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In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2

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Abstract

Falcipain-2 (FP-2) is a Plasmodium falciparum hemoglobinase widely targeted in the search for antimalarials. FP-2 can be allosterically modulated by various noncompetitive inhibitors that have been serendipitously identified. Moreover, the crystal structures of two inhibitors bound to an allosteric site, termed site 6, of the homolog enzyme human cathepsin K (hCatK) suggest that the equivalent region in FP-2 might play a similar role. Here, we conduct the rational identification of FP-2 inhibitors through virtual screenings (VS) of compounds into several pocket-like conformations of site 6, sampled during molecular dynamics (MD) simulations of the free enzyme. Two noncompetitive inhibitors, ZINC03225317 and ZINC72290660, were confirmed using in vitro enzymatic assays and their poses into site 6 led to calculated binding free energies matching the experimental ones. Our results provide strong evidence about the allosteric inhibition of FP-2 through binding of small molecules to site 6, thus opening the way toward the discovery of new inhibitors against this enzyme.

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Availability of data and material

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Code availability

MOE, Amber14, Amber18, and Gaussian 09 are commercial software. Autodock-Vina, Gromacs and Avogadro are freely available on the internet.

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Funding

JEHG and CO gratefully acknowledge financial support in the context of an Ernst Mach Scholarship (OeAD), financed by the Austrian Federal Ministry for Education, Science and Research. JEHG and LHA thank the Sao Paulo Research Foundation (FAPESP), Grant Numbers 2016/24587–9, 2018/03911–8 and 2020/10214-1 for financial support. ESS is grateful to the National Research Council (CONICET, Argentina). VBPL was funded by VBPL was funded by FAPESP Grant 2019/22540–3 and 2016/19766–1, and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). PGP thanks CNPq e Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for general financial support (Finance Code 001).

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Authors and Affiliations

  1. Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas – Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rua Cristóvão Colombo 2265, Jardim Nazareth, São José do Rio Preto, SP, CEP 15054-000, Brazil

    Jorge Enrique Hernández González, Lilian Hernández Alvarez & Vitor B. P. Leite

  2. Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofı́sica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave. Carlos Chagas Filho – Universidade Federal do Rio de Janeiro (UFRJ), Ave. Carlos Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária Ilha de Fundão, Rio de Janeiro, RJ, CEP 21941-902, Brazil

    Jorge Enrique Hernández González, Diego Enry Barreto Gomes & Pedro Geraldo Pascutti

  3. Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering – University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria

    Jorge Enrique Hernández González & Chris Oostenbrink

  4. Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina

    Emir Salas-Sarduy

  5. Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora (UFJF), Rua José Lourenço Kelmer, s/n – Campus Universitário, Bairro São Pedro, Juiz de Fora, MG, CEP 36036-900, Brazil

    Diego Enry Barreto Gomes

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  1. Jorge Enrique Hernández González
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  2. Emir Salas-Sarduy
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Correspondence to Jorge Enrique Hernández González.

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Hernández González, J.E., Salas-Sarduy, E., Hernández Alvarez, L. et al. In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J Comput Aided Mol Des 35, 1067–1079 (2021). https://doi.org/10.1007/s10822-021-00420-7

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