New Route to the Synthesis of Novel Pyrazolo[1,5-a]pyrimidines and Evaluation of their Antimicrobial Activity as RNA Polymerase Inhibitors

Page: [926 - 948] Pages: 23

  • * (Excluding Mailing and Handling)

Abstract

Aims: The current study aimed to synthesize novel pyrazolo[1,5-a]pyrimidines based on 5- aminopyrazoles 3, evaluate their antimicrobial activity, and study the minimum inhibitory concentration (MIC) for the most active compounds. In addition, molecular docking studies and RNA polymerase inhibitory activity were determined.

Background: Starting with our previously reported 5-aminopyrazoles 3, a number of novel pyrazolo[1,5- a]pyrimidines were synthesized. Due to the similarity of pyrazolopyrimidine derivatives with the purine systems, pyrazolopyrimidines are important in many different biological applications, most notably as anti-tumor, antibacterial, and hepatitis C virus inhibitors. The pharmaceutical applications of the pyrazolopyrimidine derivatives were explained in several approved drugs like Indiplon, Zaloplan, and Ocinaplon.

Objective: To prepare a novel antimicrobial agent, namely pyrazolo[1,5-a]pyrimidine, reveal their structures using different spectral data, the minimum inhibitory concentration (MIC) for the most active compounds was evaluated, and both the molecular docking and the RNA polymerase inhibitory activity were determined.

Methods: A number of different pyrazolopyrimidines namely 2-(phenylamino)-6,11-dihydrobenzo[g]pyrazolo [1,5-a]quinazoline-3-carboxamides (5a-c), (E)-5,7-dimethyl-2-(phenylamino)-6-(phenyldiazenyl)pyrazolo-[1,5- a]pyrimidine-3-carboxamides (7a-c), 7-amino-2-(phenylamino) pyrazolo[1,5-a]pyrimidine-3-carboxamides (11af), 7-amino-2-(phenylamino)-5-(2-thienyl)pyrazolo[1,5-a]pyrimidine-3-carboxamides (14-f) and ethyl 7-amino-3- carbamoyl-2-(phenylamino)-5-(4-pyridyl)pyrazolo[1,5-a]pyrimidine-6-carboxylate derivatives (14g-i) were synthesized through the reaction of 5-aminopyrazoles 3 with a variety of chemical reagents. On the other hand, the evaluation of the antimicrobial activity for all the prepared compounds was screened through different strains as Gram-positive bacteria, such as staphylococcus aureus and Streptococcus mutans, and Gram-negative bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and klebsiella. The antifungal activity was determined by Candids Albicans fungal strain, and the MIC of the most active compounds was measured. The molecular docking was recorded, and the RNA polymerase inhibitory activity was estimated for the high docking score compounds.

Results: Compounds 5a, 5b, 5c, 7a, 7b, 7c, 11d, 14b, and 14h were the most active compounds against some of the bacterial and fungal tested strains. MIC was determined for the most active tested compounds. As an antimicrobial agent, compound 7b was the most potent, with a high docking score and RNA polymerase inhibitory activity (IC50= 0.213 μg/ml) compared to Rifampicin (IC50= 0.244 μg/ml). The reactivity of the latter compound was attributed to the presence of 4-Br-C6H4 moiety. The results demonstrated that docking studies on the most active compounds in the RNA polymerase active site were consistent with in vitro assays.

Conclusion: The resultant novel bioactive pyrazolo[1,5-a]pyrimidine derivatives were synthesized based on 5- aminopyrazole derivatives 3. The current study evaluated the antimicrobial activity for all the prepared compounds, followed by the determination of the MIC for the most potent active compounds. The molecular docking study was performed, and it was appropriate with the in vitro activity. The RNA polymerase inhibitory activity was assessed for the most active antimicrobial compounds with a high docking score (7b, 7c, 14a, 14b, 14e, 14i). Compound 7b was the most potent compound inhibiting RNA polymerase enzyme compared to the reference drug Rifampicin.

Other: The novel prepared heterocyclic systems are extremely important in a variety of domains, especially biological and pharmacological ones.

Keywords: 5-Aminopyrazoles, antimicrobial activity, pyrazolo[1, 5-a]pyrimidines, docking studies, pyrazolopyrimidines, RNA polymerase inhibitors.

