Next Article in Journal
New Advances in Short Peptides: Looking Forward
Previous Article in Journal
3D Graphene Foam by Chemical Vapor Deposition: Synthesis, Properties, and Energy-Related Applications
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Molecules
Volume 27
Issue 11
10.3390/molecules27113633
molecules-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains

by
Parul Sahrawat
1,
Paweł Kowalczyk
2,*,
Dominik Koszelewski
1,
Mateusz Szymczak
3,
Karol Kramkowski
4,
Aleksandra Wypych
5 and
Ryszard Ostaszewski
1,*
1
Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland
2
Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jabłonna, Poland
3
Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
4
Department of Physical Chemistry, Medical University of Bialystok, Kilińskiego 1 Str., 15-089 Białystok, Poland
5
Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, ul. Wileńska 4, 87-100 Toruń, Poland
*
Authors to whom correspondence should be addressed.
Molecules 2022, 27(11), 3633; https://doi.org/10.3390/molecules27113633
Submission received: 4 May 2022 / Revised: 25 May 2022 / Accepted: 31 May 2022 / Published: 6 June 2022
Browse Figures
Versions Notes

Abstract

:
An efficient method for the synthesis of functionalized peptidomimetics via multicomponent Ugi reaction has been developed. The application of trifluoroethanol (TFE) as a reaction medium provided desired products with good yields. Further, using the developed cyclisation reaction, the obtained peptidomimetics were transformed into the cyclic analogues (diketopiperazines, DKPs). The goal of the performed studies was to revised and compare whether the structure of the obtained structurally flexible acyclic peptidomimetics and their rigid cycling analogue DKPs affect antimicrobial activity. We studied the potential of synthesized peptidomimetics, both cyclic and acyclic, as antimicrobial drugs on model E. coli bacteria strains (k12, R2–R4). The biological assays reveal that DKPs hold more potential as antimicrobial drugs compared to open chain Ugi peptidomimetics. We believe that it can be due to the rigid cyclic structure of DKPs which promotes the membrane penetration in the cell of studied pathogens. The obtained data clearly indicate the high antibiotic potential of synthesized diketopiperazine derivatives over tested antibiotics.

Graphical Abstract

1. Introduction

Ugi reaction is a one pot multicomponent reaction for peptidomimetics synthesis. This transformation was already successfully engaged as a crucial step for diketopiperazines (DKPs) synthesis [1,2]. Diketopiperazine derivatives are known for their well-recognized biological activities. These small, cycling and conformationally rigid molecules have multiple functional groups which can interact with receptors and so show a broad spectrum of biological actions [3]. There are plentiful reports on bioactive compounds containing DKP moiety. This scaffold is quite important due to its interesting medicinal properties such as PDE5 inhibitors [4], oxytocin antagonists [5], cancer inhibitors [6], metalloproteinase inhibitors [7], antivirals [8], antibiotics [9], antibacterial [10], neuroprotective reagents [11], anxiolytic agents [12], anti-inflammatory inhibitors [13], bio herbicides [14] and natural products [15] (Figure 1).
This work is a continuation of earlier work reported by us, in which we paid attention to the structure–activity relationship of a library of peptidomimetics synthesized via Ugi reaction to check their antimicrobial potential against E. coli strains [16]. However, here, we are more interested in assessing the effect of cyclisation with respect to the open chain Ugi peptidomimetics. In order to study the influence of structure, particularly its rigidity, it is necessary to develop the method for the synthesis of these two groups of compounds. We have exploited the diversity of Ugi reaction using several aldehydes, isocyanides, amines and acrylic acid to make a library of compounds. Reported peptidomimetics are a class of alkylating agents which should aid its antimicrobial activity but our research has shown otherwise, which may be related to cell membrane permeability in pathogens. 2-chloropropionic acid derivatives are also proven to be biologically active. For example, piracetam derivatives are known as cognitive enhancers [17] and 3CL pro inhibitors [18]. Due to antimicrobial resistance, there is a need to find new potent antimicrobial drugs. There are very few reports on the antimicrobial activities of DKPs against E. coli [19]. The goal of the presented studies is to design a method for the synthesis of DKPs and to substantiate their antimicrobial potential against model E. coli strains.

2. Materials and Methods

2.1. Microorganisms and Media

E. coli K-12, R1–R4 strains were received from Prof. Jolanta Łukasiewicz at the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy (Polish Academy of Sciences, Warsaw, Poland). Bacteria were cultivated in a tryptic soy broth (TSB; Sigma-Aldrich, Saint Louis, MI, USA) liquid medium and on agar plates containing TSB medium. N,N-Dimethylformamide (DMF) was purchased from Sigma Aldrich (CAS No. 68-12-2, Poznań, Poland), Lanes 1kb-ladder, and Quick Extend DNA ladder (New England Biolabs, Ipswich, MA, USA), with MIC and MBC tests as described in detail in the previous work [16,17,18,19,20,21,22] and analyzed by the Tukey test indicated by (p < 0.05): * p < 0.05, ** p < 0.1, *** p < 0.01.

2.2. Chemicals

Starting materials and all other reagents were purchased from Sigma-Aldrich. All solvents were of analytical grade and were used without prior distillation. Merck silica gel plates 60 F254 were used for TLC (thin layer chromatography) analysis. Crude reaction mixtures were purified using column chromatography on Merck silica gel 60/230–400 mesh, with an appropriate mixture of hexane and ethyl acetate as a solvent. THF was dried according to standard procedure. Nuclear magnetic resonance spectra (NMR) were performed on a Bruker Avance 400 and Varian 500MHz instrument. Chemical shifts are expressed in ppm and coupling constant (J) in Hz using TMS as an internal standard. High-resolution mass spectra were acquired on a Maldi SYNAPT G2-S HDMS (Waters) apparatus with a QqTOF analyser.
The bacterial tests used, and MIC and MBC were accurately described in detail in the previous work [20,21,22,23,24,25,26]. An MTT test to assess the metabolic activity of cells was performed on the basis of [27,28,29,30], with THLE-5b as the control and the caco-2 cell line derived from human adenocarcinoma.

2.3. General Procedure for Synthesis of Compounds Va-Vh

To the mixture of benzyl amine (0.25 mmol) in 2,2,2-trifluoroethanol (1 mL, 0.25 mmol) corresponding aldehyde was added and the reaction mixture was stirred for 20 min at room temperature followed by the addition of 2-chloropropionic acid (0.25 mmol). After 20 min, isocyanide (0.25 mmol) was added to the reaction mixture and was stirred continuously for 18 h at 50 °C. Then, the solvent was evaporated and the crude products were purified by column chromatography on silica gel using hexane/AcOEt as the eluent.

2.3.1. N-benzyl-2-chloro-N-(2-((4-methoxybenzyl)amino)-2-oxo-1-phenylethyl) Propanamide (Va)

Colorless oil; (dr: 1:1); 1H NMR (400 MHz, CDCl3) δ 7.38 (dd, J = 6.5, 2.8 Hz, 2H), 7.29–7.15 (m, 8H), 7.05 (d, J = 7.3 Hz, 2H), 6.84–6.76 (m, 2H), 6.13 (s, 1H), 5.76 (s, 1H), 4.99 (d, J = 18.0 Hz, 1H), 4.61 (d, J = 18.0 Hz, 1H), 4.44–4.32 (m, 2H), 3.75 (s, 3H), 1.57 (d, J = 6.5 Hz, 3H); 13C NMR (100 MHz, CDCl3) δ 170.6, 168.7, 158.9, 136.9, 134.3, 130.0, 129.8, 129.0, 128.9, 128.8, 128.6, 127.3, 126.0, 125.8, 114.0, 64.1, 55.2, 50.2, 50.1, 43.2, 20.7. HR-MS (ESI): m/z calculated for C26H27ClN2O3 [M+Na]+ 449.1629, found 449.1632.

