020, 10, 1319
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compounds (Lorentz and polarization corrections were applied) was performed using the CrysAlis
CCD [28]. All structures were solved in the monoclinic crystal system, P21/c for 13a and 14c, P21/n for
13c, space group respectively (Table S9-1), by direct methods and refined by a full-matrix least-squares
method using SHELXL14 program [29,30]. The H atoms were located from difference Fourier synthesis
and from geometrical parameters and refined using a riding model. The structure drawings were
prepared using SHELXTL and Mercury programs (Figure S9) [31].
Crystallographic data for solved structures have been deposited with the Cambridge
Crystallographic Data Centre as supplementary publication number CCDC: 1968381 for 13a, 2021711
for 13c and 2021401 for 14c. These data can be obtained free of charge via http://www.ccdc.cam.ac.uk/
conts/retrieving.html, or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge
CB2 1EZ, UK; fax: 144 1223 336 033; email: deposit@ccdc.cam.ac.uk.
3. Results and Discussion
3.1. Chemistry
Novel library of the phosphonic acid analogues of homophenylalanine and phenylalanine have
been synthesized by multistep reaction using commercially available fluorinated 3-phenylpropionic
acids and fluorinated and brominated 2-phenylacetic acids, as starting materials. Preselection of
starting substrates was done basing on previous study [10] taking into consideration their availability.
Because of limitation on the usefulness of the previously described multistep reaction (hydrogenolytic
removal of bromine from phenyl ring during reduction of oxime to amine group) and lack of products
upon synthesis of homophenylalanine analogues by this procedure, we decided to convert carboxylic
acid precursors to corresponding aldehydes. Aldehydes constitute well-known class of substrates in
the synthesis of the
of the P-C-N scaffold [32]. Preliminarily we evaluated amidoalkylation reaction of trivalent phosphorus
compounds [33 35] (Scheme 1, route A). Unfortunately, we were able to isolate only ammonium
α-aminophosphonic acids by using methods based on the simultaneous formation
–
chloride salt (most likely product of decomposition of reaction intermediates) and no expected products
were formed. Further modifications of the amine group source (replacement of acetamide by benzyl
carbamate [36,37]) also did not provide the desired product (Scheme 1, route B). Finally, the most
promising method turned out to be the three-component condensation of carbonyl compound, benzyl
carbamate and triphenyl phosphite, known as Birum-Oleksyszyn reaction [38–40].
X = F, Br, I; Y = CH2
or
X = H, F, CF3; Y = CH2CH2
Scheme 1. Amidoalkylation of trivalent phosphorus compounds: (A), reagents: AcNH2-acetamide;
AcOH-acetic acid; AcCl-acetyl chloride; PCl3-phosphorus trichloride, 12 M HCl and (B), reagents:
CbzNH2-benzyl carbamate; AcOH; AcCl; PCl3, 12M HCl.
Briefly (Scheme 2), the substituted aldehydes were obtained from aromatic carboxylic acid
counterparts (compounds
and , route ) and their reduction to alcohols (compounds
avoidance of harsh conditions, poor yields, problematic work-up upon purification we do not use direct
1
and
7
) via formation of the methyl ester hydrochlorides (compounds
2
8
A
3
and , route ) [41 42]. Due to
9
B
,

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transformation of carboxylic to hydroxyl group (e.g., by using LiAlH4 or LiBH4 and TMSCl) [43–45].
Although the reduction of esters to alcohols by using sodium borohydride considered as relatively
difficult to achieve [46] our study confirmed relevance of this reducing agent and the pure alcohols were
obtained in excellent, quantitative yields. The synthetic challenge was an oxidation of the resulting
alcohols to aldehydes (compounds
4 and 10). The procedure by Omura and Swern, where alcohols are
oxidized with oxalyl chloride/DMSO, was initially examined [47]. However, as a consequence of the
presence of substituents in aromatic fragment of substrates many unidentified products were obtained.
