New scaffolds of natural origin as Integrase–LEDGF/p75 interaction inhibitors: Virtual screening and activity assays
Open accessAbstract
The disruption of crucial interactions between HIV-1 Integrase and cellular cofactor LEDGF/p75 represents an emerging approach for the design and development of new antiretroviral agents. In this study we report the successful application of a structure-based virtual screening strategy for the discovery of natural hit structures able to inhibit Integrase-LEDGF/p75 interaction. The application of sequential filters (drug-likeness, 3D-pharmacophore mapping, docking, molecular dynamics simulations) yielded a hit list of compounds, out of which 9 were tested in the in vitro AlphaScreen assays and 8 exhibited a detectable inhibition of the interaction between the two proteins. The best inhibitors belong to different chemical classes and could be represent a good starting point for further optimization and structure-activity relationship studies.
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Development and testing of a general amber force field
Wang, J.-M., Wolf, R., Caldwell, J., Kollman, P., & Case, D. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20035 · Cited by 18,318 · see citing works
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763 · see citing works
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000) · Accounts of Chemical Research · doi:10.1021/ar000033j · Cited by 4,978 · see citing works
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T.-S., et al. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10349 · Cited by 4,271 · see citing works
ZINC: A Free Tool to Discover Chemistry for Biology
Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S. D., & Coleman, R. G. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci3001277 · Cited by 2,533 · see citing works
Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds
Pauwels, R., Balzarini, J. M., Baba, M., Snoeck, R., Schols, D., Herdewijn, P. A., Desmyter, J., & Clercq, E. D. (1988) · Journal of Virological Methods · doi:10.1016/0166-0934(88)90134-6 · Cited by 1,646 · see citing works
Christ, F., Voet, A., Marchand, A., Nicolet, S., Desimmie, B. A., Marchand, D., Bardiot, D., Van der Veken, N. J., Van Remoortel, B., Strelkov, S. V., et al. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.370 · Cited by 479 · see citing works
Self-citationStructural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75
Cherepanov, P., Ambrosio, A. L. B., Rahman, S., Ellenberger, T., & Engelman, A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506924102 · Cited by 408 · see citing works
The lentiviral integrase binding protein LEDGF/p75 and HIV-1 replication
Engelman, A., & Cherepanov, P. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000046 · Cited by 231 · see citing works
Natural products as a screening resource
Harvey, A. L. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2007.08.012 · Cited by 224 · see citing works
Christ, F., Shaw, S. M., Demeulemeester, J., Desimmie, B. A., Marchand, A., Butler, S., Smets, W. J., Chaltin, P., Westby, M., Debyser, Z., et al. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00717-12 · Cited by 176 · see citing works
Self-citationNew Class of HIV-1 Integrase (IN) Inhibitors with a Dual Mode of Action
Tsiang, M., Jones, G. S., Niedziela-Majka, A., Kan, E., Lansdon, E. B., Huang, W., Hung, M., Samuel, D., Novikov, N., Xu, Y., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.347534 · Cited by 167 · see citing works
Luca, L. D., Barreca, M. L., Ferro, S., Christ, F., Iraci, N., Gitto, R., Monforte, A., Debyser, Z., & Chimirri, A. (2009) · ChemMedChem · doi:10.1002/cmdc.200900070 · Cited by 100 · see citing works
Self-citationAl‐Mawsawi, L. Q., & Neamati, N. (2007) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2007.09.005 · Cited by 71 · see citing works
Du, L., Zhao, Y., Chen, J., Yang, L., Zheng, Y., Tang, Y., Shen, X., & Jiang, H. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.07.139 · Cited by 69 · see citing works