2.3.2. N-benzyl-2-chloro-N-(2-((4-methoxybenzyl)amino)-1-(4-methoxyphenyl)-2-oxoethyl) Propanamide (Vb)

Pale yellow oil; (dr: 3:1); 1H NMR (400 MHz, CDCl3) δ 7.34–7.26 (m, 2H), 7.25–7.18 (m, 3H), 7.18–7.14 (m, 2H), 7.06 (d, J = 7.3 Hz, 2H), 6.83–6.79 (m, 2H), 6.78–6.74 (m, 2H), 6.03–5.91 (m, 1H), 5.62 (s, 1H), 5.56 (d, J = 14.6 Hz, 1H, minor), 5.07 (t, J = 3.6 Hz, 2H, minor), 4.96 (d, J = 18.0 Hz, 1H, major), 4.56 (d, J = 18.0 Hz, 1H, major), 4.40 (t, J = 5.1 Hz, 2H, major), 3.77 (s, 3H), 3.73 (s, 3H), 3.57 (d, J = 14.6 Hz, 1H, minor), 1.64 (d, J = 7.2 Hz, 1H, minor), 1.59 (d, J = 6.4 Hz, 3H, major); 13C NMR (100 MHz, CDCl3) δ 168.9, 159.9, 159.80, 136.9, 131.1, 128.9, 128.7, 128.6, 128.1, 127.3, 125.8, 114.8, 114.3, 114.1, 63.7, 55.2, 50.2, 49.9, 43.2, 20.7. HR-MS (ESI): m/z calculated for C27H29ClN2O4 [M+Na]+ 503.1709, found 503.1714.

2.3.3. N-benzyl-2-chloro-N-(2-(cyclohexylamino)-2-oxo-1-phenylethyl) Propanamide (Vc)

Colorless oil; (dr: 3:2); 1H NMR (500 MHz, CDCl3) δ 7.39–7.30 (m, 3H), 7.30–7.23 (m, 6H), 7.22–7.18 (m, 2H), 7.12 (d, J = 7.5 Hz, 2H), 7.03 (d, J = 7.5 Hz, 1H), 6.04 (s, 1H, major), 5.79 (d, J = 8.0 Hz, 1H, major), 5.70 (s, 1H, minor), 5.57 (d, J = 7.9 Hz, 1H, minor), 4.98 (d, J = 18.0 Hz, 1H, minor), 4.66 (q, J = 17.6 Hz, 2H), 4.56 (d, J = 18.1 Hz, 1H, minor), 4.47 (q, J = 6.6 Hz, 1H, major), 4.38 (q, J = 6.6 Hz, 1H, major), 3.80 (ddtt, J = 22.7, 11.2, 7.8, 4.0 Hz, 2H), 1.89 (dd, J = 11.5, 5.5 Hz, 3H), 1.75–1.60 (m, 5H), 1.59 (dd, J = 6.5, 2.3 Hz, 5H), 1.38–1.23 (m, 4H), 1.15–1.02 (m, 4H); 13C NMR (126 MHz, CDCl3) δ 171.5, 170.5, 167.8, 167.7, 137.4, 136.9, 134.8, 134.4, 129.7, 129.1, 128.8, 128.7, 128.6, 128.6, 128.5, 127.9, 127.3, 127.2, 126.0, 125.9, 125.7, 64.1, 62.7, 50.8, 50.2, 50.0, 49.6, 48.5, 34.6, 32.8, 32.7, 32.7, 32.6, 31.5, 29.0, 25.4, 25.4, 25.2, 24.7, 24.6, 21.0, 20.7, 20.6. HR-MS (ESI): m/z calculated for C24H29ClN2O2 [M+Na]+ 435.1812, found 435.1815.

2.3.4. N-benzyl-2-chloro-N-(2-((4-methoxybenzyl)amino)-2-oxo-1-(p-tolyl)ethyl) Propanamide (Vd)

White semi-solid; (dr: 3:2); 1H NMR (400 MHz, CDCl3) δ 7.28–7.17 (m, 9H), 7.13 (dt, J = 8.3, 4.6 Hz, 5H), 7.10–6.97 (m, 6H), 6.86–6.77 (m, 4H), 6.32 (d, J = 7.1 Hz, 1H, major), 6.03 (s, 1H, minor), 5.99 (d, J = 5.9 Hz, 1H, minor), 5.61 (s, 1H, major), 4.97 (d, J = 18.0 Hz, 1H), 4.64 (d, J = 11.7 Hz, 1H), 4.55 (d, J = 18.1 Hz, 1H), 4.38 (ddd, J = 13.2, 7.3, 4.0 Hz, 4H), 3.77 (d, J = 2.1 Hz, 6H), 2.29 (s, 3H, minor), 2.26 (s, 3H, major), 1.57 (dd, J = 9.0, 6.5 Hz, 5H); 13C NMR (100 MHz, CDCl3) δ 170.5, 168.8, 158.9, 138.5, 136.9, 129.1, 128.9, 128.6, 127.2, 125.8, 114.0, 114.1, 64.2, 62.8, 55.2, 50.8, 50.2, 50.1, 43.2, 21.1, 20.7. HR-MS (ESI): m/z calculated for C27H29ClN2O3 [M+Na]+ 487.1771, found 487.1764.

2.3.5. N-benzyl-2-chloro-N-(2-(cyclohexylamino)-2-oxo-1-(p-tolyl)ethyl) Propanamide (Ve)

Colorless oil; (dr: 3:2); 1H NMR (400 MHz, CDCl3) δ 7.32–7.09 (m, 10H), 7.05 (q, J = 8.3 Hz, 5H), 6.02 (s, 1H, minor), 5.95 (d, J = 8.1 Hz, 1H, minor), 5.64 (d, J = 8.4 Hz, 2H, major), 4.94 (d, J = 18.0 Hz, 1H, major), 4.68 (d, J = 17.7 Hz, 2H, minor), 4.54 (d, J = 17.7 Hz, 1H, major), 4.44 (q, J = 6.4 Hz, 1H, minor), 4.36 (q, J = 6.5 Hz, 1H, major), 3.88–3.68 (m, 2H), 2.29 (s, 3H, minor), 2.26 (s, 3H, major), 1.96–1.81 (m, 3H), 1.69–1.59 (m, 5H), 1.55 (d, J = 6.5 Hz, 6H), 1.38–1.22 (m, 5H), 1.09 (dqd, J = 17.1, 11.7, 11.1, 4.1 Hz, 5H); 13C NMR (100 MHz, CDCl3) δ 175.6, 174.9, 169.8, 169.5, 168.1, 137.7, 129.4, 128.6, 128.5, 128.1, 127.2, 127.1, 126.1, 126.0, 56.3, 48.3, 48.0, 43.1, 42.7, 37.1, 32.8, 32.7, 32.6, 32.5, 29.4, 25.9, 25.5, 25.1, 24.7, 24.6, 24.6, 22.7, 22.6, 22.4, 22.4, 22.3. HR-MS (ESI): m/z calculated for C25H31ClN2O2 [M+Na]+ 449.1970, found 449.1972.

2.3.6. N-benzyl-2-chloro-N-(2-(cyclohexylamino)-1-(2,4-dinitrophenyl)-2-oxoethyl) Propanamide (If)

Yellow oil; (dr: 3:2); 1H NMR (400 MHz, CDCl3) δ 8.79 (d, J = 2.4 Hz, 1H, major), 8.67–8.60 (m, 1H, minor), 8.43 (dd, J = 8.6, 2.4 Hz, 1H, major), 8.35–8.28 (m, 1H, minor), 7.79 (d, J = 8.7 Hz, 1H, minor), 7.70 (d, J = 8.7 Hz, 1H, major), 7.30 (dd, J = 14.5, 6.9 Hz, 4H), 7.24 (s, 2H), 7.16 (d, J = 7.4 Hz, 3H), 7.09 (d, J = 6.7 Hz, 2H), 6.63 (s, 1H, major), 6.37 (s, 1H, minor), 6.28 (d, J = 7.9 Hz, 1H, major), 5.87 (d, J = 8.0 Hz, 1H, minor), 5.07 (d, J = 17.0 Hz, 2H, major), 4.86 (d, J = 17.7 Hz, 1H, minor), 4.61 (dt, J = 10.9, 5.5 Hz, 2H), 3.74–3.51 (m, 1H, minor), 3.31–3.17 (m, 1H, major), 1.72 (d, J = 6.5 Hz, 4H), 1.66 (d, J = 6.4 Hz, 4H), 1.62–1.55 (m, 4H), 1.54–1.44 (m, 4H), 1.29–1.16 (m, 5H), 1.12–0.93 (m, 7H); 13C NMR (126 MHz, CDCl3) δ 170.7, 170.2, 164.5, 149.7, 149.2, 147.2, 138.6, 136.0, 135.2, 131.7, 129.7, 129.3, 129.1, 128.4, 128.1, 127.2, 126.8, 126.5, 125.9, 120.4, 120.2, 60.7, 60.0, 51.5, 50.0, 49.8, 49.2, 48.9, 32.5, 31.7, 25.3, 25.3, 24.4, 20.7, 20.3. HR-MS (ESI): m/z calculated for C24H27ClN4O6 [M-H]+ 501.1537, found 501.1541.