Graphical Abstract

[1]
Liu, Y.; Laufer, R.; Patel, N.K.; Ng, G.; Sampson, P.B.; Li, S-W.; Lang, Y.; Feher, M.; Brokx, R.; Beletskaya, I.; Hodgson, R.; Plotnikova, O.; Awrey, D.E.; Qiu, W.; Chirgadze, N.Y.; Mason, J.M.; Wei, X.; Lin, D.C-C.; Che, Y.; Kiarash, R.; Fletcher, G.C.; Mak, T.W.; Bray, M.R.; Pauls, H.W. Discovery of Pyrazolo[1,5-a]pyrimidine TTK Inhibitors: CFI-402257 is a potent, selective, bioavailable anticancer agent. ACS Med. Chem. Lett., 2016, 7(7), 671-675.
[http://dx.doi.org/10.1021/acsmedchemlett.5b00485] [PMID: 27437075]
[2]
Zhao, M.; Ren, H.; Chang, J.; Zhang, D.; Yang, Y.; He, Y.; Qi, C.; Zhang, H. Design and synthesis of novel pyrazolo[1,5-a]pyrimidine derivatives bearing nitrogen mustard moiety and evaluation of their antitumor activity in vitro and in vivo. Eur. J. Med. Chem., 2016, 119, 183-196.
[http://dx.doi.org/10.1016/j.ejmech.2016.04.068] [PMID: 27162123]
[3]
Al-Adiwish, W.M.; Tahir, M.I.M.; Siti-Noor-Adnalizawati, A.; Hashim, S.F.; Ibrahim, N.; Yaacob, W.A. Synthesis, antibacterial activity and cytotoxicity of new fused pyrazolo[1,5-a]pyrimidine and pyrazolo[5,1-c][1,2,4]triazine derivatives from new 5-aminopyrazoles. Eur. J. Med. Chem., 2013, 64, 464-476.
[http://dx.doi.org/10.1016/j.ejmech.2013.04.029] [PMID: 23669354]
[4]
Abdallah, A.E.M.; Elgemeie, G.H. Design, synthesis, docking, and antimicrobial evaluation of some novel pyrazolo[1,5-a] pyrimidines and their corresponding cycloalkane ring-fused derivatives as purine analogs. Drug Des. Devel. Ther., 2018, 12, 1785-1798.
[http://dx.doi.org/10.2147/DDDT.S159310] [PMID: 29950813]
[5]
Drev, M.; Grošelj, U.; Mevec, Š.; Pušavec, E.; Štrekelj, J. Golobič A.; Dahmann, G.; Stanovnik, B.; Svete, J. Regioselective synthesis of 1-and 4-substituted 7-oxopyrazolo[1,5-a]pyrimidine-3-carboxamides. Tetrahedron, 2014, 70, 8267-8279.
[http://dx.doi.org/10.1016/j.tet.2014.09.020]
[6]
Popovici-Muller, J.; Shipps, G.W., Jr; Rosner, K.E.; Deng, Y.; Wang, T.; Curran, P.J.; Brown, M.A.; Siddiqui, M.A.; Cooper, A.B.; Duca, J.; Cable, M.; Girijavallabhan, V. Pyrazolo[1,5-a]pyrimidine-based inhibitors of HCV polymerase. Bioorg. Med. Chem. Lett., 2009, 19(22), 6331-6336.
[http://dx.doi.org/10.1016/j.bmcl.2009.09.087] [PMID: 19819138]
[7]
Mukaiyama, H.; Nishimura, T.; Shiohara, H.; Kobayashi, S.; Komatsu, Y.; Kikuchi, S.; Tsuji, E.; Kamada, N.; Ohnota, H.; Kusama, H. Discovery of novel 2-anilinopyrazolo[1,5-a]pyrimidine derivatives as c-Src kinase inhibitors for the treatment of acute ischemic stroke. Chem. Pharm. Bull. (Tokyo), 2007, 55(6), 881-889.
[http://dx.doi.org/10.1248/cpb.55.881] [PMID: 17541186]
[8]
Shiota, T.; Yamamori, T.; Sakai, K.; Kiyokawa, M.; Honma, T.; Ogawa, M.; Hayashi, K.; Ishizuka, N.; Matsumura, K.; Hara, M.; Fujimoto, M.; Kawabata, T.; Nakajima, S. Synthesis and structure-activity relationship of a new series of potent angiotensin II receptor antagonists: Pyrazolo[1,5-a]pyrimidine derivatives. Chem. Pharm. Bull. (Tokyo), 1999, 47(7), 928-938.
[http://dx.doi.org/10.1248/cpb.47.928] [PMID: 10434395]
[9]
