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Savino DF, Silva JV, da Silva Santos S, Lourenço FR, Giarolla J. How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease? J Mol Model 2024; 30:54. [PMID: 38289526 DOI: 10.1007/s00894-024-05843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
CONTEXT AND RESULTS Flavivirus diseases' cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. METHODS The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).
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Affiliation(s)
- Débora Feliciano Savino
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - João Vitor Silva
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Felipe Rebello Lourenço
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil.
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Santos SS, Gonzaga RV, Scarim CB, Giarolla J, Primi MC, Chin CM, Ferreira EI. Drug/Lead Compound Hydroxymethylation as a Simple Approach to Enhance Pharmacodynamic and Pharmacokinetic Properties. Front Chem 2022; 9:734983. [PMID: 35237565 PMCID: PMC8883432 DOI: 10.3389/fchem.2021.734983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
Hydroxymethylation is a simple chemical reaction, in which the introduction of the hydroxymethyl group can lead to physical–chemical property changes and offer several therapeutic advantages, contributing to the improved biological activity of drugs. There are many examples in the literature of the pharmaceutical, pharmacokinetic, and pharmacodynamic benefits, which the hydroxymethyl group can confer to drugs, prodrugs, drug metabolites, and other therapeutic compounds. It is worth noting that this group can enhance the drug’s interaction with the active site, and it can be employed as an intermediary in synthesizing other therapeutic agents. In addition, the hydroxymethyl derivative can result in more active compounds than the parent drug as well as increase the water solubility of poorly soluble drugs. Taking this into consideration, this review aims to discuss different applications of hydroxymethyl derived from biological agents and its influence on the pharmacological effects of drugs, prodrugs, active metabolites, and compounds of natural origin. Finally, we report a successful compound synthesized by our research group and used for the treatment of neglected diseases, which is created from the hydroxymethylation of its parent drug.
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Affiliation(s)
- Soraya S. Santos
- Laboratório de Planejamento e Síntese de Quimioterápicos Potencialmente Ativos Em Doenças Negligenciadas (LAPEN), Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo – USP, São Paulo, Brazil
| | - Rodrigo V. Gonzaga
- Laboratório de Planejamento e Síntese de Quimioterápicos Potencialmente Ativos Em Doenças Negligenciadas (LAPEN), Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo – USP, São Paulo, Brazil
| | - Cauê B. Scarim
- Laboratório de Pesquisa e Desenvolvimento de Fármacos (LAPDESF), Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual de São Paulo “Júlio de Mesquita Filho” (UNESP), Araraquara, Brazil
| | - Jeanine Giarolla
- Laboratório de Planejamento e Síntese de Quimioterápicos Potencialmente Ativos Em Doenças Negligenciadas (LAPEN), Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo – USP, São Paulo, Brazil
| | | | - Chung M. Chin
- Laboratório de Pesquisa e Desenvolvimento de Fármacos (LAPDESF), Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual de São Paulo “Júlio de Mesquita Filho” (UNESP), Araraquara, Brazil
- Centro de Pesquisa Avançada Em Medicina (CEPAM), Faculdade de Medicina, União Das Faculdades Dos Grande Lagos (UNILAGO), São José Do Rio Preto, Brazil
| | - Elizabeth I. Ferreira
- Laboratório de Planejamento e Síntese de Quimioterápicos Potencialmente Ativos Em Doenças Negligenciadas (LAPEN), Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo – USP, São Paulo, Brazil
- *Correspondence: Elizabeth I. Ferreira,
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Dias AP, da Silva Santos S, da Silva JV, Parise-Filho R, Igne Ferreira E, Seoud OE, Giarolla J. Dendrimers in the context of nanomedicine. Int J Pharm 2019; 573:118814. [PMID: 31759101 DOI: 10.1016/j.ijpharm.2019.118814] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/23/2023]
Abstract
Dendrimers are globular structures, presenting an initiator core, repetitive layers starting radially from the core and terminal groups on the surface, resembling tree architecture. These structures have been studied in many biological applications, as drug, DNA, RNA and proteins delivery, as well as imaging and radiocontrast agents. With reference to that, this review focused in providing examples of dendrimers used in nanomedicine. Although most studies emphasize cancer, there are others which reveal action in the neurosystem, reducing either neuroinflammation or protein aggregation. Dendrimers can carry bioactive compounds by covalent bond (dendrimer prodrug), or by ionic interaction or adsortion in the internal space of the nanostructure. Additionally, dendrimers can be associated with other polymers, as PEG (polyethylene glycol), and with targeting structures as aptamers, antibodies, folic acid and carbohydrates. Their products in preclinical/clinical trial and those in the market are also discussed, with a total of six derivatives in clinical trials and seven products available in the market.
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Affiliation(s)
- Ana Paula Dias
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - João Vitor da Silva
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Omar El Seoud
- Department of Organic Chemistry, Institute of Chemistry, University of São Paulo - USP, São Paulo, SP, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil.
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da Silva Santos S, Igne Ferreira E, Giarolla J. Dendrimer Prodrugs. Molecules 2016; 21:E686. [PMID: 27258239 PMCID: PMC6274429 DOI: 10.3390/molecules21060686] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
The main objective of this review is to describe the importance of dendrimer prodrugs in the design of new drugs, presenting numerous applications of these nanocomposites in the pharmaceutical field. Therefore, the use of dendrimer prodrugs as carrier for drug delivery, to improve pharmacokinetic properties of prototype, to promote drug sustained-release, to increase selectivity and, consequently, to decrease toxicity, are just some examples of topics that have been extensively reported in the literature, especially in the last decade. The examples discussed here give a panel of the growing interest dendrimer prodrugs have been evoking in the scientific community.
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Affiliation(s)
- Soraya da Silva Santos
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil.
| | - Elizabeth Igne Ferreira
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil.
| | - Jeanine Giarolla
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil.
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da Silva Santos S, Giarolla J, Pasqualoto KF, Ferreira EI. In silicostudy to analyse the disassembly of quercetin-targeted dendrimers potentially leishmanicide. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.994622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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