Andre Filipe Rodrigues Miranda

@ubi.pt

PhD Student in Biochemistry
Centro de Investigação em Ciências da Saúde (CICS)

Andre Filipe Rodrigues Miranda


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https://researchid.co/andre.miranda

RESEARCH, TEACHING, or OTHER INTERESTS

Biophysics, Biochemistry, Structural Biology, Biotechnology
22

Scopus Publications

273

Scholar Citations

10

Scholar h-index

10

Scholar i10-index

Scopus Publications

  • Therapeutic Applications of Nucleic Acid Aptamers
    Springer Handbooks, 2026
  • Cellular modulation of a G-quadruplex structure found in the lung cancer-related microRNA-3196
    Daniela Alexandre, Joana Polido, André Miranda, Robert H.E. Hudson, David Monchaud, et al.
    International Journal of Biological Macromolecules, 2025
  • Sensitive fluorescent detection of SARS-CoV-2 RNA using an enzymatic-based method
    André Miranda, Bruno Baptista, Marília Figueira, Fani Sousa, Cláudio J. Maia, et al.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, 2025
  • Exploring the G-Quadruplex Formation of AS1411 Derivatives
    Pedro Lourenço, David Moreira, André Miranda, Jéssica Lopes-Nunes, Izamara Maocha, et al.
    Molecules, 2025
    AS1411 is a G-quadruplex (G4) aptamer that binds tightly to nucleolin (NCL) on the cell surface and has shown strong anticancer effects. However, this aptamer is highly polymorphic, presenting different types of G4s, which may hinder its preclinical application. Several modifications have been made to decrease the polymorphism of this aptamer. In this work, we designed six AS1411 derivatives by substituting guanine with thymine in the central linker and modifying the number of thymines either in the linker itself and/or at both ends of the sequence. The G4 formation, stability, and NCL binding were evaluated by several biophysical techniques and computational and cell studies. Overall, a decrease in polymorphism of G4-forming sequences compared to AS1411 is observed by size exclusion chromatography (SEC) and circular dichroism (CD) spectroscopy in the presence of potassium salt. The melting experiments reveal a higher ability of the derivatives without thymine at both sequence ends to form a G4, consistent with the G4H score predictions. Additionally, it is possible to conclude that deletions of T in the central core increase the ability to form G4. Moreover, the AS1411 derivatives bind NCL with high affinity (KD values in the 10−9 M range), particularly the sequences with only thymine modifications in the central linker. In silico studies reveal structural insights and demonstrate that AS1411 derivatives interact with NCL, establishing multiple interactions with the different domains, thereby further supporting the experimental findings. By using a lung cancer cell line with high cell surface NCL expression, we evaluate the internalization and uptake of AS1411 derivatives, identifying the derivative-lacking thymines in the central core as the ones with the highest internalization and cellular uptake.
  • I-motif formation in the promoter region of the B-MYB proto-oncogene
    André Alves, André Miranda, Irene Zanin, Sara N. Richter, Jean-Louis Mergny, et al.
    International Journal of Biological Macromolecules, 2025
  • Synthesis of 1,10-Phenanthroline-2,9-bistriazoles: Evaluation as G-Quadruplex Binders and Anti-Tumor Activity
    Joana Figueiredo, Israel Carreira‐Barral, Pedro Lourenço, André Miranda, Jéssica Lopes‐Nunes, et al.
    Chemmedchem, 2025
    Novel 1,10‐phenanthroline‐2,9‐bistriazoles derivatives have been synthesized by copper‐catalyzed azide/alkyne cycloaddition reactions and assessed for their ability to bind and stabilize G‐quadruplex (G4) structures. Ten novel compounds were evaluated using Förster resonance energy transfer (FRET) melting, circular dichroism (CD), and fluorescence spectroscopy on several G4 sequences. Biophysical characterization led to the identification of compounds 4 a, 4 b, and 5 b as good G4 ligands of KRAS G4 sequences. The impact on cell viability of all derivatives was also assessed, revealing weak effects. However, compound 2 a exhibited cytotoxicity activity on A549 and H1299 cancer cells and low cytotoxicity towards MRC‐5 non‐malignant cells MRC‐5 not connected with its G4‐binding ability. Flow cytometry showed that 2 a induced a cell viability decrease in S and G2/M phases for A549 and H1299; thus, more studies should be performed to explore the proteins involved in cell cycle regulation.
  • Detecting mir-155-3p through a Molecular Beacon Bead-Based Assay
    David Moreira, Daniela Alexandre, André Miranda, Pedro Lourenço, Pedro V. Baptista, et al.
    Molecules, 2024