Thus, we decided to evaluate Corey reagent—pyridinium chlorochromate (PCC) as an oxidizing agent
(route C) [48,49]. Oxidation of the fluorinated 3-phenylpropylalcohols (compounds 3) gave mixtures of
two main products: the desired major product—substituted 3-phenylpropionaldehydes (compounds
4d–4h)—and the symmetric esters (substituted 3-phenylpropyl-3-phenylpropionates - compounds
5d–5h) as side products, most likely via oxidative esterification as reported earlier by Hunsen and
Viana [50,51]. Hunsen and coworkers obtained corresponding ester upon oxidizing of phenylethanol
to its suitable carbonyl derivative, by using PCC and periodic acid as co-oxidant. Viana and coworkers
during the oxidation of brominated arylethers, mediated by PCC or mixture PCC/BF3*OEt2, reported
the formation of esters as a main product (with 46%–76% yield). During PCC oxidation of the
phenylethanols 9a and 9b, desired products—substituted 2-phenylacetaldehydes (compounds 10a
and 10b) and expected esters (substituted 2-phenylacetyl-2-phenylacetates) (compounds 11a and 11b
were obtained. Quite unexpectedly, we also observed the formation of appropriate benzaldehydes
(compounds 12a and 12b). Such cleavage of C-C bond during oxidation of homobenzylic alcohols
by PCC was reported earlier by Fernandes [52]. The loss of the one methylene group caused by
oxidative breakage of the C-C bond in the presence of PCC constitute very rare process in synthetic
organic chemistry. Noteworthy, modification of molar ratio between alcohol and PCC (from 1:3 to 1:1)
did not change the direction of the reaction. Moreover, elongation of the oxidation time promoted
by-products production (esters or/and benzaldehydes). In order to increase the yield of the aldehydes,
)
we decided to apply oxidation by using Dess-Martin periodinane (DMP) as catalyst (route
D) [53,54].
The reaction was conducted in dry CH2Cl2 and the optimal molar ratio between alcohol and oxidizer
was established as 1:1.2. Also the sequence of the addition of the reactants seems to play a significant
role in the course of this reaction and depended on the character of the transformed alcohol. While
DMP was added to the solution of alcohol, the reappearance of esters were observed, whereas the
quick addition of the alcohol solution into the DMP in dry CH2Cl2 resulted only in aldehyde formation
(compounds 4b
13), were prepared by condensation of the freshly prepared aldehyde, benzyl carbamate and triphenyl
phosphite in standard conditions (route ) [27 55 56]. In most cases the products were precipitated
from methanol at
20◦C or from acetone/hexane at 4 ◦C (see experimental Section 2.6). Due to rotation
around the C-N bond of the carbamate group in the obtained diphenyl esters they exist as mixtures of
trans- and cis-forms in solutions, with trans-form being a predominating one [49 57]. We succeeded
, 4c, 10c–10e). Cbz-protected diphenyl 1-aminoalkylphosphonates (compounds 6 and
E
, ,
−
,
in obtaining two diphenyl 1-(N-benzyloxycarbonylamino)-2-phenylethylphosphonates (compounds
13a and 13c) in a form suitable for X-ray analysis (Figure S9A,B). The final aminophosphonic acids
(compounds 15a
amino groups in concentrated HCl in acetic acid (Scheme 3, route
,
15d
,
15e
,
15g
,
17a
-
17c) were formed by acidic deprotection of the phosphoryl and
) and further recrystallization from
F
EtOH/H2O followed by adding a few drops of pyridine (to pH = 6). In the case of some diphenyl
esters, the classic acidic hydrolysis (in concentrated HCl or HBr) led to removal only carbobenzoxyl
group and diphenyl 1-aminoalkylphosphonates were identified (compounds 18b, 18c, 18f, 18h, 19d
and 19e, see experimental Section 2.9). Thus, the transesterification of Cbz-protected diphenyl
1-aminoalkylphosphonates (compounds 6b, 6c, 6f, 6h, 13d and 13e) with methanol in the presence
of KF/18-crown-ether (Scheme 3, route
dimethyl 1-{[(N-benzyloxy)carbonyl]amino)alkylphosphonates 14 and 16 and their further hydrolysis
with 12 M HCl (route F*) provided the desired products—compounds 15b
15c 15f 15h 17d 17e. The
crystal structure of compound 14c was included in Supplementary Material (Figure S9C).