Villain-Guillot, P.; Gualtieri, M.; Bastide, L.; Roquet, F.; Martinez, J.; Amblard, M.; Pugniere, M.; Leonetti, J-P. Structure-activity relation-ships of phenyl-furanyl-rhodanines as inhibitors of RNA polymerase with antibacterial activity on biofilms. J. Med. Chem., 2007, 50(17), 4195-4204.
[http://dx.doi.org/10.1021/jm0703183] [PMID: 17665895]
[10]
Elgaher, W.A.M.; Fruth, M.; Groh, M.; Haupenthal, J.; Hartmann, R.W. Expanding the scaffold for bacterial RNA polymerase inhibitors: Design, synthesis and structure–activity relationships of ureido-heterocyclic-carboxylic acids. RSC Advances, 2014, 4, 2177-2194.
[http://dx.doi.org/10.1039/C3RA45820B]
[11]
Elgemeie, G.H.; Ali, H.A. Potential purine analogue antagonists: Synthesis of novel cycloalkane ring-fused pyrazolo[1,5-a]pyrimidines. Synth. Commun., 2002, 32, 253-264.
[http://dx.doi.org/10.1081/SCC-120002010]
[12]
Elgemeie, G.H.; Hani, A.A.; Jones, P.G. 2-Phenyl-7,8-dihydro-6H-cyclopenta[e]pyrazolo[1,5-a]pyrimidine. Acta Crystallogr., 2002, E58, 1247-1249.
[13]
Elgemeie, G.H.; El-Ezbawy, S.E.; Ali, H.A.; Mansour, A.K. Novel synthesis of mercaptopurine and pentaaza-as-indacene analogues: Reac-tion of [bis(methylthio)methylene]malononitrile and ethyl 2-cyano-3,3-bis(methylthio)acrylate with 5-aminopyrazoles. Bull. Chem. Soc. Jpn., 1994, 67, 738-741.
[http://dx.doi.org/10.1246/bcsj.67.738]
[14]
Abu-Zaied, M.A.; Loutfy, S.A.; Hassan, A.E.; Elgemeie, G.H. Novel purine thioglycoside analogs: Synthesis, nanoformulation and biolog-ical evaluation in in vitro human liver and breast cancer models. Drug Des. Devel. Ther., 2019, 13, 2437-2457.
[http://dx.doi.org/10.2147/DDDT.S201249] [PMID: 31440030]
[15]
Elgemeie, G.H.; Elghandour, A.H.; Elzanate, A.M.; Ahmed, S.A. Synthesis of some novel α-cyanoketene S,S-acetals and their use in het-erocyclic synthesis. J. Chem. Soc., Perkin Trans. 1, 1997, 21, 3285-3290.
[http://dx.doi.org/10.1039/a702343j]
[16]
Elgemeie, G.H.; Elghandour, A.H.; Abd-Elaziz, G.W. Potassium 2-cyanoethylene-1-thiolate derivative: A new preparative route to 2-cyanoketene S,N-acetals and pyrazole derivatives. Synth. Commun., 2004, 34, 3281-3291.
[http://dx.doi.org/10.1081/SCC-200030549]
[17]
Elgemeie, G.H.; Jones, P.G. 5-Amino-3-anilino-N-(chlorophenyl)-1H-pyrazole-4-carboxamide ethanol solvent. Acta Crystallogr., 2004, E60, 01616-01618.
[18]
Kurz, T.; Widyan, K.; Elgemeie, G.H. Novel synthesis of fluorinated cyanoketene N,S-acetals (IV) and their conversions to fluorinated pyrazole derivatives (V). Phosphorus Sulfur Silicon Relat. Elem., 2006, 181, 299-304.
[http://dx.doi.org/10.1080/104265090970368]
[19]
Elgemeie, G.H.; Zaghary, W.A.; Amin, K.M.; Nasr, T.M. A direct route to a new class of acrylamide thioglycosides. J. Carbohydr. Chem., 2008, 27, 373-378.
[http://dx.doi.org/10.1080/07328300802262786]
[20]
Elgemeie, G.H.; Elghandour, A.H.; Abd Elaziz, G.W. Novel cyanoketene N,S-acetals and pyrazole derivatives using potassium 2-cyanoethylene-1-thiolates. Synth. Commun., 2007, 37, 2827-2834.
[http://dx.doi.org/10.1080/00397910701473317]
[21]
Elgemeie, G.H.; Elsayed, S.H.; Hassan, A.S. Direct route to a new class of acrylamide thioglycosides and their conversions to pyrazole derivatives. Synth. Commun., 2008, 38, 2700-2706.