2.3.7. N-benzyl-2-chloro-N-(2-(cyclohexylamino)-1-(4-(dimethylamino)phenyl)-2-oxoethyl) Propanamide (Vg)

Pale yellow oil; (dr: 3:2); 1H NMR (400 MHz, CDCl3) δ 7.31 (q, J = 2.5, 1.6 Hz, 1H), 7.19 (dt, J = 18.3, 7.1 Hz, 12H), 7.08 (d, J = 7.5 Hz, 2H), 6.59 (dd, J = 8.5, 4.0 Hz, 4H), 5.92 (s, 1H), 5.67 (d, J = 8.1 Hz, 1H), 5.54 (d, J = 8.4 Hz, 2H), 4.92 (d, J = 18.0 Hz, 1H), 4.66–4.48 (m, 3H), 4.44 (d, J = 6.5 Hz, 1H), 4.34 (q, J = 6.4 Hz, 1H), 3.78 (ddtd, J = 20.1, 16.5, 8.6, 8.2, 4.3 Hz, 2H), 2.90 (d, J = 4.6 Hz, 12H), 1.99–1.82 (m, 5H), 1.56 (t, J = 6.6 Hz, 7H), 1.38–1.24 (m, 7H), 1.15–1.00 (m, 7H); 13C NMR (100 MHz, CDCl3) δ 170.4, 168.4, 150.5, 137.5, 130.7, 130.4, 129.6, 128.6, 128.5, 128.3, 127.1, 127.1, 126.2, 125.8, 112.3, 112.3, 64.0, 62.8, 51.1, 50.3, 49.7, 49.2, 48.5, 40.2, 32.7, 26.9, 25.5, 24.8, 24.7, 21.1, 20.7. HR-MS (ESI): m/z calculated for C26H34ClN3O2 [M+Na]+ 478.2239, found 478.2237.

2.3.8. N-benzyl-2-chloro-N-(2-(cyclohexylamino)-1-(4-nitrophenyl)-2-oxoethyl) Propanamide (Vh)

Colorless oil; (dr: 3:2); 1H NMR (400 MHz, CDCl3) δ 8.24–8.19 (m, 1H, minor), 8.11–8.07 (m, 1H, major), 8.02 (d, J = 8.7 Hz, 2H), 7.50 (dd, J = 16.3, 8.7 Hz, 4H), 7.31–7.29 (m, 2H), 7.16 (h, J = 4.4, 3.6 Hz, 4H), 7.10 (d, J = 7.4 Hz, 2H), 6.95–6.90 (m, 2H), 6.40 (d, J = 7.9 Hz, 1H, major), 6.06 (s, 1H, minor), 6.01 (d, J = 8.1 Hz, 1H, minor), 5.88 (s, 1H, major), 5.40 (d, J = 14.7 Hz, 1H, minor), 5.00 (d, J = 17.8 Hz, 1H, major), 4.60 (d, J = 17.8 Hz, 1H, major), 4.50 (q, J = 5.6, 4.7 Hz, 1H, minor), 4.45 (dd, J = 8.3, 4.7 Hz, 1H, major), 3.93 (d, J = 14.7 Hz, 1H, minor), 3.84–3.64 (m, 2H), 1.92–1.82 (m, 2H), 1.67–1.54 (m, 14H), 1.34–1.25 (m, 4H), 1.12 (q, J = 12.0, 10.1 Hz, 6H); 13C NMR (126 MHz, CDCl3) δ 171.1, 170.7, 166.6, 164.5, 148.4, 147.7, 142.3, 141.5, 138.8, 135.9, 130.5, 129.4, 129.2, 128.9, 128.8, 128.7, 128.6, 128.4, 127.9, 127.8, 127.1, 126.0, 125.7, 124.6, 124.5, 123.7, 123.6, 63.1, 61.9, 61.5, 60.3, 50.5, 50.3, 50.1, 48.7, 48.6, 32.7, 32.6, 31.1, 25.3, 24.6, 24.0, 21.0, 20.6, 20.5, 16.6, 14.2. HR-MS (ESI): m/z calculated for C24H28ClN3O4 [M+Na]+ 480.1668, found 480.1666.

2.4. General Procedure for Synthesis of Compounds VIa-VIh

Compound V (0.25 mmol) obtained in step 1 was dissolved in THF (3 mL) and cooled to 0 °C in an ice bath. After 5 min, sodium hydride (NaH 3 eq.) was added to it portion wise and the reaction mixture was refluxed for 3 hrs. The solvent was evaporated and the crude mixture was purified by column chromatography on silica gel using hexane/AcOEt as the eluent.

2.4.1. 1-benzyl-4-(4-methoxybenzyl)-3-methyl-6-phenylpiperazine-2,5-dione (VIa)

Colorless oil; (dr: 99.9:0.1); 1H NMR (500 MHz, CDCl3) δ 7.42 (d, J = 3.8 Hz, 5H), 7.22–7.14 (m, 5H), 6.92 (d, J = 8.5 Hz, 2H), 6.81 (d, J = 8.6 Hz, 2H), 5.85 (s, 1H), 4.67 (d, J = 15.4 Hz, 1H), 4.25 (dd, J = 14.3, 6.1 Hz, 1H), 4.03 (dd, J = 14.3, 6.1 Hz, 1H), 3.83 (s, 3H), 3.79 (dd, J = 8.4, 6.5 Hz, 1H), 3.64 (d, J = 15.4 Hz, 1H), 1.33 (d, J = 7.5 Hz, 3H); 13C NMR (126 MHz, CDCl3) δ 172.1, 168.4, 159.1, 136.3, 135.9, 129.3, 129.1, 129.0, 128.7, 128.5, 128.1, 127.4, 114.0, 57.5, 55.3, 45.0, 42.9, 30.3, 29.7, 11.1. HR-MS (ESI): m/z calculated for C26H26N2O3 [M+Na]+ 437.1792, found 437.1796.

2.4.2. 1-benzyl-4-(4-methoxybenzyl)-6-(4-methoxyphenyl)-3-methylpiperazine-2,5-dione (VIb)

Pale yellow oil; (dr: 95:5); 1H NMR (500 MHz, CDCl3) δ 7.32–7.29 (m, 2H), 7.20–7.12 (m, 5H), 6.92–6.88 (m, 4H), 6.81–6.76 (m, 2H), 5.83 (s, 1H), 4.64 (d, J = 15.3 Hz, 1H), 4.21 (dd, J = 14.2, 6.1 Hz, 1H), 4.00 (dd, J = 14.3, 6.1 Hz, 1H), 3.73 (q, J = 7.5 Hz, 1H), 3.61 (d, J = 15.3 Hz, 1H), 1.29 (d, J = 7.5 Hz, 3H); 13C NMR (126 MHz, CDCl3) δ 172.2, 168.7, 159.7, 159.1, 136.4, 129.5, 129.3, 129.1, 128.8, 128.5, 128.1, 127.7, 114.3, 113.9, 71.3, 57.4, 55.4, 55.3, 44.8, 42.9, 11.1. HR-MS (ESI): m/z calculated for C27H28N2O4 [M+Na]+ 467.1946, found 467.1947.

2.4.3. 1-benzyl-4-cyclohexyl-3-methyl-6-phenylpiperazine-2,5-dione (VIc)

Colorless Oil; (dr: 85:15); 1H NMR (500 MHz, CDCl3) δ 7.44 (d, J = 4.2 Hz, 4H), 7.42–7.31 (m, 6H), 7.27 (dd, J = 8.4, 2.2 Hz, 3H), 5.56 (d, J = 8.3 Hz, 1H, major), 5.29 (d, J = 8.3 Hz, 1H, minor), 4.86 (d, J = 15.8 Hz, 1H, minor), 4.74 (d, J = 15.4 Hz, 1H, major), 4.15 (d, J = 15.8 Hz, 1H, minor), 4.11–4.02 (m, 1H, minor), 3.81 (q, J = 7.5 Hz, 1H), 3.67 (dtd, J = 11.3, 7.7, 4.0 Hz, 1H, major), 3.51 (d, J = 15.4 Hz, 1H, major), 1.73–1.63 (m, 1H), 1.56 (dd, J = 10.9, 6.7 Hz, 5H), 1.37 (d, J = 7.5 Hz, 3H, major), 1.31–1.19 (m, 4H), 0.96 (ddd, J = 17.6, 13.5, 10.5 Hz, 1H), 0.85 (d, J = 7.6 Hz, 3H, minor), 0.62 (qd, J = 12.2, 3.5 Hz, 1H), 0.49–0.39 (m, 1H); 13C NMR (126 MHz, CDCl3) δ 172.5, 167.6, 136.8, 136.3, 136.1, 134.3, 129.4, 128.9, 128.8, 128.8, 128.7, 128.6, 128.5, 128.3, 128.2, 127.9, 127.7, 127.5, 125.9, 71.7, 71.5, 57.4, 54.8, 48.5, 48.0, 45.1, 44.8, 32.6, 32.5, 32.4, 32.1, 29.6, 25.3, 25.2, 24.7, 24.6, 11.1, 10.2. HR-MS (ESI): m/z calculated for C24H28N2O2 [M+Na]+ 399.2048, found 399.2073.