G, see experimental Section 2.7) [58] yielded corresponding
,
,
,
,
,

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Scheme 2. Synthetic route to Cbz-protected diphenyl 1-aminoalkylphosphonates. Reagents and
conditions: (A) TMSCl-chlorotrimethylsilane, MeOH, 6–12 h, rt; (B) NaBH4-sodium borohydride, THF,
MeOH, reflux; (C) pyridinium chlorochromate, CH2Cl2, rt; (D) Dess-Martin periodinane, dry CH2Cl2,
1h, rt, Ar; (E) benzyl carbamate, triphenyl phosphite, AcOH, 80–90 ◦C, 1–2 h.

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Scheme 3. Deprotection of the diphenyl 1-(N-benzyloxycarbonyl)aminoalkylphosphonates to the
phosphonic acid analogues of the homophenylalanine (compounds 15) and phenylalanine (compounds
17). Reagents and conditions: (F) 10 M HCl in acetic acid, 12–24 h, reflux; (G) KF, 18-crown-6, MeOH,
1h, reflux; (F*) 12M HCl, 6–8 h, reflux.
3.2. Evaluation of Inhibitory Activity
Medium-throughput screening on a collection of preselected compounds against defined molecular
target is one of the means for discovery of novel lead compounds or for determination of the most
appropriate building blocks useful in medicinal chemistry. Thus, the obtained set of racemic phosphonic
acid analogues of homophenylalanine (compounds 15) and phenylalanine (compounds 17) were
examined for their inhibitory effects on human (hAPN) and porcine (pAPN) alanine aminopeptidases.
The results of the enzymatic studies, presented in Table 1, indicate quite significant potency of these
compounds towards both enzymes. The data in Table 1 are supplemented with literature inhibitory
constants obtained for compounds 17t, 17o and 17s [10], which are analogues of compounds 17c, 17d
and 17e differing in that they contain chlorine in place of bromine in aromatic rings.
When comparing the two studied enzymes, the higher affinity of all the tested inhibitors towards
hAPN over pAPNs is visible, with the differences in Ki values being of at least about an order in
magnitude smaller for the first ones.

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Table 1. Structures and inhibitory properties of the phosphonic acid analogues of homophenylalanine
(15) and phenylalanine (17) towards human (hAPN) and porcine (pAPN) aminopeptidases.
hAPN
Ki [µM]
pAPN
Ki [µM]
hAPN
Ki [µM]
pAPN
Ki [µM]
Cpd.
Substituents
Cpd.
Substituents
15a
15b
15c
15d
15e
15f
all-H
2-F
3-F
0.707 ± 0.176
0.506 ± 0.038
0.129 ± 0.025
0.249 ± 0.025
0.661 ± 0.105
0.149 ± 0.011
0.347 ± 0.062
0.804 ± 0.122
7.64 ± 0.11
12.7 ± 0.8
17a
17b
17c
2-Br, 4-F
2-Br, 5-F
3-Br, 4-F
3-Cl, 4F
4-Br, 2-F
4-Cl, 2F
4-Br, 3-F
4-Cl, 3-F
14.0 ± 0.4
41.7 ± 7.4
70.0 ± 6.6
379 ± 126
2.22 ± 0.14
6.93 ± 0.78
82.5 ± 2.0
160 ± 11
2.63 ± 0.18
1.69 ± 0.81
1.71 ± 0.46
1.02 ± 0.30
0.976 ± 0.099
7.49 ± 0.58
0.248 ± 0.024
0.542 ± 0.152
7.36 ± 0.21
17.8 ± 2.09
0.670 ± 0.049
1.01 ± 0.16
4-F
17t
2,4-diF
3,4-diF
4-CF3
2-CF3
a
17d
17o a
17e
15g
15h
4.23 ± 0.44
14.8 ± 0.9
17s a
Data from previous studies with letters conforming to the described compounds [10].
