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Charoenkwan P, Schaduangrat N, Lio P, Moni MA, Chumnanpuen P, Shoombuatong W. iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides. ACS OMEGA 2022; 7:41082-41095. [PMID: 36406571 PMCID: PMC9670693 DOI: 10.1021/acsomega.2c04465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antimalarial peptides (AMAPs) varying in length, amino acid composition, charge, conformational structure, hydrophobicity, and amphipathicity reflect their diversity in antimalarial mechanisms. Due to the worldwide major health problem concerning antimicrobial resistance, these peptides possess great therapeutic value owing to their low incidences of drug resistance as compared to conventional antibiotics. Although well-known experimental methods are able to precisely determine the antimalarial activity of peptides, these methods are still time-consuming and costly. Thus, machine learning (ML)-based methods that are capable of identifying AMAPs rapidly by using only sequence information would be beneficial for the high-throughput identification of AMAPs. In this study, we propose the first computational model (termed iAMAP-SCM) for the large-scale identification and characterization of peptides with antimalarial activity by using only sequence information. Specifically, we employed an interpretable scoring card method (SCM) to develop iAMAP-SCM and estimate propensities of 20 amino acids and 400 dipeptides to be AMAPs in a supervised manner. Experimental results showed that iAMAP-SCM could achieve a maximum accuracy and Matthew's coefficient correlation of 0.957 and 0.834, respectively, on the independent test dataset. In addition, SCM-derived propensities of 20 amino acids and selected physicochemical properties were used to provide an understanding of the functional mechanisms of AMAPs. Finally, a user-friendly online computational platform of iAMAP-SCM is publicly available at http://pmlabstack.pythonanywhere.com/iAMAP-SCM. The iAMAP-SCM predictor is anticipated to assist experimental scientists in the high-throughput identification of potential AMAP candidates for the treatment of malaria and other clinical applications.
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Affiliation(s)
- Phasit Charoenkwan
- Modern
Management and Information Technology, College of Arts, Media and
Technology, Chiang Mai University, Chiang Mai50200, Thailand
| | - Nalini Schaduangrat
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok10700, Thailand
| | - Pietro Lio
- Department
of Computer Science and Technology, University
of Cambridge, CambridgeshireCB3 0FD, U.K.
| | - Mohammad Ali Moni
- Artificial
Intelligence & Digital Health, School of Health and Rehabilitation
Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St LuciaQLD 4072, Australia
| | - Pramote Chumnanpuen
- Department
of Zoology, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
- Omics Center
for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok10900, Thailand
| | - Watshara Shoombuatong
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok10700, Thailand
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Pedron CN, Silva AF, Torres MDT, Oliveira CSD, Andrade GP, Cerchiaro G, Pinhal MAS, de la Fuente-Nunez C, Oliveira Junior VX. Net charge tuning modulates the antiplasmodial and anticancer properties of peptides derived from scorpion venom. J Pept Sci 2021; 27:e3296. [PMID: 33442881 DOI: 10.1002/psc.3296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022]
Abstract
VmCT1, a linear helical antimicrobial peptide isolated from the venom of the scorpion Vaejovis mexicanus, displays broad spectrum antimicrobial activity against bacteria, fungi, and protozoa. Analogs derived from this peptide containing single Arg-substitutions have been shown to increase antimicrobial and antiparasitic activities against Trypanossoma cruzi. Here, we tested these analogs against malaria, an infectious disease caused by Plasmodium protozoa, and assessed their antitumoral properties. Specifically, we tested VmCT1 synthetic variants [Arg]3 -VmCT1-NH2 , [Arg]7 -VmCT1-NH2 , and [Arg]11 -VmCT1-NH2 , against Plasmodium gallinaceum sporozoites and MCF-7 mammary cancer cells. Our screen identified peptides [Arg]3 -VmCT1-NH2 and [Arg]7 -VmCT1-NH2 as potent antiplasmodial agents (IC50 of 0.57 and 0.51 μmol L-1 , respectively), whereas [Arg]11 -VmCT1-NH2 did not show activity against P. gallinaceum sporozoites. Interestingly, all peptides presented activity against MCF-7 and displayed lower cytotoxicity toward healthy cells. We demonstrate that increasing the net positive charge of VmCT1, through arginine substitutions, modulates the biological properties of this peptide family yielding novel antiplasmodial and antitumoral molecules.