2.4.4. 1-benzyl-4-(4-methoxybenzyl)-3-methyl-6-(p-tolyl)piperazine-2,5-dione (VId)

White sticky compound; (dr: 3:2); 1H NMR (500 MHz, CDCl3) δ 7.27 (dd, J = 4.8, 2.6 Hz, 6H), 7.25–7.19 (m, 4H), 7.20–7.15 (m, 6H), 7.14 (dd, J = 6.6, 3.2 Hz, 2H), 7.12–7.09 (m, 1H), 6.92–6.87 (m, 4H), 6.81–6.75 (m, 4H), 5.82 (d, J = 6.3 Hz, 1H, major), 5.61 (s, 1H, minor), 4.80 (d, J = 15.7 Hz, 1H, minor), 4.64 (d, J = 15.4 Hz, 1H, major), 4.23 (d, J = 6.1 Hz, 1H, minor), 4.20 (d, J = 6.1 Hz, 1H, minor), 4.17–4.14 (m, 1H, major), 4.13 (d, J = 5.2 Hz, 1H), 4.04–4.01 (m, 1H, minor), 4.01–3.99 (m, 1H), 3.81 (s, 3H, major), 3.78 (s, 3H, minor), 3.75 (d, J = 7.5 Hz, 1H), 3.63 (d, J = 15.4 Hz, 1H, major), 2.36 (s, 3H, major), 2.35 (s, 3H, minor), 1.30 (d, J = 7.4 Hz, 3H, major), 1.21 (d, J = 6.2 Hz, 3H, minor); 13C NMR (126 MHz, CDCl3) δ 172.3, 172.2, 169.8, 168.6, 159.0, 138.6, 138.5, 136.4, 136.0, 132.8, 131.1, 129.6, 129.5, 129.5, 129.3, 129.1, 128.8, 128.5, 128.1, 128.0, 127.8, 127.5, 127.3, 114.0, 113.9, 71.52, 71.4, 64.3, 57.3, 55.3, 55.2, 54.3, 45.1, 44.9, 43.3, 42.9, 25.3, 21.0, 11.1, 10.3. HR-MS (ESI): m/z calculated for C27H28N2O3 [M+Na]+ 451.1997, found 451.1998.

2.4.5. 1-benzyl-4-cyclohexyl-3-methyl-6-(p-tolyl)piperazine-2,5-dione (VIe)

Colorless Oil; (dr: 85:15); 1H NMR (500 MHz, CDCl3) δ 7.34 (q, J = 7.8, 7.0 Hz, 3H), 7.31–7.23 (m, 4H), 7.20 (d, J = 8.0 Hz, 2H), 5.52 (d, J = 8.3 Hz, 1H, major), 5.28 (d, J = 7.9 Hz, 1H, minor), 4.80 (d, J = 15.7 Hz, 1H, minor), 4.69 (d, J = 15.4 Hz, 1H, major), 4.11 (d, J = 15.8 Hz, 1H, minor), 4.05 (q, J = 7.6 Hz, 1H, minor), 3.75 (q, J = 7.5 Hz, 1H, major), 3.64 (dtd, J = 11.7, 8.0, 4.0 Hz, 1H), 3.49 (d, J = 15.4 Hz, 1H, major), 2.36 (s, 3H), 1.68–1.58 (m, 1H), 1.52 (d, J = 14.2 Hz, 4H), 1.33 (d, J = 7.5 Hz, 3H), 1.29–1.15 (m, 5H); 13C NMR (126 MHz, CDCl3) δ 172.58, 169.13, 167.74, 138.57, 138.37, 136.89, 136.43, 132.88, 131.12, 129.63, 129.43, 129.33, 128.94, 128.86, 128.25, 128.17, 127.87, 127.64, 127.38, 71.37, 57.21, 54.61, 48.52, 48.01, 47.89, 45.02, 44.71, 32.63, 32.59, 32.49, 32.11, 31.52, 29.63, 26.87, 25.24, 24.76, 24.74, 24.64, 21.01, 20.99, 14.04, 11.11, 10.19. HR-MS (ESI): m/z calculated for C25H30N2O2 [M-H]+ 389.2225, found 389.2229.

2.4.6. 1-benzyl-4-cyclohexyl-6-(2,4-dinitrophenyl)-3-methylpiperazine-2,5-dione (VIf)

Yellow oil; (dr: 85:15); 1H NMR (500 MHz, CDCl3) δ 8.91 (d, J = 2.4 Hz, 1H), 8.21 (dd, J = 8.5, 2.4 Hz, 1H), 7.37 (d, J = 8.6 Hz, 1H), 7.33 (q, J = 2.9 Hz, 5H), 5.54 (d, J = 7.6 Hz, 1H), 4.55 (d, J = 15.1 Hz, 1H), 4.26 (d, J = 15.1 Hz, 1H), 4.10–4.07 (m, 1H), 3.51 (dtdt, J = 14.3, 10.4, 6.4, 3.4 Hz, 1H), 1.71–1.50 (m, 10H), 1.45–1.41 (m, 1H), 1.40–1.19 (m, 7H), 0.91 (d, J = 7.4 Hz, 3H); 13C NMR (126 MHz, CDCl3) δ 171.0, 165.5, 149.0, 147.7, 138.6, 135.3, 131.28, 129.3, 129.2, 129.0, 128.8, 128.3, 126.9, 120.6, 72.7, 64.3, 56.5, 49.6, 49.2, 46.3, 33.9, 32.8, 32.4, 30.6, 29.7, 25.6, 25.3, 24.9, 24.8, 24.7, 17.6, 14.1, 13.6, 11.2. HR-MS (ESI): m/z calculated for C24H26N4O6 [M+Na]+ 489.1793, found 489.1795.

2.4.7. 1-benzyl-4-cyclohexyl-6-(4-(dimethylamino)phenyl)-3-methylpiperazine-2,5-dione (VIg)

Yellow oil; (dr: 85:15); 1H NMR (500 MHz, CDCl3) δ 7.38–7.33 (m, 3H), 7.30–7.25 (m, 5H), 6.75–6.72 (m, 2H), 5.54 (d, J = 8.4 Hz, 1H), 4.69 (d, J = 15.3 Hz, 1H), 3.75 (q, J = 7.5 Hz, 1H), 3.67 (tdq, J = 11.6, 7.9, 3.8 Hz, 1H), 3.56 (d, J = 15.3 Hz, 1H), 3.00 (s, 5H), 1.61–1.49 (m, 5H), 1.35 (d, J = 7.5 Hz, 3H), 1.28–1.18 (m, 3H), 1.00–0.92 (m, 1H), 0.90–0.85 (m, 1H); 13C NMR (126 MHz, CDCl3) δ 172.9, 172.8, 169.6, 168.1, 150.4, 150.1, 137.1, 136.6, 129.2, 128.8, 128.7, 128.4, 128.2, 128.1, 127.7, 122.6, 120.5, 112.3, 112.0, 76.7, 71.5, 71.4, 60.3, 56.8, 54.5, 48.4, 47.9, 47.8, 44.8, 44.6, 40.2, 40.2, 32.6, 32.6, 32.5, 32.1, 25.3, 25.2, 24.7, 24.7, 24.6, 20.9, 14.1, 11.1, 10.2. HR-MS (ESI): m/z calculated for C24H33N3O2 [M+H]+ 442.2474 found 442.2470.