Phosphonic acids analogues of homophenylalanine displayed submicromolar and micromolar
activity towards human and porcine aminopeptidases, respectively. Non-substituted precursor
(compound 15a) has Ki values, which are in good agreement with those published in the literature
for its racemic mixtures (0.8 µM for hAPN and 3.69–15.9 µM for pAPN) [23,59,60]. Substitution of
their phenyl moieties with fluorine atoms at any position is beneficial. Position of those substitutions
seems to be less pronounced than found for analogues of phenylalanine [10]. However, it does not
significantly change their affinities to both aminopeptidases, with compound 15c being only 5 times
better inhibitor than 15a. Nonetheless, this is the most active inhibitor of hAPN amongst simple
aminophosphonic acids and ranks amongst the most efficient low-molecular inhibitors of both enzymes.
The substitution of the phenyl rings of phosphonic acid analogues of homophenylalanine with fluorine
atoms only resulted in slightly better inhibitory potencies than compound 15a, which indicates a good
acceptance of fluorine atoms by both enzymes. It is of some importance since compound 15a is quite
commonly used as building block for the development of very potent aminopeptidase inhibitors [8].
Supplementation of the previously described set of phosphonic acid analogues of
phenylalanine [10] had shown that they display lowest affinities towards the studied aminopeptidases.
Albeit, the replacement of chlorine by bromine is favorable, especially in the case of porcine enzyme.
Similarly to previous work [10], the substituents in para and meta positions of the phenyl ring are
better accepted by binding sites of both aminopeptidases, whereas the presence of substituents in ortho
position reduced inhibitory activities.
3.3. Molecular Docking
The set of compounds described in this work exhibits the best inhibitory activities determined
for low molecular weight inhibitors of aminopeptidases. Therefore, it seems to be of importance to
understand their interactions with enzymes at the molecular level. In order to establish architecture of
enzyme-inhibitor complexes, molecular modeling techniques had been used.
Homophenylalanine analogues 15, similarly to analogues of phenylalanine and phenylglycine
studied earlier [9,
10], binds in the two hydrophobic pockets S1 and S10. Porcine aminopeptidase,
despite a more open structure, has a shallower S1 pocket, consequently hPheP analogues show a higher
affinity for the S10 cavity (Figure 1).
Compound 15g, bearing a para-trifluoromethyl substituent, exhibited the highest affinity to the
porcine enzyme. Mode of binding of both enantiomers of this compound is also depicted in Figure 1.
The obligatory prerequisite for all the aminophosphonic inhibitors are interactions of phosphonate
moiety with catalytic zinc ion and tyrosine (Y472) and binding of their amino groups with acid catalytic
amino acids E350 and E384. Usually stereoisomerism does not significantly affect the arrangement of
the phenyl ring. It is arranged between hydrophobic amino acids from S10 pocket and amino acids
lying on the border of two pockets: G347 and A348. However, enantiomers of compound 15g are
bound differently. The (R)-isomer (corresponding to the D-isomer) is not so close to the enzyme surface,
which assures interaction with asparagine (N360). Its (S)-enantiomer (corresponding to L-isomer) binds

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similarly but may be affected by the presence of two arginines—R358 and R376. This alongside with
typical binding of the amino moiety causes, that phosphonic acid group is pushed out of the optimal
position of binding and interactions with Y472 and H383. Thus, calculations predict significantly
higher efficiency S isomer over R isomer.
Figure 1. General view of the crystal structure of pAPN (PDB: 4FKE) with marked zinc ion, substrate
binding cavities S1 (yellow) and S10 (pink), in the lack and presence of inhibitor (green). An
interaction between compound 15g and the active center and binding domains of the enzyme serves as
representative example. The isomer (S) is shown on the left side, when the (R)-isomer on the right side.