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Affiliation(s)
- Cibele Nicolaski Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Adriana Farias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, 19102, USA
| | | | - Gislaine Patricia Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, 19102, USA
| | - Vani Xavier Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
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3
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Torres MDT, Silva AF, Andrade GP, Pedron CN, Cerchiaro G, Ribeiro AO, Oliveira VX, de la Fuente‐Nunez C. The wasp venom antimicrobial peptide polybia-CP and its synthetic derivatives display antiplasmodial and anticancer properties. Bioeng Transl Med 2020; 5:e10167. [PMID: 33005737 PMCID: PMC7510464 DOI: 10.1002/btm2.10167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
The wasp venom-derived antimicrobial peptide polybia-CP has been previously shown to exhibit potent antimicrobial activity, but it is also highly toxic. Previously, using a physicochemical-guided peptide design strategy, we reversed its toxicity while preserving and even enhancing its antibacterial properties. Here, we report on several additional unanticipated biological properties of polybia-CP and derivatives, namely their ability to target Plasmodium sporozoites and cancer cells. We leverage a physicochemical-guided approach to identify features that operate as functional hotspots making these peptides viable antiplasmodial and anticancer agents. Helical content and net positive charge are identified as key structural and physicochemical determinants for antiplasmodial activity. In addition to helicity and net charge, hydrophobicity-related properties of polybia-CP and derivatives were found to be equally critical to target cancer cells. We demonstrate that by tuning these physicochemical parameters, it is possible to design synthetic peptides with enhanced submicromolar antiplasmodial potency and micromolar anticancer activity. This study reveals novel and previously undescribed functions for Polybia-CP and analogs. Additionally, we demonstrate that a physicochemical-guided rational design strategy can be used for identifying functional hotspots in peptide molecules and for tuning structure-function to generate novel and potent new-to-nature therapies.
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Affiliation(s)
- Marcelo D. T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Adriana F. Silva
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
- Departamento de BioquímicaUniversidade Federal de São PauloSão PauloSPBrazil
| | - Gislaine P. Andrade
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Cibele N. Pedron
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Giselle Cerchiaro
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Anderson O. Ribeiro
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Vani X. Oliveira
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
- Departamento de BiofísicaUniversidade Federal de São PauloSão PauloSPBrazil
| | - Cesar de la Fuente‐Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Der Torossian Torres M, de la Fuente-Nunez C. Reprogramming biological peptides to combat infectious diseases. Chem Commun (Camb) 2019; 55:15020-15032. [PMID: 31782426 DOI: 10.1039/c9cc07898c] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
With the rapid spread of resistance among parasites and bacterial pathogens, antibiotic-resistant infections have drawn much attention worldwide. Consequently, there is an urgent need to develop new strategies to treat neglected diseases and drug-resistant infections. Here, we outline several new strategies that have been developed to counter pathogenic microorganisms by designing and constructing antimicrobial peptides (AMPs). In addition to traditional discovery and design mechanisms guided by chemical biology, synthetic biology and computationally-based approaches offer useful tools for the discovery and generation of bioactive peptides. We believe that the convergence of such fields, coupled with systematic experimentation in animal models, will help translate biological peptides into the clinic. The future of anti-infective therapeutics is headed towards specifically designed molecules whose form is driven by computer-based frameworks. These molecules are selective, stable, and active at therapeutic doses.
