Frecer, V., Ho, B., Ding, J. L.: De novo design of potent antimicrobial peptides. Antimicrob. Agents Chemother. 48(9), 3349-3357 (2004). [133 citations WoS]

Frecer, V., Ho, B., Ding, J. L.: Interpretation of biological activity data of bacterial endotoxins by simple molecular models of mechanism of action. Eur. J. Biochem. 267(3), 837-852 (2000). [57 citations WoS]

Frecer, V.: QSAR Analysis of Antimicrobial and haemolytic effects of cyclic cationic antimicrobial peptides derived from Protegrin-1. Bioorgan. Med. Chem. 14(17), 6065-6074 (2006). [56 citations WoS]

Udommaneethanakit, T., Rungrotmongkol, T., Bren, U., Frecer, V., Miertuš, S.: Dynamic behavior of avian influenza A virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues. J. Chem. Inf. Model. 49(10), 2323-2332 (2009). [51 citations WoS]

Frecer, V., Kabelac, M., De Nardi, P., Pricl, S., Miertuš, S.: Design of inhibitors of hepatitis C virus NS3 serine protease. J. Mol. Graphics Model. 22(3), 209-220 (2004). [45 citations WoS]

Frecer, V., Miertus, S.: Antiviral agents against COVID-19: structure-based design of specific peptidomimetic inhibitors of SARS-CoV-2 main protease. RSC Advances 10(66) , 40244-40263 (2020). [32 citations WoS]

Hajzer, V., Fisera, R., Latika, A., Durmis, J., Kollar, J., Frecer, V., Tucekova, Z., Miertus, S., Kostolansky, F., Vavreckova, E., Sebesta, R.: Stereoisomers of oseltamivir - synthesis, in silico prediction and biological evaluation. Org. Biomol. Chem. 15(8) , 1828-1841 (2017). [11 citations WoS]

Kollar, J., Frecer, V.: How accurate is the description of ligand-protein interactions by a hybrid QM/MM approach? J. Mol. Model. 24(1), Art. No. 11 (2018). [13 citations WoS]

Nemčovičová, I., Lopušná, K., Štibrániová, I., Benedetti, F., Berti, F., Felluga, F., Drioli, S., Vidali, M., Katrlík, J., Pažitná, L., Holazová, A., Blahutová, J., Lenhartová, S., Sláviková, M., Klempa, B., Ondrejovič, M., Chmelová, D., Legerská, B., Miertuš, S., Klacsová, M., Uhríková, D., Kerti, L., Frecer, V.*: Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. J. Enz. Inhib. Med. Chem. 39(1), art. no. 2301772 (2024). [I.F. = 5,60, Q1, citations: 0 WoS]

Kerti, L., Frecer, V.*: Design of inhibitors of SARS-CoV-2 papain-like protease deriving from GRL0617: Structure-activity relationships. Bioorg. Med. Chem.  113, art. no. 117909 (2024).  [I.F. = 3,30, Q1, citations: 0 WoS]

 Publication 1.

a) Costa, L., Sousa, E., Fernandes, C.: Cyclic Peptides in Pipeline: What Future for These Great Molecules? Pharmaceuticals 16(7), art. no. 996 (2023).

b) Wu, Y.M., Chen, K., Wang, J.Z., Chen, M.Z., Chen, Y., She, Y.R., Yan, Z., Liu, R.: Host defense peptide mimicking antimicrobial amino acid polymers and beyond: Design, synthesis and biomedical applications. Prog. Polym. Sci. 141, art. no. 101679 (2023).

c) Modak, B., Girkar, S., Narayan, R., Kapoor, S.: Mycobacterial Membranes as Actionable Targets for Lipid-Centric Therapy in Tuberculosis. J. Med. Chem. 65(4), 3046-3065 (2022).

d) Vishweshwaraiah, Y.L., Acharya, A., Hegde, V., Prakash, B.: Rational design of hyperstable antibacterial peptides for food preservation. NPJ Sci. Food 5(1), art. no. 26 (2021).

e) Shi, W.W., Chen, F.F., Zou, X.M., Jiao, S., Wang, S.Q., Hu, Y., Lan, L.F., Tang, F., Huang, W.: Design, synthesis, and antibacterial evaluation of vancomycin-LPS binding peptide conjugates. Bioorg. Med. Chem. Lett. 45, art. no. 128122 (2021). 

Publication 2.

a) Tram, N.D.T., Xu, J., Mukherjee, D., Obanel, A.E., Mayandi, V., Selvarajan, V., Zhu, X., Teo, J., Barathi, V.A., Lakshminarayanan, R., Ee, P.L.R.: Bacteria-Responsive Self-Assembly of Antimicrobial Peptide Nanonets for Trap-and-Kill of Antibiotic-Resistant Strains. Adv. Func. Mat. 33(5), art. 10858 (2023).

b) Kumari, T., D.P., Kuldeep, J., Dhanabal, V.B., Verma, N.K., Sahai, R., Tripathi, A.K., Saroj, J., Ali, M., Mitra, K., Siddiqi, M.I., Bhattacharjya, S., Ghosh, J.K.: 10-Residue MyD88-Peptide Adopts beta-Sheet Structure, Self-Assembles, Binds to Lipopolysaccharides, and Rescues Mice from Endotoxin-Mediated Lung-Infection and Death. ACS Chem. Biol. 17(12) 3420-3434 (2022).

c) Achour, A.: Identification of oligopeptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non structural protein 8 (NSP8) and their imilarities with type 1 angiotensin II receptor key sites. Biomedicine & Pharmacotherapy 141, art. no. 111722 (2021).

d) Cochet, F., Peri, F.: The Role of Carbohydrates in the Lipopolysaccharide (LPS)/Toll-Like Receptor 4 (TLR4) Signalling. Int. J. Mol. Sci. 18(11), art. no. 2318 (2017).

e) Le, C.F., Fang, C.M., Sekaran, S.D.: Intracellular Targeting Mechanisms by Antimicrobial Peptides. Antimic. Agents Chemother. 61(4), art. no. e02340 (2017).