The enzyme is shown as ribbon representation, with the blue surface. The zinc atoms are shown as
grey spheres. Selected amino acids and inhibitors are shown as sticks. Red color depicts oxygen atoms
of the phosphonate groups and nitrogen atoms are colored blue.
Compared to the compound of similar activity—15f (Figure S7-2) it can be concluded that the
correct stabilization of the aromatic ring and the amino group has a major influence on the affinity
to pAPN.
Compounds shorter by a methylene group, analogues of phenylalanine, containing bromine in
their structure have been chosen because of the large size of bromine. It would fit better to the spacious
S1’ site of pAPN (and most likely to the S1 site of hAPN). However, these derivatives appeared to

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be less active. The presence of bromine atom as a substituent negatively affects the position of the
key elements of the enzyme-inhibitor puzzle. Bromine strongly interacts with H383 in the case of
(S)-17c, whereas in the case of (R)-17c its lack caused that aromatic ring is somewhat pushed back
in the direction of V380 (Figure S7-4). Thus, once more the S isomer is bound preferentially over R
one. On the other hand, when the compound has bromine in the ortho position, as it is in the case of
(S)-17b, it moves the phenyl ring away from the enzyme surface of S1’ pocket (Figure S7-3). Quite
interestingly modeling predicts that its enantiomer, compound (R)-17b, is preferentially bound in the
S1 cavity. However, in this case bromine also pushes out the phenyl ring from this domain.
On the contrary to the porcine enzyme, modeling predicts that human aminopeptidase binds the
aromatic fragment of the studied inhibitors in its long S1 pocket (Figure 2). Earlier studies suggested
that analogues of homophenylalanine should be more efficient that analogues of phenylalanine. Indeed,
elongation of the alkyl chain caused some increase in activity.
Also, in this case the most vital for the inhibitory activity is complexation of aminophosphonate
fragment, which is very similar for all the inhibitors (as it is seen for representative example of
compound 15c in Figure 2). Similarly, as in case of porcine enzyme, phosphonate group is bound to
zinc ion and tyrosine (Y477), whereas amine is interacting with two glutamic acids (E355 and E411).
Compounds with submicromolar activity interact with the amino acids at the bottom of the S1 pocket
composed of: Q211, N350; and its perpendicular wall: S895, F896, S897. These residues have the
greatest influence on inhibitor binding. Aromatic ring arrangement is determined by isomerism: for
(S)-isomers it is arranged mainly by face-to-face interactions with F896, whereas for compounds of
(R) configuration, face-to-edge interaction is preferred. This result form more optimal binding of
phosphonic moiety with participation of Y477 and form different binding of fluorine by S897.
Although modeling predicts, that 15e and 15f containing two fluorine substituents should increase
the affinity towards the enzyme, it was not observed. The calculations predict the favorable interactions
(Figure S8-1) for both enantiomers of compound 15f between fluorine substituents and enzyme,
by interactions with A351 and N350 observed for both isomers. These interactions simultaneously
can stiffen inhibitor location at the bottom of the cavity. It is worth to mention that in the case of
phenylalanine analogues, the triple substitution of phenyl ring with fluorine at 3,4 and 5 positions
appeared to be highly beneficial [10]. Unfortunately, we were not able to obtain tri, tetra and penta
substituted phosphonic acid analogues of the homophenylalanine.

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Figure 2. General view of the crystal structure of hAPN (PDB: 4FYT) with marked substrate cavities S1
(yellow) and S1’ (pink) in the lack and presence of inhibitor (green). The interactions of the enzyme
with compound 15c are shown as representative example. The isomer (S) is on the left side, when the
(R)-isomer is on the right side of the Figure. The coloring scheme is identical as in Figure 1.
In the case of replacement of chlorine atoms in already described inhibitors of hAPN [10] by
more bulky bromine, resulting in compounds 17a–17e, did not bring expected results and the novel
inhibitors are only slightly more effective than their counterparts. Although bromine fills well the
hydrophobic pocket S1 and interacts with several of its amino acid side chains simultaneous shift of
the inhibitor away from the bottom of S1 cavity causes that it is not optimally bound. This is well
illustrated by the architectures of the complexes of both enantiomers of compound 17b and hAPN
(Figure 3).