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Affiliation(s)
- Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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5
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Torres MDT, Andrade GP, Sato RH, Pedron CN, Manieri TM, Cerchiaro G, Ribeiro AO, de la Fuente-Nunez C, Oliveira VX. Natural and redesigned wasp venom peptides with selective antitumoral activity. Beilstein J Org Chem 2018; 14:1693-1703. [PMID: 30013694 PMCID: PMC6036970 DOI: 10.3762/bjoc.14.144] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/13/2018] [Indexed: 12/16/2022] Open
Abstract
About 1 in 8 U.S. women (≈12%) will develop invasive breast cancer over the course of their lifetime. Surgery, chemotherapy, radiotherapy, and hormone manipulation constitute the major treatment options for breast cancer. Here, we show that both a natural antimicrobial peptide (AMP) derived from wasp venom (decoralin, Dec-NH2), and its synthetic variants generated via peptide design, display potent activity against cancer cells. We tested the derivatives at increasing doses and observed anticancer activity at concentrations as low as 12.5 μmol L−1 for the selective targeting of MCF-7 breast cancer cells. Flow cytometry assays further revealed that treatment with wild-type (WT) peptide Dec-NH2 led to necrosis of MCF-7 cells. Additional atomic force microscopy (AFM) measurements indicated that the roughness of cancer cell membranes increased significantly when treated with lead peptides compared to controls. Biophysical features such as helicity, hydrophobicity, and net positive charge were identified to play an important role in the anticancer activity of the peptides. Indeed, abrupt changes in peptide hydrophobicity and conformational propensity led to peptide inactivation, whereas increasing the net positive charge of peptides enhanced their activity. We present peptide templates with selective activity towards breast cancer cells that leave normal cells unaffected. These templates represent excellent scaffolds for the design of selective anticancer peptide therapeutics.
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Affiliation(s)
- Marcelo D T Torres
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil.,Synthetic Biology Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, The Center for Microbiome Informatics and Therapeutics, Cambridge, 02139, MA, United States of America
| | - Gislaine P Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Roseli H Sato
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Cibele N Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Tania M Manieri
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Anderson O Ribeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, The Center for Microbiome Informatics and Therapeutics, Cambridge, 02139, MA, United States of America
| | - Vani X Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210580, SP, Brazil
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Silva AF, Torres MDT, Silva LDS, Alves FL, Pinheiro AADS, Miranda A, Capurro ML, Oliveira VX. New linear antiplasmodial peptides related to angiotensin II. Malar J 2015; 14:433. [PMID: 26537730 PMCID: PMC4634797 DOI: 10.1186/s12936-015-0974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023] Open
Abstract
Background Antiplasmodial activities of angiotensin II and its analogues have been extensively investigated in Plasmodium gallinaceum and Plasmodium falciparum parasite species. Due to its vasoconstrictor property angiotensin II cannot be used as an anti-malarial drug. Methods This work presents the solid-phase syntheses and liquid chromatography and mass spectrometry characterization of ten linear peptides related to angiotensin II against mature P. gallinaceum sporozoites and erythrocyte invasion by P. falciparum. Conformational analyses were performed by circular dichroism. IC50 assays were performed to identify the ideal concentration used on the biological tests and haemolytical erythrocytic assays were made to verify the viability of the biological experiments. The contractile responses of the analogues were made to evaluate if they are promising candidates to be applied as antiplasmodial drugs. Results The results indicate two short-peptides constituted by hydrophobic residues (5 and 6) with antiplasmodial activity in these models, 89 and 94 % of biological activity against P. gallinaceum sporozoite, respectively, and around 50 % of activity against P. falciparum. Circular dichroism spectra suggested that all the peptides adopted β-turn conformation in different solutions, except peptide 3. Besides the biological assays IC50, the haemolysis assays and contractile response activities were applied for peptides 5 and 6, which did not present expressive results. Conclusions The hydrophobic portion and the arginine, tyrosine, proline, and phenylalanine, when present on peptide primary sequence, tend to increase the antiplasmodial activity. This class of peptides can be explored, as anti-malarial drugs, after in vivo model tests.The most active peptide presented 94 % activity on P. gallinaceum sporozoites and 53 % inhibited P. falciparum ring forms invasion ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0974-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adriana Farias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
| | - Marcelo Der Torossian Torres
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
| | - Leandro de Souza Silva
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Flávio Lopes Alves
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Ana Acácia de Sá Pinheiro
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Antonio Miranda
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Margareth Lara Capurro
- Departamento de Parasitologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Vani Xavier Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
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