[http://dx.doi.org/10.1080/00397910802222605]
[22]
Ahmed, S.A.; Hussein, A.M.; Hozayen, W.G.M.; El-Ghandour, A.H.H.; Abdelhamid, A.O. Synthesis of some pyrazolopyrimidines as purine analogues. J. Heterocycl. Chem., 2007, 44, 803-810.
[http://dx.doi.org/10.1002/jhet.5570440408]
[23]
Ahmed, O.M.; Mohamed, M.A.; Ahmed, R.R.; Ahmed, S.A. Synthesis and anti-tumor activities of some new pyridines and pyrazolo[1,5-a]pyrimidines. Eur. J. Med. Chem., 2009, 44(9), 3519-3523.
[http://dx.doi.org/10.1016/j.ejmech.2009.03.042] [PMID: 19398146]
[24]
Ammar, Y.A.; Aly, M.M.; Al-Sehemi, A.G.; Salem, M.A.; El-Gaby, M.S.A. Cyanoacetanilides intermediates in heterocyclic synthesis. Part 5: Preparation of hitherto unknown 5-aminopyrazole and pyrazolo[1,5-a]pyrimidine derivatives containing sulfamoyl moiety. J. Chin. Chem. Soc. (Taipei), 2009, 56, 1064-1071.
[http://dx.doi.org/10.1002/jccs.200900154]
[25]
Hussein, A.M. Synthesis of some new purine-related compounds: Regioselective one-pot synthesis of new tetrazolo[1,5-a]pyrimidine, pyrazolo[1,5-a]pyrimidine and pyrimido[1,6-a]pyrimidine derivatives. J. Saudi Chem. Soc., 2010, 14, 61-68.
[http://dx.doi.org/10.1016/j.jscs.2009.12.010]
[26]
Hussein, A.M. Novel synthesis of some new pyrimido[1,6-a]pyrimidines and pyrazolo[1,5-a]pyrimidine derivatives. J. Heterocycl. Chem., 2012, 49, 446-451.
[http://dx.doi.org/10.1002/jhet.852]
[27]
Hassan, A.S.; Hafez, T.S.; Osman, S.A.M.; Ali, M.M. Synthesis and in vitro cytotoxic activity of novel pyrazolo[1,5-a]pyrimidines and related Schiff bases. Turk. J. Chem., 2015, 39, 1102-1113.
[http://dx.doi.org/10.3906/kim-1504-12]
[28]
Hassan, A.S.; Hafez, T.S.; Osman, S.A. Synthesis, characterization, and cytotoxicity of some new 5-aminopyrazole and pyrazolo[1,5-a]pyrimidine derivatives. Sci. Pharm., 2015, 83(1), 27-39.
[http://dx.doi.org/10.3797/scipharm.1409-14] [PMID: 26839799]
[29]
Hassan, A.S.; Mady, M.F.; Awad, H.M.; Hafez, T.S. Synthesis and antitumor activity of some new pyrazolo[1,5-a]pyrimidines. Chin. Chem. Lett., 2017, 28, 388-393.
[http://dx.doi.org/10.1016/j.cclet.2016.10.022]
[30]
Hafez, T.S.; Osman, S.A.; Yosef, H.A.A.; El-All, A.S.; Hassan, A.S.; El-Sawy, A.A.; Abdallah, M.M.; Youns, M. Synthesis, structural elucidation, and in vitro antitumor activities of some pyrazolopyrimidines and Schiff bases derived from 5-amino-3-(arylamino)-1H-pyrazole-4-carboxamides. Sci. Pharm., 2013, 81(2), 339-357.
[http://dx.doi.org/10.3797/scipharm.1211-07] [PMID: 23833708]
[31]
Hassan, A.S.; Moustafa, G.O.; Awad, H.M. Synthesis and in vitro anticancer activity of pyrazolo[1,5-a]pyrimidines and pyrazolo[3,4-d][1,2,3]triazines. Synth. Commun., 2017, 47, 1963-1972.
[http://dx.doi.org/10.1080/00397911.2017.1358368]
[32]
Sayed, A.Z.; Aboul-Fetouh, M.S.; Hesham, S.; Nassar, H.S. Synthesis, biological activity and dyeing performance of some novel azo dis-perse dyes incorporating pyrazolo[1,5-a]pyrimidines for dyeing of polyester fabrics. J. Mol. Struct., 2012, 1010, 146-151.
[http://dx.doi.org/10.1016/j.molstruc.2011.11.046]
[33]