Publication 3.

a) You, Y.H., Liu, H.Y., Zhu, Y.Z., Zheng, H.: Rational design of stapled antimicrobial peptides. Amino Acids 55(4), 421-442 (2023).

b) Jukic, M., Bren, U.: Machine Learning in Antibacterial Drug Design. Front. Pharmacol. 13, art. no. 864412 (2022).

c) Waghu, F.H., Gawde, U., Gomatam, A., Coutinho, E., Idicula-Thomas, S.: A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity. Chem. Biol. Drug Des. 96(6), 1408-1417 (2020).

d) Cardoso, M.H., Meneguetti, B.T., Costa, B.O., Buccini, D.F., Oshiro, K.G.N., Preza, S.L.E., Carvalho, C.M.E., Migliolo, L., Franco, O.L.: Non-Lytic Antibacterial Peptides That Translocate Through Bacterial Membranes to Act on Intracellular Targets. Int. J. Mol. Sci. 20(19), art. no. 4877 (2019).

e) Chaudhary, K., Kumar, R., Singh, S., Tuknait, A., Gautam, A., Mathur, D., Anand, P., Varshney, G.C., Raghava, G.P.S.: A Web Server and Mobile App for Computing Hemolytic Potency of Peptides. Sci Rep. 6, art. no. 22843 (2016). 

Publication 4.

a) Shi, L., Zhang, X.Y., Cheng, L.P.: Design, synthesis and biological evaluation of 1,3,4- triazole-3-acetamide derivatives as potent neuraminidase inhibitors. Bioorg. Med. Chem. Lett. 61, art. no. 128590 (2022).

b) Hanpaibool, C., Leelawiwat, M., Takahashi, K., Rungrotmongkol, T.: Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J. Comp-Aided Mol. Des. 34(1), 27-37 (2020).

c) Shie, J.J., Fang, J.M.: Development of effective anti-influenza drugs: congeners and conjugates - a review. J. Biomed. Sci. 26(1), art. no 84 (2019).

d) Racek, T., Pazurikova, J., Varekova, R.S., Geidl, S., Krenek, A., Falginella, F.L., Horsky, V., Hejret, V., Koca, J.: NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminform. 8, art. no. 57 (2016).

e) Wang, P.C., Fang, J.M., Tsai, K.C., Wang, S.Y., Huang, W.I., Tseng, Y.C., Cheng, Y.S.E., Cheng, T.J.R., Wong, C.H.: Peramivir Phosphonate Derivatives as Influenza Neuraminidase Inhibitors. J. Med. Chem. 59(11), 5297-5310 (2016).

Publication 5.

a) Boonma, T., Nutho, B., Darai, N., Rungrotmongkol, T., Nunthaboot, N., Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study. J. Biomol. Struct. Dyn. 40(12), 5283-5294 (2022).

b) Isik, G.O., Ozer, A.N., Prediction of substrate specificity in NS3/4A serine protease by biased sequence search threading. J. Biomol. Struct. Dyn. 35(5), 1102-1114 (2017).

c) Ganesan, A., Barakat, K.: Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Curr. Topics Med. Chem. 16(12), 1351-1361 (2016).

d) Ezat, A.A., Mostafa, H.I., El-Bialy, N.S., Saleh, N.A., Ibrahim, M.A.: Computational Approaches to Study Peptidomimetic and Macrocyclic Hepatitis C Virus NS3 Protease Inhibitors. J. Comput. Theor. Nanosci. 12(1), 52-59 (2015).

e) Weber, F., Brune, S., Korpis, K., Bednarski, P.J., Laurini, E., Dal Col, V., Pricl, S., Schepmann, D., Wunsch, B.: Synthesis, Pharmacological Evaluation, and sigma(1) Receptor Interaction Analysis of Hydroxyethyl Substituted Piperazines. J. Med. Chem. 57(7), 2884-2894 (2014).

APVV-21-0108 Antiviral drugs against COVID-19: Design, synthesis and biological activity testing of specific inhibitors of viral proteases of coronavirus SARS-CoV-2, 2021-2026, principal investigator

PP-COVID-20-0010 New Antiviral Drugs: Design, Synthesis and Activity Evaluation of Specific Inhibitors of Viral Proteases of Coronavirus SARS-CoV-2, 2020-2021, investigator

APVV-17-0239 Computational Design, Synthesis, Testing and Disposition of Inhibitors of Neuraminidazes of Influenza A Virus as Potential Antiviral Compounds, 2018-2022, principal investigator

VEGA 1/0228/17 Research of antimicrobial compounds and their effect on model membranes, 2017-2020, principal investigator

APVV-15-0111 Design and complex characterization of biocompatible tubular 3D-scaffolds made of biosynthetic extracellular matrix intended as potential substitutes of damaged human urethra, 2016-2020, investigator

APVV-14-0294 Manufacturing and testing of custom made bone scaffolds made of hydroxyapatite (HA) by use of 3D printing technology , 2015-2019, investigator