Allosteric Inhibitor Development Targeting HIV‐1 Integrase
Al‐Mawsawi, L. Q., & Neamati, N. (2011) · ChemMedChem · doi:10.1002/cmdc.201000443 · Cited by 62 · see citing works
Small molecules targeting the interaction between HIV-1 integrase and LEDGF/p75 cofactor
Luca, L. D., Ferro, S., Gitto, R., Barreca, M. L., Agnello, S., Christ, F., Debyser, Z., & Chimirri, A. (2010) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2010.08.051 · Cited by 59 · see citing works
Self-citationAl‐Mawsawi, L. Q., Christ, F., Dayam, R., Debyser, Z., & Neamati, N. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.02.076 · Cited by 55 · see citing works
Self-citationPeat, T. S., Rhodes, D. I., Vandegraaff, N., Le, G. T., Smith, J. A., Clark, L. J., Jones, E. D., Coates, J. A. V., Thienthong, N., Newman, J. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040147 · Cited by 52 · see citing works
Fan, X. H., Zhang, F.-H., Al-Safi, R. I., Zeng, L., Shabaik, Y., Debnath, B., Sanchez, T. W., Odde, S., Neamati, N., & Long, Y. (2011) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2011.06.058 · Cited by 49 · see citing works
HIV-1 integrase inhibitors: 2007-2008 update
Ramkumar, K., Serrao, E., Odde, S., & Neamati, N. (2010) · Medicinal Research Reviews · doi:10.1002/med.20194 · Cited by 39 · see citing works
Inhibitors of the Interactions between HIV‐1 IN and the Cofactor LEDGF/p75
Luca, L. D., Ferro, S., Morreale, F. E., Grazia, S. D., & Chimirri, A. (2011) · ChemMedChem · doi:10.1002/cmdc.201100071 · Cited by 36 · see citing works
Self-citationCellular Cofactors of Lentiviral Integrase: From Target Validation to Drug Discovery
Taltynov, O., Desimmie, B. A., Demeulemeester, J., Christ, F., & Debyser, Z. (2012) · Molecular Biology International · doi:10.1155/2012/863405 · Cited by 34 · see citing works
Self-citationLuca, L. D., Ferro, S., Morreale, F. E., & Chimirri, A. (2011) · Mini-Reviews in Medicinal Chemistry · doi:10.2174/138955711796268787 · Cited by 25 · see citing works
Self-citationHu, G., Li, X., Sun, X., Lü, W., Liu, G., Huang, J. Y., Shen, X., & Tang, Y. (2012) · Journal of Molecular Modeling · doi:10.1007/s00894-012-1494-0 · Cited by 23 · see citing works
Luca, L. D., Gitto, R., Christ, F., Ferro, S., Grazia, S. D., Morreale, F. E., Debyser, Z., & Chimirri, A. (2011) · Antiviral Research · doi:10.1016/j.antiviral.2011.07.005 · Cited by 21 · see citing works
Self-citationLuca, L. D., Morreale, F. E., & Chimirri, A. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300361e · Cited by 20 · see citing works
Self-citationLuca, A. D., Marazzi, M. C., Mancinelli, S., Ceffa, S., Altan, A. M. D., Buonomo, E., Prosperi, F. M. C., Pedruzzi, B., Majid, N., Scarcella, P., et al. (2011) · JAIDS Journal of Acquired Immune Deficiency Syndromes · doi:10.1097/qai.0b013e31824276e9 · Cited by 19 · see citing works
Fragment hopping approach directed at design of HIV IN-LEDGF/p75 interaction inhibitors
Luca, L. D., Ferro, S., Morreale, F. E., Christ, F., Debyser, Z., Chimirri, A., & Gitto, R. (2012) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.3109/14756366.2012.703184 · Cited by 14 · see citing works
Self-citationFerro, S., Grazia, S. D., Luca, L. D., Gitto, R., Faliti, C. E., Debyzer, Z., & Chimirri, A. (2011) · Molecules · doi:10.3390/molecules16086858 · Cited by 7 · see citing works
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Sorted by citations
Modulators of Protein–Protein Interactions
Milroy, L.-G., Grossmann, T. N., Hennig, S., Brunsveld, L., & Ottmann, C. (2014) · Chemical Reviews · doi:10.1021/cr400698c · Cited by 497 · see citing works
Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends
Zhan, P., Pannecouque, C. C., Clercq, E. D., & Liu, X. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00497 · Cited by 316 · see citing works
Hierarchical virtual screening approaches in small molecule drug discovery
Kumar, A., & Zhang, K. Y. J. (2014) · Methods · doi:10.1016/j.ymeth.2014.07.007 · Cited by 157 · see citing works
Panwar, U., & Singh, S. K. (2017) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1384400 · Cited by 48 · see citing works