El-Naggar, M.; Hassan, A.S.; Awad, H.M.; Mady, M.F. Design, synthesis and antitumor evaluation of novel pyrazolopyrimidines and pyrazoloquinazolines. Molecules, 2018, 23(6), 1249-1269.
[http://dx.doi.org/10.3390/molecules23061249] [PMID: 29882908]
[34]
Mehranpour, A.; Hashemnia, S.; Bornak, M. Synthesis and characterization of new pyrido- and pyrazolopyrimidine derivatives using 2-substituted vinamidinium salts. Chem. Heterocycl. Compd., 2019, 55, 1087-1091.
[http://dx.doi.org/10.1007/s10593-019-02582-7]
[35]
Leung, S.S.F.; Mijalkovic, J.; Borrelli, K.; Jacobson, M.P. Testing physical models of passive membrane permeation. J. Chem. Inf. Model., 2012, 52(6), 1621-1636.
[http://dx.doi.org/10.1021/ci200583t] [PMID: 22621168]
[36]
Rezai, T.; Yu, B.; Millhauser, G.L.; Jacobson, M.P.; Lokey, R.S. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J. Am. Chem. Soc., 2006, 128(8), 2510-2511.
[http://dx.doi.org/10.1021/ja0563455] [PMID: 16492015]
[37]
Leung, S.S.F.; Sindhikara, D.; Jacobson, M.P. Simple predictive models of passive membrane permeability incorporating size-dependent membrane-water partition. J. Chem. Inf. Model., 2016, 56(5), 924-929.
[http://dx.doi.org/10.1021/acs.jcim.6b00005] [PMID: 27135806]
[38]
Schrödinger, L.L.C. Release. Prime. New York, 2019, 2019, 1.
[39]
Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 1996, 118, 11225-11236.
[http://dx.doi.org/10.1021/ja9621760]
[40]
Kaminski, G.A.; Friesner, R.A.; Tirado-Rives, J.; Jorgensen, W.L. Evaluation and reparametrization of the OPLS-AA force field for pro-teins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B, 2001, 105, 6474-6487.
[http://dx.doi.org/10.1021/jp003919d]
[41]
Schrodinger, L.L.C. Macromodel Version 10.2. New York (NY), 2013.
[42]
Chlenov, M.; Masuda, S.; Murakami, K.S.; Nikiforov, V.; Darst, S.A.; Mustaev, A. Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase β′ subunit. J. Mol. Biol., 2005, 353(1), 138-154.
[http://dx.doi.org/10.1016/j.jmb.2005.07.073] [PMID: 16154587]
[43]
Marras, S.A.E.; Gold, B.; Kramer, F.R.; Smith, I.; Tyagi, S. Real-time measurement of in vitro transcription. Nucleic Acids Res., 2004, 32(9), e72.
[http://dx.doi.org/10.1093/nar/gnh068] [PMID: 15155820]
[44]
Friesner, R.A.; Murphy, R.B.; Repasky, M.P.; Frye, L.L.; Greenwood, J.R.; Halgren, T.A.; Sanschagrin, P.C.; Mainz, D.T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem., 2006, 49(21), 6177-6196.
[http://dx.doi.org/10.1021/jm051256o] [PMID: 17034125]
[45]
Naseem, S.; Khalid, M.; Tahir, M.N.; Halim, M.A.; Braga, A.A.C.; Naseer, M.M.; Shafiq, Z. Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand. J. Mol. Struct., 2017, 1143, 235-244.
[http://dx.doi.org/10.1016/j.molstruc.2017.04.093]
[46]
Scott, A.C. Laboratory control of antimicrobial therapy.Mackie and MacCartney Practical Medical Microbiology; 13th Ed; Collee, J.G.; Duguid, J.P.; Fraser, A.G.; Marmion, B.P., Eds.; Churchill Livingstone: Edinburgh, Scotland, 1989, p. 161-181.
[47]
Wiegand, I.; Hilpert, K.; Hancock, R.E. Agar and broth dilution methods to determine the Minimal Inhibitory Concentration (MIC) of an-timicrobial substances. Nat. Protoc., 2008, 3(2), 163-175.
[http://dx.doi.org/10.1038/nprot.2007.521] [PMID: 18274517]