2.4.8. 1-benzyl-4-cyclohexyl-3-methyl-6-(4-nitrophenyl)piperazine-2,5-dione (VIh)

Colorless oil; (dr: 1:1); 1H NMR (500 MHz, CDCl3) δ 8.28–8.22 (m, 4H), 7.69–7.65 (m, 2H), 7.58–7.54 (m, 2H), 7.42–7.33 (m, 9H), 7.28–7.26 (m, 2H), 5.62 (d, J = 8.3 Hz, 1H), 5.36 (d, J = 7.9 Hz, 1H), 4.90 (d, J = 15.6 Hz, 1H), 4.83 (d, J = 15.4 Hz, 1H), 4.16–4.10 (m, 1H), 4.02 (q, J = 7.6 Hz, 1H), 3.74 (q, J = 7.5 Hz, 1H), 3.63 (ddtd, J = 26.1, 11.3, 7.8, 3.9 Hz, 2H), 3.47 (d, J = 15.3 Hz, 1H), 1.74–1.64 (m, 3H), 1.64–1.50 (m, 9H), 1.38 (d, J = 7.5 Hz, 3H), 1.31–1.20 (m, 6H), 1.04–0.91 (m, 2H), 0.87 (d, J = 7.6 Hz, 3H); 13C NMR (126 MHz, CDCl3) δ 171.6, 171.5, 167.9, 166.5, 147.8, 143.5, 141.7, 136.2, 135.9, 129.6, 129.3, 128.9, 128.8, 128.7, 128.6, 128.5, 128.4, 123.9, 123.6, 76.7, 71.3, 70.7, 60.3, 59.1, 56.3, 48.7, 48.3, 45.4, 45.1, 32.6, 32.4, 32.1, 25.1, 24.7, 24.7, 24.6, 20.9, 14.1, 11.1, 10.2. HR-MS (ESI): m/z calculated for C24H27N3O4 [M+H]+ 444.1904 found 444.1899.

3. Results & Discussion

3.1. Chemistry

Diketopiperazines possess a variety of biological activities. They are found in numerous natural products and are also obtained from the degradation of polypeptides in foodstuff. Their small, conformationally strained structure makes them more attractive along with the possibility of instigating several substituents at six different positions. Due to their rigid backbone, they are quite popular in drug discovery as an important pharmacophore. Post-Ugi transformation for the synthesis of diketopiperazines has been reported [31,32] but these transformations were using reagents such as PPh3 which make the purification process hard. In this study, we synthesized a library of differently substituted diketopiperazines varying the substrates for the Ugi multicomponent reaction. To see the effect of substituents on cyclic and acyclic peptidomimetics we used different isocyanides (p-methoxybenzylisocyanide and isocyanocyclohexane) and eight different aldehydes. Diketopiperazines were synthesized in a two-step process. First, target peptidomimetics were obtained via Ugi multicomponent reaction (Scheme 1). A model Ugi reaction was carried out using 2-chloropropionic acid, benzyl amine, benzaldehyde and p-methoxybenzylisocyanide as substrates (Scheme 2) in methanol at room temperature following the same procedure reported by us [33], which resulted in product Va with 30% yield. To check the effect of temperature on reaction yield we performed the reaction with methanol at 30 °C and obtained product Va with 32% yield. A further increase in temperature to 50 °C led to a gradual increase in yield but when the temperature was increased to 60 °C, the reaction yield remained the same which indicates 50 °C as an optimal temperature for this reaction. Since we know that solvent can also affect the progress of the reaction and hence the yield, so we screened various polar protic solvents known for the Ugi reaction and we found Trifluoroethanol to be an efficient solvent for this transformation (Table 1, entry 8). Then we further increased the temperature to 60 °C (entry 9) and yield dropped down to 42%. The mechanistic reason is unclear but it can be that the non-nucleophilic nature of TFE is suppressing the side reactions [34] and increasing the overall yield of product. So, we took the best conditions found in optimization (Table 1, entry 8) for the synthesis of compounds Va–Vh with good yield (Figure 2). This Ugi reaction led to the formation of a diastereomeric mixture of peptidomimetics.
Naliapara et. al. reported the cyclisation of Ugi peptidomimetic using a transition metal catalyst [35]. We modified the conditions for our reaction to eliminate the usage of a metal catalyst (Table 2, Scheme 3, Entry 1). This reaction yielded 25% product. Then, the same reaction was performed at a lower temperature (90 °C; Table 2, entry 2) as well as a high temperature (110 °C; Table 2, entry 3) but yield remained the same. Since the solvent is known to be a crucial parameter in terms of modulating the yield, several different organic solvents were applied (Table 2, entry 4). Further model reaction was conducted at different temperatures (Table 2, entries 4–6); however, it was observed that at high temperatures, the yield decreases (Table 2, entry 6), which may be due to product decomposition. It indicates 65 °C as the optimal temperature for the studied cyclisation reaction. The application of various solvents (Table 2, entry 9–11) resulted in maximum yield (49%) with THF. Having optimized the solvent and temperature for the model reaction, we screened various organic and inorganic bases (Table 2, entry 12–16) and observed that NaH in THF at 65 °C gives product VIa with a good yield of 70%. These conditions were further used to obtain DKPs VIa–VIh with the yields ranging from 44% to 70%. Upon cyclisation, we observed the change in diastereomeric ratios varying with the attached substituents in the peptidomimetic scaffold.

3.2. Cytotoxic Studies of the Synthesized Compounds

The obtained results indicate that all tested Diketopiperazines show cytotoxic activity in all analyzed E.coli strains differing in LPS length. Different inhibitory activity was found depending on the nature of the R1 and R2 substituents attached to the chlorine atom of the tested compounds. Among all tested compounds, the compounds from VIa–VIh showed a stronger antibacterial effect than Va–Vh. It is worth noting that the introduction of the chlorine atom into the structure of the tested compounds had a significant impact on their activity and cytotoxicity and high selectivity against selected E. coli model strains in the MIC and MBC tests, which is often observed in various types of compounds showing strong microbiological activity on cells [12]. These compounds showed higher activity against strains R2, R3 and R4 than commonly used antibiotics (Figure 3, Figure 4, Figure 5, Figure 6 and Figure 7). The values of the MIC and MBC tests for each model of E. coli R2–R4 and K12 strains were visible on all analyzed growth microplates after the addition of resazurin.
The analyzed bacterial strains used in the experiments were used in 48-well plates; which were treated with the analyzed compounds in the MIC and MBC assays. On the basis of their analysis, color changes were observed for all tested compounds, but at different levels and at different dilutions. The most sensitive to the effects of the analyzed compounds were the bacterial strains R3 and R4 due to the increasing length of their LPS (visible dilutions 10−2 corresponding to a concentration of 0.0015 μM); more than strains K12 and R2 (visible dilutions of 10−6 corresponding to a concentration of 0.0015 µM). Strain R4 was the most sensitive, possibly due to the longest length of lipopolysaccharide (LPS) in the bacterial membrane. In all analyzed cases, the MBC test values were approximately 75 times higher than the MIC test values in eight analyzed compounds including Cl (Figure 3, Figure 4 and Figure 5 and Table 3).

3.3. Analysis of R2–R4 E. coli Strains Modified with Tested Compounds diketopiperazines

The obtained MIC values, as well as our previous studies with various types of the analyzed compounds [20,21,22,23,24,25,26,27,28,29,30], indicate that derivatives of diketopiperazines also show a strong toxic effect of the analyzed model strains of bacteria. The three compounds analyzed were selected for further analysis by modifying their DNA. Modified bacterial DNA was digested with Fpg as previously described [36,37,38,39,40,41]. All selected analyzed derivatives of diketopiperazines including various types of alkoxy groups, substituents located at aromatic rings and the length of the alkyl chain can strongly change the bacterial DNA topology. After Fpg digestion, approximately 3.5% of the oxidative damage was identified, which, similar to previous observations, indicates very strong oxidative damage in bacterial DNA [7,8,9]. Different types of alkoxy groups, substituents located on the aromatic ring and the length of the alkyl chain, may determine the toxicity of the analyzed E. coli strains, including in particular R4, as evidenced by the obtained MIC, MBC and MTT values. The obtained results for individual compounds were statistically significant at the level of p < 0.05 (Figure 6, Figure 7 and Figure 8).

3.4. R2–R4 E. coli Strains with Tested Peptidomimetics

The performed studies support the concept that the synthesized compounds can be considered drug candidates for further studies (Supplementary Materials Figure S3).

