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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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2
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Hernández González JE, de Araujo AS. Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein-Protein Interfaces Considering Fixed and Variable Protonation States. J Chem Inf Model 2023; 63:6807-6822. [PMID: 37851531 DOI: 10.1021/acs.jcim.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The calculation of relative free energies (ΔΔG) for charge-changing mutations at protein-protein interfaces through alchemical methods remains challenging due to variations in the system's net charge during charging steps, the possibility of mutated and contacting ionizable residues occurring in various protonation states, and undersampling issues. In this study, we present a set of strategies, collectively termed TIRST/TIRST-H+, to address some of these challenges. Our approaches combine thermodynamic integration (TI) with the prediction of pKa shifts to calculate ΔΔG values. Moreover, special sets of restraints are employed to keep the alchemically transformed molecules separated. The accuracy of the devised approaches was assessed on a large and diverse data set comprising 164 point mutations of charged residues (Asp, Glu, Lys, and Arg) to Ala at the protein-protein interfaces of complexes with known three-dimensional structures. Mean absolute and root-mean-square errors ranging from 1.38 to 1.66 and 1.89 to 2.44 kcal/mol, respectively, and Pearson correlation coefficients of ∼0.6 were obtained when testing the approaches on the selected data set using the GPU-TI module of Amber18 suite and the ff14SB force field. Furthermore, the inclusion of variable protonation states for the mutated acid residues improved the accuracy of the predicted ΔΔG values. Therefore, our results validate the use of TIRST/TIRST-H+ in prospective studies aimed at evaluating the impact of charge-changing mutations to Ala on the stability of protein-protein complexes.
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Brogi S, Ibba R, Rossi S, Butini S, Calderone V, Gemma S, Campiani G. Covalent Reversible Inhibitors of Cysteine Proteases Containing the Nitrile Warhead: Recent Advancement in the Field of Viral and Parasitic Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082561. [PMID: 35458759 PMCID: PMC9029279 DOI: 10.3390/molecules27082561] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/29/2022]
Abstract
In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.
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Affiliation(s)
- Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Roberta Ibba
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Sara Rossi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
- Correspondence:
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
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Barbosa Da Silva E, Sharma V, Hernandez-Alvarez L, Tang AH, Stoye A, O’Donoghue AJ, Gerwick WH, Payne RJ, McKerrow JH, Podust LM. Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi. J Med Chem 2022; 65:4255-4269. [DOI: 10.1021/acs.jmedchem.1c02063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elany Barbosa Da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Vandna Sharma
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Lilian Hernandez-Alvarez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Arthur H. Tang
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexander Stoye
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
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Hernández González JE, Alberca LN, Masforrol González Y, Reyes Acosta O, Talevi A, Salas-Sarduy E. Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site. J Chem Inf Model 2021; 62:159-175. [PMID: 34962803 DOI: 10.1021/acs.jcim.1c01189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric inhibitors regulate enzyme activity from remote and usually specific pockets. As they promise an avenue for less toxic and safer drugs, the identification and characterization of allosteric inhibitors has gained great academic and biomedical interest in recent years. Research on falcipain-2 (FP-2), the major papain-like cysteine hemoglobinase of Plasmodium falciparum, might benefit from this strategy to overcome the low selectivity against human cathepsins shown by active site-directed inhibitors. Encouraged by our previous finding that methacycline inhibits FP-2 noncompetitively, here we assessed other five tetracycline derivatives against this target and characterized their inhibition mechanism. As previously shown for methacycline, tetracycline derivatives inhibited FP-2 in a noncompetitive fashion, with Ki values ranging from 121 to 190 μM. A possible binding to the S' side of the FP-2 active site, similar to that described by X-ray crystallography (PDB: 6SSZ) for the noncompetitive inhibitor E-chalcone 48 (EC48), was experimentally discarded by kinetic analysis using a large peptidyl substrate spanning the whole active site. By combining lengthy molecular dynamics (MD) simulations that allowed methacycline to diffuse from solution to different FP-2 surface regions and free energy calculations, we predicted the most likely binding mode of the ligand. Of note, the proposed binding pose explains the low differences in Ki values observed for the tested tetracycline derivatives and the calculated binding free energies match the experimental values. Overall, this study has implications for the design of novel allosteric inhibitors against FP-2 and sets the basis for further optimization of the tetracycline scaffold to produce more potent and selective inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto, São Paulo CEP 15054-000, Brazil
| | - Lucas N Alberca
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | | | - Osvaldo Reyes Acosta
- Chemistry and Physics Department, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Alan Talevi
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde"─Universidad Nacional de San Martín─CONICET, San Martín B1650HMP, Buenos Aires, Argentina
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Hernández González JE, Salas-Sarduy E, Hernández Alvarez L, Barreto Gomes DE, Pascutti PG, Oostenbrink C, Leite VBP. In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J Comput Aided Mol Des 2021; 35:1067-1079. [PMID: 34617191 DOI: 10.1007/s10822-021-00420-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/24/2021] [Indexed: 01/05/2023]
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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Affiliation(s)
- Jorge Enrique Hernández González
- 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. .,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. .,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.
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
| | - Lilian Hernández Alvarez
- 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
| | - Diego Enry Barreto Gomes
- 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.,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
| | - Pedro Geraldo Pascutti
- 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
| | - Chris Oostenbrink
- 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
| | - Vitor B P Leite
- 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
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Armacost KA, Riniker S, Cournia Z. Exploring Novel Directions in Free Energy Calculations. J Chem Inf Model 2020; 60:5283-5286. [PMID: 33222441 DOI: 10.1021/acs.jcim.0c01266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kira A Armacost
- Computational and Structural Chemistry, MRL, Merck & Co., Inc. West Point, Pennsylvania 19486, United States
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece
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