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Figure 3. The mode of binding of compound 17b ((S) isomer–left, (R) isomer–right) by hAPN (PDB:
4FYT). The coloring scheme is identical as in Figure 1. The bromine atom is shown as dark red stick.
4. Conclusions
Present studies and literature data point out that the introduction of halogen atoms into the
aromatic ring of phosphonic acid analogues of phenylalanine or homophenylalanine results in the
elevation of the affinities of novel phosphonates towards aminopeptidases. The higher potency of
homophenylalanine analogues most likely is caused by flexibility of longer aliphatic linker between
aminophosphonate part of inhibitors and their phenyl rings. It ensured better fit of homophenylalanines
to the hydrophobic pockets of the studied enzymes. Introduction of fluorine atoms into the phenyl
ring is beneficial. Replacement of hydrogen atoms by fluorine becomes a standard since the resulting
compounds are not only well accepted by enzymes and other receptor proteins but also are involved in
additional interactions with them. Our study resulted in finding the most potent aminophosphonate
inhibitor of hAPN-1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound 15c).
Introduction of bromine into phenyl ring of phenylalanine derivatives caused increase of inhibitory
potency of novel analogues. However, these compounds are significantly less effective than analogues
of homophenylalanine, which derives from bulky character of bromine resulting in lower flexibility of
the inhibitor molecule. This, in turn, often resulted in its non-optimal placement in the hydrophobic
binding sites of aminopeptidases.
Since porcine enzyme is considered as a good model of human one it is worth to express that
aromatic aminophosphonates are bound in two, albeit similar to each other, different sites: S1 in the
case of hAPN and S10 in the case of pAPN. This explains why phosphonic acid analogues are far
more effective inhibitors of human enzyme. However, the structure-activity relationship found for the
two enzymes supports the possibility of using pAPN as a model of hAPN and shows that S1 and S10
binding sites of hAPN and pAPN, respectively are quite similar. Nevertheless, some reservations is
suggested here.
Supplementary Materials: The following are available online at http://www.mdpi.com/2218-273X/10/9/1319/s1.
Section S1: The characterization data of the compounds 2c–2h and 8a–8e. Section S2: The characterization data of
the compounds 3c–3h and 9a–9e. Section S3: The characterization data of the compounds 4e–4h, 10a and 10b
.
Section S4: The characterization data of the compounds 4b
,
4c
13e. Section S6: The characterization data of the compounds 14c
) and 19F (
) NMR spectra for 3-(4-fluorophenyl)propyl-3-(4-fluorophenyl)propionate
), 1H-31P HMQC ( ) and 1H-13C HMQC (
) NMR spectra for 1-amino-3-(4-fluorophenyl)
,
10c–10e. Section S5
:
The characterization data of the
compounds 6b
-
A
6h and 13a
-
,
14f 14h 16d and 16e.