4. Conclusions

An efficient method for the synthesis of peptidomimetics was developed using the Ugi reaction; these were then used to synthesis diketopiperazines. The established protocol was used to synthesize a series of target products containing differently substituted aldehydes and isocyanides. This protocol ensures the efficient, gentle and metal-free synthesis of the target products with good yields (49%–70%). The cytotoxic effect of the obtained cyclic and acyclic peptidomimetics was assessed on model E. coli strain and its mutants. The analyzed diketopiperazines derivatives are able to modify all model strains of E. coli (R2–R4) and their bacterial DNA, changing the spatial structure of LPS contained in their cell membranes. Compared to the derivatives, the most active among the tested derivatives turned out to be those with cyclic structures VI–VIh. We have found that the stiffening of the peptidomimetic structure is responsible for increase in their antimicrobial activity. Figure 3 reveals that compounds VIa, VIb, VIc and VIg have the highest potential as anti-bacterial drug candidates among the tested DKPs. Our studies also show that synthesized DKPs have a lower MIC value compared to well-known antibiotics, which allows us to say that DKPs hold more potential as antibiotic drug candidates due to high anti-bacterial activity for all the tested mutants. The results of the presented research are important for understanding the biological properties of the studied derivative diketopiperazines as a function of potential new antibiotics and their toxic effects on gram-negative bacteria and cancer cell lines in the face of the growing drug resistance pandemic. Referring to our previous work related to the characteristics of the E. coli K12 and R2–R4 models it is worth continuing this research on the separation of diastereomers of the analyzed compounds and their studies on E. coli strains and on human cell lines in various types of cancer.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/molecules27113633/s1, Figure S1. Examples of MIC and MBC on microplates with different concentration of studied compounds (mg L−1). Figure S2. An example of an agarose gel electrophoresis separation of isolated plasmids DNA on R4 strains modified with selected compounds (Panel A) from 8 selected compounds, as shown in Figure 3, and digested with repair Fpg protein (Panel B). M = marker. Figure S3. Example of an agarose gel electrophoresis separation of isolated plasmids DNA from R2–R4 strains modified with antibiotics: bleomycin, ciprofloxacin, and cloxacillin digested with repair enzymes Fpg. M = marker. Figure S4: Structure of antibiotics. Figure S5: NMR spectra of synthesized compounds Va–Vh & VIa–VIh.

Author Contributions

Conceptualization, P.K., P.S. and R.O.; methodology, P.S., P.K., R.O. investigation, P.K., A.W. and M.S.; resources, R.O., P.K.; data curation, K.K., M.S. and A.W.; writing—original draft preparation, P.K., P.S. and R.O. and D.K.; writing—review and editing, D.K., R.O. and P.K.; supervision, R.O. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by a grant from the Medical University of Białystok SUB/2/DN/22/001/2201 and by National Science Centre, Poland project OPUS No. 2019/33/B/ST4/01118.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

On request of those interested.

Acknowledgments

The authors thank Jolanta Łukasiewicz from Ludwik Hirszfeld Institute of Immunology and Experimental Therapy (Polish Academy of Sciences) for providing the strains of E. coli.

Conflicts of Interest

The authors declare no conflict of interest.

Sample Availability

On request of those interested.

Abbreviations

MICminimum inhibitory concentration
MBCminimum bactericidal concentration
Ocopen circle
Ccccovalently closed circle
BERbase excision repair
FpgDNA-formamidopyrimidine glycosylase