Synthesis of dihydropyrimidine α,γ-diketobutanoic acid derivatives targeting HIV integrase
Sari, O., Roy, V., Métifiot, M., Marchand, C., Pommier, Y. G., Bourg, S., Bonnet, P., Schinazi, R. F., & Agrofoglio, L. A. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.09.015 · Cited by 36 · see citing works
Kumar, D., Sharma, P., Shabu, Kaur, R., Lobe, M. M. M., Gupta, G. K., & Ntie‐Kang, F. (2021) · RSC Advances · doi:10.1039/d0ra10655k · Cited by 27 · see citing works
Ferro, S., Luca, L. D., Surdo, G. L., Morreale, F. E., Christ, F., Debyser, Z., Gitto, R., & Chimirri, A. (2014) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2014.02.012 · Cited by 18 · see citing works
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Weydert, C., Rijck, J. D., Christ, F., & Debyser, Z. (2015) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026615666150901115106 · Cited by 16 · see citing works
Self-citationAgharbaoui, F. E., Hoyte, A. C., Ferro, S., Gitto, R., Buemi, M. R., Fuchs, J. R., Kvaratskhelia, M., & Luca, L. D. (2016) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2016.07.077 · Cited by 10 · see citing works
Self-citationLuca, L. D., Agharbaoui, F. E., Gitto, R., Buemi, M. R., Christ, F., Debyser, Z., & Ferro, S. (2016) · Molecular Informatics · doi:10.1002/minf.201501034 · Cited by 9 · see citing works
Self-citationOptimization of rhodanine scaffold for the development of protein–protein interaction inhibitors
Ferro, S., Luca, L. D., Agharbaoui, F. E., Christ, F., Debyser, Z., & Gitto, R. (2015) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2015.04.072 · Cited by 4 · see citing works
Self-citationGu, W.-G., Liu, B., & Yuan, J. (2014) · Journal of drug targeting · doi:10.3109/1061186x.2014.959020 · Cited by 4 · see citing works
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Li, Y., Tian, Y., Yao, X., Qin, Z., & Yan, A. (2019) · Current Computer - Aided Drug Design · doi:10.2174/1573409915666190919153959 · Cited by 3 · see citing works
Ribone, S. R., & Quevedo, M. A. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.05.019 · Cited by 2 · see citing works
Sun, H., Wu, H., Wang, T., Chen, A., & Yu, R. (2025) · Journal of Chemometrics · doi:10.1002/cem.70037 · Cited by 1 · see citing works
Kehinde, I. O., Madlala, P., Pellicane, G., Rotondo, A., Kehinde, S. O., Faya, M. A., & Soliman, M. E. S. (2025) · Journal of Computational Biophysics and Chemistry · doi:10.1142/s2737416526500432
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Zarghi, A., & Hajimahdi, Z. (2026) · Archiv der Pharmazie · doi:10.1002/ardp.70221
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- Authors
- De Luca, L., Morreale, F., Christ, F., Debyser, Z., Ferro, S., & Gitto, R.
- Affiliations
- University of Messina (IT)
- KU Leuven (BE)
- Venue
- European Journal of Medicinal Chemistry
- Publisher
- Elsevier BV
- Published
- 2013-10
- Volume
- 68
- Pages
- 405-411
- ISSN
- 0223-5234 (ISSN-L)
- OpenAlex
- W2012839858
- Cited by
- 17
- References
- 30
- Citations by year
- 2026: 1 · 2025: 2 · 2021: 1 · 2019: 1 · 2017: 2 · 2016: 2 · 2015: 4 · 2014: 4
- FWCI
- 4.01
- Type
- journal article
- Language
- en
- Open access
- green
- zenodo.org
- Licence
- Locations
- European Journal of Medicinal Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Lirias (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
- Funders
- European Commission
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Keywords
- HIV-1 integrase, LEDGF/p75, natural product scaffolds, structure-based virtual screening, antiretroviral drugs, protein-protein interaction inhibition, molecular docking, molecular dynamics simulation
- MeSH terms
- Biological Assay, Biological Products, Drug Evaluation, Preclinical, Enzyme Activation, Humans, Models, Molecular, Molecular Structure, Crystallography, X-Ray, HIV Integrase Inhibitors, Integrase Inhibitors, Intercellular Signaling Peptides and Proteins, Molecular Docking Simulation
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