Biopolym. Cell. 2024; 40(1):68-80.
Bioorganic Chemistry
Synthesis and antibiofilm activity of novel 1,4-dihydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidine-2-carboxamides
1Muzychka L. V., 2Humeniuk N. I., 2Boiko I. O., 2Vrynchanu N. O., 1Smolii O. B.
  1. V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the NAS of Ukraine,
    1, Academician Kukhar Str., Kyiv, Ukraine, 02094
  2. Institute of Pharmacology and Toxicology of National Medical Academy of Science of Ukraine
    14, Anton Tsedyk Str., Kyiv, Ukraine, 03057


Aim. Synthesis of novel alkyl-substituted 4-oxo-1,4-dihydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidine-2-carboxamides and evaluation of their antibiofilm activity in vitro. Methods. Organic synthesis, analytical and spectral methods, broth microilution method, biofilm formation on abiotic surface. Results. A simple and efficient method for the synthesis of new 1,4-dihydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidine-2-carboxylic acid derivatives was developed. The results of antibiofilm activity screening showed that among the synthesized alkyl-substituted 1,4-dihydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidine-2-carboxamides there are the compounds capable to disrupt the formation of biofilm of methicillin-resistant strain S. aureus 222, E. coli 311 and P. aeruginosa 449. Compound 6g is active against biofilms of E. coli 311, biomass decreases by 91.2%, and against S. aureus 222 (reduction by 54.0 %). Compound 6d is active against biofilms of P. aeruginosa 449 and S. aureus 222 (reduction by 78.7 % and 50.2 %, respectively). Conclusions. A series of novel substituted 1-alkyl-4-oxo-1,4-dihydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidine-2-carboxamides were synthesized. The activity of the synthesized pyrido[1,2-a]pyrrolo[2,3-d]pyrimidines towards the S. aureus 222, E. coli 311 and P. aeruginosa 449 biofilm formation was investigated, and the compounds with the pronounced antibiofilm activity were found.
Keywords: pyrido[1,2-a]pyrrolo[2,3-d]pyrimidines, pyrido[1,2-a]pyrimidine-3-carbaldehydes, synthesis, antibiofilm activity


[1] Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals (Basel). 2023; 16(11):1615.
[2] Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science. 1999; 284(5418):1318-22.
[3] Wang S, Zhao Y, Breslawec AP, Liang T, Deng Z, Kuperman LL, Yu Q. Strategy to combat biofilms: a focus on biofilm dispersal enzymes. NPJ Biofilms Microbiomes. 2023; 9(1):63.
[4] Sharma D, Misba L, Khan AU. Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrob Resist Infect Control. 2019; 8:76.
[5] Shree P, Singh CK, Sodhi KK, Surya JN, Singh DK. Biofilms: Understanding the structure and contribution towards bacterial resistance in antibiotics. Med Microecol. 2023; 16:100084.
[6] Sharma S, Mohler J, Mahajan SD, Schwartz SA, Bruggemann L, Aalinkeel R. Microbial Biofilm: A Review on Formation, Infection, Antibiotic Resistance, Control Measures, and Innovative Treatment. Microorganisms. 2023; 11(6):1614.
[7] Li Y, Xiao P, Wang Y, Hao Y. Mechanisms and Control Measures of Mature Biofilm Resistance to Antimicrobial Agents in the Clinical Context. ACS Omega. 2020; 5(36):22684-90.
[8] Worthington RJ, Richards JJ, Melander C. Small molecule control of bacterial biofilms. Org Biomol Chem. 2012; 10(37):7457-74.
[9] Roy R, Tiwari M, Donelli G, Tiwari V. Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action. Virulence. 2018; 9(1):522-54.
[10] Sambanthamoorthy K, Gokhale AA, Lao W, Parashar V, Neiditch MB, Semmelhack MF, Lee I, Waters CM. Identification of a novel benzimidazole that inhibits bacterial biofilm formation in a broad-spectrum manner. Antimicrob Agents Chemother. 2011; 55(9):4369-78.
[11] Dinicola S, De Grazia S, Carlomagno G, Pintucci JP. N-acetylcysteine as powerful molecule to destroy bacterial biofilms. A systematic review. Eur Rev Med Pharmacol Sci. 2014; 18(19):2942-8.
[12] Abraham NM, Lamlertthon S, Fowler VG, Jefferson KK. Chelating agents exert distinct effects on biofilm formation in Staphylococcus aureus depending on strain background: role for clumping factor B. J Med Microbiol. 2012; 61(Pt 8):1062-70.