References

  1. Ugi, I. The α-addition of immonium ions and anions to isonitriles accompanied by secondary reactions. Angew. Chem. Int. Ed. 1962, 1, 8–21. [Google Scholar] [CrossRef]
  2. Hulme, C.; Gore, V. Multi-component Reactions: Emerging Chemistry in Drug Discovery ‘From Xylocain to Crixivan’. Curr. Med. Chem. 2003, 10, 51–80. [Google Scholar] [CrossRef] [PubMed]
  3. Borthwick, A.D. 2, 5-Diketopiperazines: Synthesis, reactions, medicinal chemistry, and bioactive natural products. Chem. Rev. 2012, 112, 3641–3716. [Google Scholar] [CrossRef] [PubMed]
  4. Daugan, A.; Grondin, P.; Ruault, C.; Le Monnier de Gouville, A.-C.; Coste, H.; Linget, J.M.; Kirilovsky, J.; Hyafil, F.; Labaudiniere, R. The discovery of tadalafil: A novel and highly selective PDE5 inhibitor. 2: 2, 3, 6, 7, 12, 12a-hexahydropyrazino [1‘, 2‘: 1, 6] pyrido [3, 4-b] indole-1, 4-dione analogues. J. Med. Chem. 2003, 46, 4533–4542. [Google Scholar] [CrossRef] [PubMed]
  5. Wyatt, P.G.; Allen, M.J.; Borthwick, A.D.; Davies, D.E.; Exall, A.M.; Hatley, R.J.D.; Irving, W.R.; Livermore, D.G.; Miller, N.D.; Nerozzi, F.; et al. 2, 5-Diketopiperazines as potent and selective oxytocin antagonists 1: Identification, stereochemistry and initial SAR. Bioorg. Med. Chem. Lett. 2005, 15, 2579–2582. [Google Scholar] [CrossRef]
  6. Allen, J.D.; van Loevezijn, A.; Lakhai, J.M.; van der Valk, M.; van Tellingen, O.; Reid, G.; Schellens, J.H.M.; Koomen, G.J.; Schinkel, A.H. Potent and Specific Inhibition of the Breast Cancer Resistance Protein Multidrug Transporter in Vitro and in Mouse Intestine by a Novel Analogue of Fumitremorgin C1. Mol. Cancer Ther. 2002, 1, 417–425. [Google Scholar]
  7. Szardenings, A.K.; Antonenko, V.; Campbell, D.A.; DeFrancisco, N.; Ida, S.; Shi, L.H.; Sharkov, N.; Tien, D.; Wang, Y.W.; Navre, M. Identification of highly selective inhibitors of collagenase-1 from combinatorial libraries of diketopiperazines. J. Med. Chem. 1999, 42, 1348–1357. [Google Scholar] [CrossRef]
  8. Mas, V.; Falco, A.; Brocal, I.; Perez, L.; Coll, J.M.; Estepa, A. Identification of selective inhibitors of VHSV from biased combinatorial libraries of N, N′-disubstituted 2, 5-piperazinediones. Antivir. Res. 2006, 72, 107–115. [Google Scholar] [CrossRef]
  9. Miyoshi, T.; Miyairi, N.; Aoki, H.; Kohsaka, M.; Sakai, H.; Imanaka, H. Bicyclomycin, a new antibiotic I. Taxonomy, isolation and characterization. J. Antibiot. 1972, 25, 569–575. [Google Scholar] [CrossRef] [Green Version]
  10. Miyamura, S.; Ogasawara, N.; Otsuka, H.; Niwayama, S.; Tanaka, H.; Take, T.; Uchiyama, T.; Ochiai, H.; Abe, K. Antibiotic No. 5879, a new water-soluble antibiotic against Gram-negative bacteria. J. Antibiot. 1972, 25, 610–612. [Google Scholar] [CrossRef] [Green Version]
  11. Andersen, O.A.; Dixon, M.J.; Eggleston, I.M.; van Aalten, D.M. Natural product family 18 chitinase inhibitors. Nat. Prod. Rep. 2005, 22, 563–579. [Google Scholar] [CrossRef] [PubMed]
  12. Guan, J.; Mathai, S.; Harris, P.; Wen, J.Y.; Zhang, R.; Brimble, M.; Gluckman, P. Peripheral administration of a novel diketopiperazine, NNZ 2591, prevents brain injury and improves somatosensory-motor function following hypoxia–ischemia in adult rats. Neuropharmacology 2007, 53, 749–762. [Google Scholar] [CrossRef] [PubMed]
  13. Lopez-Rodrıguez, M.L.; Rosado, M.L.; Benhamu, B.; Morcillo, M.J.; Fernandez, E.; Schaper, K.J. Synthesis and Structure− Activity Relationships of a New Model of Arylpiperazines. 2. Three-Dimensional Quantitative Structure− Activity Relationships of Hydantoin−Phenylpiperazine Derivatives with Affinity for 5-HT1A and α1 Receptors. A Comparison of CoMFA Models. J. Med. Chem. 1997, 40, 1648–1656. [Google Scholar] [PubMed]
  14. Shimazaki, N.; Shima, I.; Okamoto, M.; Yoshida, K.; Hemmi, K.; Hashimoto, M. PAF inhibitory activity of diketopiperazines: Structure-activity relationships. In Platelet-Activating Factor and Structurally Related Alkyl Ehter Lipids. AOCS Pub. 1991, 26, 223–226. [Google Scholar]
  15. Bobylev, M.M.; Bobyleva, L.I.; Cutler, H.G.; Cutler, S.J.; Strobel, G.A. Growth regulating activity of maculosin analogs in the etiolated wheat coleoptile bioassay (Triticum aestivum L. cv. Wakeland). PGRSA Q. 1999, 27, 105–118. [Google Scholar]
  16. Williams, R.M.; Stocking, E.M.; Sanz-Cervera, J.F. Biosynthesis of prenylated alkaloids derived from tryptophan. Biosyn 2000, 209, 97–173. [Google Scholar]
  17. Kowalczyk, P.; Madej, A.; Szymczak, M.; Ostaszewski, R. α-Amidoamids as New Replacements of Antibiotics—Research on the Chosen K12, R2–R4 E. coli Strains. Materials 2020, 13, 5169. [Google Scholar] [CrossRef]
  18. Ku, I.W.; Kang, S.B.; Keum, G.C.; Kim, Y.S. Synthesis of α, β-unsaturated 2-Oxopyrrolidinyl acetamide derivatives by application of the Ugi/RCM reaction sequence. Bull. Korean Chem. Soc. 2011, 32, 3167–3170. [Google Scholar] [CrossRef] [Green Version]
  19. Sutanto, F.; Shaabani, S.; Oerlemans, R.; Eris, D.; Patil, P.; Hadian, M.; Dömling, A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew. Chem. Int. Ed. 2021, 60, 18231–18239. [Google Scholar] [CrossRef]
  20. Wang, W.; Wang, Y.; Tao, H.; Peng, X.; Liu, P.; Zhu, W. Cerebrosides of the halotolerant fungus Alternaria raphani isolated from a sea salt field. J. Nat. Prod. 2009, 72, 1695–1698. [Google Scholar] [CrossRef]
  21. Samsonowicz-Górski, J.; Kowalczyk, P.; Koszelewski, D.; Brodzka, A.; Szymczak, M.; Kramkowski, K.; Ostaszewski, R. The Synthesis and Evaluation of Amidoximes as Cytotoxic Agents on Model Bacterial E. coli Strains. Materials 2021, 14, 7577. [Google Scholar] [CrossRef] [PubMed]
  22. Kowalczyk, P.; Trzepizur, D.; Szymczak, M.; Skiba, G.; Kramkowski, K.; Ostaszewski, R. 1,2-Diarylethanols—A New Class of Compounds That Are Toxic to E. coli K12, R2–R4 Strains. Materials 2021, 14, 1025. [Google Scholar] [CrossRef] [PubMed]
  23. Laskowska, M.; Pastukh, O.; Fedorchuk, A.; Schabikowski, M.; Kowalczyk, P.; Zalasiński, M.; Laskowski, Ł. Nanostructured Silica with Anchoring Units: The 2D Solid Solvent for Molecules and Metal Ions. Int. J. Mol. Sci. 2020, 21, 8137. [Google Scholar] [CrossRef]
  24. Kowalczyk, P.; Borkowski, A.; Czerwonka, G.; Cłapa, T.; Cieśla, J.; Misiewicz, A.; Borowiec, M.; Szala, M. The microbial toxicity of quaternary ammonium ionic liquids is dependent on the type of lipopolysaccharide. J. Mol. Liq. 2018, 266, 540–547. [Google Scholar] [CrossRef]
  25. Borkowski, A.; Kowalczyk, P.; Czerwonka, G.; Ciésla, J.; Cłapa, T.; Misiewicz, A.; Szala, M.; Drabik, M. Interaction of quaternary ammonium ionic liquids with bacterial membranes—Studies with Escherichia coli R1–R4-type lipopolysaccharides. J. Mol. Liq. 2017, 246, 282–289. [Google Scholar] [CrossRef]
  26. Kowalczyk, P.; Gawdzik, B.; Trzepizur, D.; Szymczak, M.; Skiba, G.; Raj, S.; Kramkowski, K.; Lizut, R.; Ostaszewski, R. δ-Lactones—A New Class of Compounds That Are Toxic to E. coli K12 and R2–R4 Strains. Materials 2021, 14, 2956. [Google Scholar] [CrossRef]
  27. Maciejewska, A.; Kaszowska, M.; Jachymek, W.; Lugowski, C.; Lukasiewicz, J. Lipopolysaccharide-linked Enterobacterial Common Antigen (ECALPS) Occurs in Rough Strains of Escherichia coli R1, R2, and R4. Int. J. Mol. Sci. 2020, 21, 6038. [Google Scholar] [CrossRef]
  28. Prost, M.E.; Prost, R. Basic parameters of evaluation of the effectiveness of antibiotic therapy. Ophth. Ther. 2017, 4, 233–236. [Google Scholar]
  29. Al-Jaidi, B.A.; Telfah, S.T.; Bardaweel, S.K.; Deb, P.K.; Borah, P.; Venugopala, K.N.; Bataineh, Y.A.; Al Khames Aga, Q.A. Anticancer Activity and In Silico ADMET Properties of 2,4,5-Trisubstitutedthiazole Derivatives. Curr. Drug Metab. 2021, 22, 532–536. [Google Scholar] [CrossRef]
  30. Simic, M.; Petkovic, M.; Jovanovic, P.; Jovanovic, M.; Tasic, G.; Besu, I.; Zizak, Z.; Aleksic, I.; Nikodinovic-Runic, J.; Savic, V. Fragment-type 4-azolylcoumarin derivatives with anticancer properties. Arch. Pharm. 2021, 354, 2100238. [Google Scholar] [CrossRef] [PubMed]
  31. Balalaie, S.; Ramezani Kejani, R.; Ghabraie, E.; Darvish, F.; Rominger, F.; Hamdan, F.; Bijanzadeh, H.R. Diastereoselective synthesis of functionalized diketopiperazines through post-transformational reactions. J. Org. Chem. 2017, 82, 12141–12152. [Google Scholar] [CrossRef] [PubMed]
  32. Halimehjani, A.Z.; Sharifi, M. Synthesis of a novel category of Ugi adducts using succinic acid, succinic anhydride and maleic anhydride and their application in post-Ugi reactions for synthesis of functionalized piperazine 2, 5-diones. Tetrahedron 2017, 73, 5778–5783. [Google Scholar] [CrossRef]
  33. Kowalczyk, P.; Wilk, M.; Parul, P.; Szymczak, M.; Kramkowski, K.; Raj, S.; Skiba, G.; Sulejczak, D.; Kleczkowska, P.; Ostaszewski, R. The Synthesis and Evaluation of Aminocoumarin Peptidomimetics as Cytotoxic Agents on Model Bacterial E. coli Strains. Materials 2021, 14, 5725. [Google Scholar] [CrossRef] [PubMed]