,
,
1
Figure S1: H (
), 13C (
B
C
(
5d). Figure S2: 1H (
A
B
C
propylphosphonic acid (15d). Section S7: Molecular docking simulations of the inhibitors 15c, 15f,
17b and 17c binding to active site of pAPN (PDB: 4FKE). Figure S7-1: Binding mode of the
1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound 15c) with the pAPN. Figure S7-2: Binding mode of
the 1-amino-3-(3,4-difluorophenyl) propylphosphonic acid (compound 15f) with the pAPN. Figure S7-3: Binding
mode of the 1-amino-2-(2-bromo-5-fluorophenyl) ethylphosphonic acid (compound 17b) with the pAPN. Figure
S7-4: Binding mode of the 1-amino-2-(3-bromo-4-fluorophenyl) ethylphosphonic acid (compound 17c) with the
pAPN. Section S8: Molecular docking simulations of the inhibitors 15f
, 15g and 17c binding to active site of hAPN
(PDB: 4FYT). Figure S8-1: Binding mode of the 1-amino-3-(3,4-difluorophenyl) propylphosphonic acid (compound

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15f) with the hAPN. Figure S8-2: Binding mode of the 1-amino-3-(4-trifluoromethylphenyl) propylphosphonic
acid (compound 15g) with the hAPN. Figure S8-3: Binding mode of the 1-amino-2-(3-bromo-4-fluorophenyl)
ethylphosphonic acid (compound 17c) with the hAPN. Section S9: X-Ray analysis of compounds 13a
13c and 14c Section S9: X-Ray analysis of compounds 13a, 13c and 14c Figure S9: Molecular
structures of diphenyl [(N-benzyloxycarbonylamino)-2-(2-bromo-4-fluoro)phenylethyl]phosphonate (13a)( ),
diphenyl [(N-benzyloxycarbonylamino)-2-(3-bromo-4-fluoro)phenylethyl]phosphonate (13c) ( ) and dimethyl
[(N-benzyloxycarbonylamino)-3-(3-fluoro)phenylpropyl]phosphonate (14c) (C). Table S9-1: Crystal parameters
and experimental details of the X-Ray data collection for structure 13a 13c and 14c. Table S9-2: Selected geometric
parameters for crystal structure 13a (Å, ). Table S9-3: Selected hydrogen-bond parameters for structure 13a. Table
S9-4: Selected geometric parameters for crystal structure 13c (Å, ). Table S9-5: Selected geometric parameters
,
.
.
A
B
,
º
º
for crystal structure 14c (Å,
º
). Table S9-6: Selected hydrogen-bond parameters for structure 14c. Section S10:
1
Characterization of the Final Compounds 15a–15h and 17a–17e by 1H, 13C, 19F, 31P NMR. Figure S10-1: H (
A
),
31P ( ) NMR spectra for compound 15a. Figure S10-2: 1H ( ),13C ( ), 19F ( ), 31P (
B A B C D) NMR spectra for compound
15b. Figure S10-3: 1H (A),13C (B), 19F (C), 31P (D) NMR spectra for compound 15c. Figure S10-4: 1H (A),13C (B),
19F (
C
), 31P (
D) NMR spectra for compound 15d. Figure S10-5: H (
A
),13C (
B
), 19F (
C
), 31P (
D
) NMR spectra for
1
1
1
compound 15e. Figure S10-6: H (
A
),13C (
B
), 19F (
C
), 31P (
D
) NMR spectra for compound 15f. Figure S10-7: H
(A B C D A B C D) NMR
),13C ( ), 19F ( ), 31P ( ) NMR spectra for compound 15g. Figure S10-8: 1H ( ),13C ( ), 19F ( ), 31P (
spectra for compound 15h. Figure S10-9: 1H (
A
),13C (
B
), 19F (
C
), 31P (
D
) NMR spectra for compound 17a. Figure
1
1
S10-10: H (
A
), 19F (
B
), 31P (
C
) NMR spectra for compound 17b. Figure S10-11: H (
A
),13C (
B
), 19F (
C
), 31P (
D
)
1
NMR spectra for compound 17c. Figure S10-12: H (
A
),13C (
B
), 19F (
C
), 31P (
D
) NMR spectra and HPLC (
E
) for
compound 17d. Figure S10-13: 1H (A),13C (B), 19F (C), 31P (D) NMR spectra for compound 17e.
Author Contributions: Conceptualization, W.W.; methodology, W.W., M.T.; formal analysis, W.W., M.T., B.D.,
P.K.; investigation, W.W., M.T., B.D.; writing—original draft preparation, W.W., M.T., P.K.; writing—editing and
review, W.W., P.K.; visualization, W.W., M.T., B.D.; funding acquisition, P.K. All authors have read and agreed to
the published version of the manuscript.
Funding: The research was funded by National Science Center of Poland, grant number 017/26/M/ST5/00437.
Conflicts of Interest: The authors declare no conflict of interest.
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