[13] Rabin N, Zheng Y, Opoku-Temeng C, Du Y, Bonsu E, Sintim HO. Biofilm formation mechanisms and targets for developing antibiofilm agents. Future Med Chem. 2015; 7(4):493-512.
[14] Mirghani R, Saba T, Khaliq H, Mitchell J, Do L, Chambi L, Diaz K, Kennedy T, Alkassab K, Huynh T, Elmi M, Martinez J, Sawan S, Rijal G. Biofilms: Formation, drug resistance and alternatives to conventional approaches. AIMS Microbiol. 2022; 8(3):239-77.
[15] Bhawale RT, Chillal AS, Kshirsagar UA. 4H-Pyrido[1,2-a]pyrimidin-4-one, biologically important fused heterocyclic scaffold: Synthesis and functionalization. J Heterocycl Chem. 2023; 60(8):1356-73.
[16] Yuan P, Jiang X, Wang S, Shao X, Yang Q, Qian X. X-ray Structure and Molecular Docking Guided Discovery of Novel Chitinase Inhibitors with a Scaffold of Dipyridopyrimidine-3-carboxamide. J Agric Food Chem. 2020; 68(47):13584-93.
[17] Jiang X, Kumar A, Motomura Y, Liu T, Zhou Y, Moro K, Zhang KYJ, Yang Q. A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors. J Med Chem. 2020; 63(3):987-1001.
[18] Park DS, Jo E, Choi J, Lee M, Kim S, Kim HY, Nam J, Ahn S, Hwang JY, Windisch MP. Characterization and structure-activity relationship study of iminodipyridinopyrimidines as novel hepatitis C virus inhibitor. Eur J Med Chem. 2017; 140:65-73.
[19] Dong Z, Wang Z, Guo ZQ, Gong S, Zhang T, Liu J, Luo C, Jiang H, Yang CG. Structure-Activity Relationship of SPOP Inhibitors against Kidney Cancer. J Med Chem. 2020; 63(9):4849-66.
[20] Pilyo SG, Demydchuk BA, Moskvina VS, Shablykina OV, Brovarets VS. A combinatorial library of substituted 3-sulfonyl-2-imino-1,2-dihydro-5H-dipyrido[1,2-a:2',3'-d]pyrimidin-5-ones and their anticancer activities. Biopolym Cell. 2022; 38(4): 242-56.
[21] Aljuhani A, Ahmed HEA, Ihmaid SK, Omar AM, Althagfan SS, Alahmadi YM, Ahmad I, Patel H, Ahmed S, Almikhlafi MA, El-Agrody AM, Zayed MF, Turkistani SA, Abulkhair SH, Almaghrabi M, Salama SA, Al-Karmalawy AA, Abulkhair HS. In vitro and computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-MPro inhibitors. RSC Adv. 2022; 12(41):26895-907.
[22] Horváth Ág, Hermecz I. Nitrogen bridgehead compounds. Part 65. Vilsmeier-haack formylation of 4H-pyrido[1,2-a]pyrimidin-4-ones. Part 6. J Heterocycl Chem. 1986; 23(5):1295-8.
[23] The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 13.0, 2023.
[24] ISO 20776-1:2019. Susceptibility testing of infectious agents and evaluation of performance of antimicrobial susceptibility test devices Part 1: Broth microdilution reference method for testing the in vitro activity of antimicrobial agents against rapidly growing aerobic bacteria involved in infectious diseases//Geneva: International Organization for Standardization. 2019. https://www.iso. org/standard/70464.html (accepted Oct 25, 2022).
[25] O'Toole GA. Microtiter dish biofilm formation assay. J Vis Exp. 2011; (47):2437.
[26] Verves EV, Kucher AV, Muzychka LV, Smolii OB. Synthesis of 7-alkyl-4-amino-7H-pyrrolo[2,3-d]pyrimidine-6-carboxylic acids. Chem Heterocycl Compd. 2013; 48(12):1844-52.
[27] Muzychka LV, Yaremchuk IO, Verves EV, Smolii OB. Pyrrolo[2,3-d]pyrimidine derivatives in the synthesis of a novel heterocyclic system 2a,5a,7-triazaacenaphthylene. Chem Heterocycl Compd. 2019; 55(4-5):397-400.
[28] Ranieri MR, Whitchurch CB, Burrows LL. Mechanisms of biofilm stimulation by subinhibitory concentrations of antimicrobials. Curr Opin Microbiol. 2018; 45:164-9.