  34. Thompson, M.J.; Chen, B. Ugi reactions with ammonia offer rapid access to a wide range of 5-aminothiazole and oxazole derivatives. J. Org. Chem. 2009, 74, 7084–7093. [Google Scholar] [CrossRef] [PubMed]
  35. Radadia, A.C.; Rajapara, J.G.; Naliapara, Y.T. An efficient protocol for the synthesis of N-fused 2, 5-diketopiperazine via base catalyzed Ugi-type MCR. Org. Chem. 2018, 2018, 174–183. [Google Scholar] [CrossRef] [Green Version]
  36. Pobłocki, K.; Jacewicz, D.; Walczak, J.; Gawdzik, B.; Kramkowski, K.; Drzeżdżon, J.; Kowalczyk, P. Preparation of Allyl Alcohol Oligomers Using Dipicolinate Oxovanadium(IV) Coordination Compound. Materials 2022, 15, 695. [Google Scholar] [CrossRef] [PubMed]
  37. Qian, Z.; Liu, T.; Liu, Y.Y.; Briesewitz, R.; Barrios, A.M.; Jhiang, S.M.; Pei, D. Efficient delivery of cyclic peptides into mammalian cells with short sequence motifs. ACS Chem. Biol. 2013, 8, 423–431. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Cascales, L.; Henriques, S.T.; Kerr, M.C.; Huang, Y.H.; Sweet, M.J.; Daly, N.L.; Craik, D.J. Identification and characterization of a new family of cell-penetrating peptides: Cyclic cell-penetrating peptides. J. Biol. Chem. 2011, 286, 36932–36943. [Google Scholar] [CrossRef] [Green Version]
  39. Mandal, D.; Shirazi, A.N.; Parang, K. Cell-penetrating homochiral cyclic peptides as nuclear-targeting molecular transporters. Angew. Chem. Int. Ed. 2011, 50, 9633–9637. [Google Scholar] [CrossRef]
  40. Traboulsi, H.; Larkin, H.; Bonin, M.A.; Volkov, L.; Lavoie, C.L.; Marsault, E. Macrocyclic cell penetrating peptides: A study of structure-penetration properties. Bioconjugate Chem. 2015, 26, 405–411. [Google Scholar] [CrossRef]
  41. Feni, L.; Jütten, L.; Parente, S.; Piarulli, U.; Neundorf, I.; Diaz, D. Cell-penetrating peptides containing 2, 5-diketopiperazine (DKP) scaffolds as shuttles for anti-cancer drugs: Conformational studies and biological activity. Chem. Commun. 2022, 56, 5685–5688. [Google Scholar] [CrossRef]
Molecules 27 03633 g001 550
Figure 1. Biologically active DKPs.
Figure 1. Biologically active DKPs.
Molecules 27 03633 g001
Molecules 27 03633 sch001 550
Scheme 1. Proposed two step synthesis of DKPs.
Scheme 1. Proposed two step synthesis of DKPs.
Molecules 27 03633 sch001
Molecules 27 03633 sch002 550
Scheme 2. Model Ugi reaction.
Scheme 2. Model Ugi reaction.
Molecules 27 03633 sch002
Molecules 27 03633 g002 550
Figure 2. Structures of investigated peptidomimetics and DKPs with isolated yield and diastereomeric ratio in brackets.
Figure 2. Structures of investigated peptidomimetics and DKPs with isolated yield and diastereomeric ratio in brackets.
Molecules 27 03633 g002
Molecules 27 03633 sch003 550
Scheme 3. Model cyclisation reaction.
Scheme 3. Model cyclisation reaction.
Molecules 27 03633 sch003
Molecules 27 03633 g003 550
Figure 3. Minimum inhibitory concentration (MIC) of the phosphonate derivatives in model bacterial strains. The x-axis features compounds 1–16 used sequentially. The y-axis shows the MIC value in μg/mL−1 Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Figure 3. Minimum inhibitory concentration (MIC) of the phosphonate derivatives in model bacterial strains. The x-axis features compounds 1–16 used sequentially. The y-axis shows the MIC value in μg/mL−1 Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Molecules 27 03633 g003
Molecules 27 03633 g004 550
Figure 4. Minimum bactericidal concentration (MBC) of the phosphonate derivatives. The x-axis features compounds Va–Vh and VIa–VIh used sequentially. The y-axis shows the MIC value in μg/mL−1. Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Figure 4. Minimum bactericidal concentration (MBC) of the phosphonate derivatives. The x-axis features compounds Va–Vh and VIa–VIh used sequentially. The y-axis shows the MIC value in μg/mL−1. Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Molecules 27 03633 g004
Molecules 27 03633 g005 550
Figure 5. The ratio of MBC/MIC of the phosphonate derivatives. The x-axis features compounds Va–Vh and VIa–VIh used sequentially. The y-axis shows the MIC value. Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Figure 5. The ratio of MBC/MIC of the phosphonate derivatives. The x-axis features compounds Va–Vh and VIa–VIh used sequentially. The y-axis shows the MIC value. Investigated strains of E. coli K12 as control (blue), R2 strains (orange), R3 strain (grey), and R4 strain (yellow). The y-axis shows the MBC value in μg/mL−1. The order in which the compounds were applied to the plate is shown in Supplementary Materials Figure S1.
Molecules 27 03633 g005
Molecules 27 03633 g006 550
Figure 6. Percentage of plasmid DNA recognized by Fpg enzyme (y-axis) with model bacterial, K12, and R2–R4 strains (x-axis). All analyzed compounds numbered were statistically significant at <0.05 * (see Table 2 and Supplementary Materials Figure S2 panel A and B).
Figure 6. Percentage of plasmid DNA recognized by Fpg enzyme (y-axis) with model bacterial, K12, and R2–R4 strains (x-axis). All analyzed compounds numbered were statistically significant at <0.05 * (see Table 2 and Supplementary Materials Figure S2 panel A and B).
Molecules 27 03633 g006
Molecules 27 03633 g007 550
Figure 7. Examples of MIC with model bacterial strains K12, R2, R3, and R4 for studying antibiotics ciprofloxacin (cipro), bleomycin (bleo), and cloxacillin (clox). The x-axis features antibiotics used sequentially. The y-axis features the MIC value in μg/mL−1. Supplementary Materials Figure S1.
Figure 7. Examples of MIC with model bacterial strains K12, R2, R3, and R4 for studying antibiotics ciprofloxacin (cipro), bleomycin (bleo), and cloxacillin (clox). The x-axis features antibiotics used sequentially. The y-axis features the MIC value in μg/mL−1. Supplementary Materials Figure S1.
Molecules 27 03633 g007
Molecules 27 03633 g008 550
Figure 8. Percentage of bacterial DNA recognized by Fpg enzyme in model bacterial strains after ciprofloxacin, bleomycin, and cloxacillin treatment. The compounds were statistically significant at p < 0.05. (See Supplementary Materials Figure S3).
Figure 8. Percentage of bacterial DNA recognized by Fpg enzyme in model bacterial strains after ciprofloxacin, bleomycin, and cloxacillin treatment. The compounds were statistically significant at p < 0.05. (See Supplementary Materials Figure S3).
Molecules 27 03633 g008
Table
Table 1. Influence of solvent on model Ugi reaction.
Table 1. Influence of solvent on model Ugi reaction.
EntrySolventTemperature (°C)Yield (%)
1Methanol2530
2Methanol3032
3Methanol4033
4Methanol5039
5Methanol6039
6Ethanol5033
7Isopropanol5037
8TFE5053
9TFE6042
Table
Table 2. Optimization for model cyclisation reaction.
Table 2. Optimization for model cyclisation reaction.
EntryBaseSolventTemperatureYield (%)
1K2CO3DMF10025
2K2CO3DMF9027
3K2CO3DMF11026
4K2CO3Ethanol5030
5K2CO3Ethanol6539
6K2CO3Ethanol7528
7K2CO3THF6549
8K2CO3DMF6530
9K2CO3DMSO6532
10K2CO3Toluene6529
11K2CO3Methanol6534
12CsFTHF6533
13NaHCO3THF6536
14KOtBuTHF6527
15KOHTHF6519
16NaHTHF6570
Table
Table 3. Statistical analysis of all analyzed compounds by MIC, MBC, and MBC/MIC; <0.05 *, <0.01 **, <0.001 ***.
Table 3. Statistical analysis of all analyzed compounds by MIC, MBC, and MBC/MIC; <0.05 *, <0.01 **, <0.001 ***.
No. of SamplesVaVbVcVdVeVfVgVhType of Test
K12*************MIC
R2*************MIC
R3*************MIC
R4*************MIC
K12***********MBC
R2***********MBC
R3***********MBC
R4***********MBC
K12***********MBC/MIC
R2************MBC/MIC
R3************MBC/MIC
R4************MBC/MIC
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Sahrawat, P.; Kowalczyk, P.; Koszelewski, D.; Szymczak, M.; Kramkowski, K.; Wypych, A.; Ostaszewski, R. Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains. Molecules 2022, 27, 3633. https://doi.org/10.3390/molecules27113633

AMA Style

Sahrawat P, Kowalczyk P, Koszelewski D, Szymczak M, Kramkowski K, Wypych A, Ostaszewski R. Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains. Molecules. 2022; 27(11):3633. https://doi.org/10.3390/molecules27113633

Chicago/Turabian Style

Sahrawat, Parul, Paweł Kowalczyk, Dominik Koszelewski, Mateusz Szymczak, Karol Kramkowski, Aleksandra Wypych, and Ryszard Ostaszewski. 2022. "Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains" Molecules 27, no. 11: 3633. https://doi.org/10.3390/molecules27113633

APA Style

Sahrawat, P., Kowalczyk, P., Koszelewski, D., Szymczak, M., Kramkowski, K., Wypych, A., & Ostaszewski, R. (2022). Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains. Molecules, 27(11), 3633. https://doi.org/10.3390/molecules27113633

Article Metrics

Back to TopTop