    Lung cancer (LC) is recognized as one of the most prevalent and lethal cancers worldwide, underscoring an urgent need for innovative diagnostic and therapeutic approaches. MicroRNAs (miRNAs) have emerged as promising biomarkers for several diseases and their progression, such as LC. However, traditional methods for detecting and quantifying miRNAs, such as PCR, are time-consuming and expensive. Herein, we used a molecular beacon (MB) bead-based assay immobilized in a microfluidic device to detect miR-155-3p, which is frequently overexpressed in LC. The assay relies on the fluorescence enhancement of the MB upon binding to the target miRNA via Watson and Crick complementarity, resulting in a conformational change from a stem–loop to a linear structure, thereby bringing apart the fluorophores at each end. This assay was performed on a microfluidic platform enabling rapid and straightforward target detection. We successfully detected miR-155-3p in a saline solution, obtaining a limit of detection (LOD) of 42 nM. Furthermore, we evaluated the method’s performance in more complex biological samples, including A549 cells’ total RNA and peripheral blood mononuclear cells (PBMCs) spiked with the target miRNA. We achieved satisfactory recovery rates, especially in A549 cells’ total RNA.
  • G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene
    André Miranda, Anne Cucchiarini, Cyril Esnault, Jean-Christophe Andrau, Paula A. Oliveira, et al.
    International Journal of Biological Macromolecules, 2024
  • Targeting proto-oncogene B-MYB G-quadruplex with a nucleic acid–based fluorescent probe
    Pedro Lourenço, André Miranda, Maria Paula Cabral Campello, António Paulo, Jean Louis-Mergny, et al.
    International Journal of Biological Macromolecules, 2024
  • Targeting of G-quadruplex DNA with 99mTc(I)/Re(I) Tricarbonyl Complexes Carrying Pyridostatin Derivatives
    Elisa Palma, Cigdem Içhedef, Célia Fernandes, Ana Belchior, Paula Raposinho, et al.
    Chemistry A European Journal, 2024
    The main goal of this work was to elucidate the potential relevance of (radio)metal chelates of 99mTc and Re targeting G‐quadruplex structures for the design of new tools for cancer theranostics. 99mTc provides the complexes with the ability to perform single‐photon‐emission computed tomography imaging studies, while the Re complexes should act as anticancer agents upon interaction with specific G4 DNA or RNA structures present in tumor tissues. Towards this goal, we have developed isostructural 99mTc(I) and Re(I) tricarbonyl complexes anchored by a pyrazolyl‐diamine (Pz) chelator carrying a pendant pyridostatin (PDS) fragment as the G4‐binding motif. The interaction of the PDF‐Pz‐Re (8) complex with different G4‐forming oligonucleotides was studied by circular dichroism, fluorescence spectroscopy and FRET‐melting assays. The results showed that the Re complex retained the ability to bind and stabilize G4‐structures from different DNA or RNA sequences, namely those present on the SRC proto‐oncogene and telomeric RNA (TERRA sequence). PDF‐Pz‐Re (8) showed low to moderate cytotoxicity in PC3 and MCF‐7 cancer cell lines, as typically observed for G4‐binders. Biodistribution studies of the congener PDF‐Pz‐99mTc (12) in normal mice showed that the complex undergoes a fast blood clearance with a predominant hepatobiliary excretion, pointing also for a high in vitro stability.
  • Gallic Acid–Triethylene Glycol Aptadendrimers Synthesis, Biophysical Characterization and Cellular Evaluation
    André Miranda, Roi Lopez-Blanco, Jéssica Lopes-Nunes, Ana M. Melo, Maria Paula Cabral Campello, et al.
    Pharmaceutics, 2022
  • G-Quadruplex Aptamer-Ligand Characterization
    David Moreira, Daniela Leitão, Jéssica Lopes-Nunes, Tiago Santos, Joana Figueiredo, et al.
    Molecules, 2022
  • Stabilization of a DNA aptamer by ligand binding
    Tiago Santos, Jéssica Lopes-Nunes, Daniela Alexandre, André Miranda, Joana Figueiredo, et al.
    Biochimie, 2022
  • Targeting a G-quadruplex from let-7e pre-miRNA with small molecules and nucleolin
    Tiago Santos, André Miranda, Lionel Imbert, David Monchaud, Gilmar F. Salgado, et al.
    Journal of Pharmaceutical and Biomedical Analysis, 2022
  • Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin
    Tiago Santos, André Miranda, Lionel Imbert, Andreia Jardim, Catarina R.F. Caneira, et al.
    European Journal of Pharmaceutical Sciences, 2022
  • Aptamer-based microfluidics for circulating tumor cells
    Carla Cruz, André Miranda, Tiago Santos
    Aptamers Engineered Nanocarriers for Cancer Therapy, 2022
  • Molecular beacon assay development for severe acute respiratory syndrome coronavirus 2 detection
    Josué Carvalho, Jéssica Lopes-Nunes, Joana Figueiredo, Tiago Santos, André Miranda, et al.
    Sensors, 2021
  • Ligands as stabilizers of g-quadruplexes in non-coding rnas
    Joana Figueiredo, Tiago Santos, André Miranda, Daniela Alexandre, Bernardo Teixeira, et al.
    Molecules, 2021
  • Recognition of nucleolin through interaction with RNA G-quadruplex
    Tiago Santos, André Miranda, Maria P.C. Campello, António Paulo, Gilmar Salgado, et al.
    Biochemical Pharmacology, 2021
  • Targeting nucleolin by RNA G-quadruplex-forming motif
    Joana Figueiredo, André Miranda, Jéssica Lopes-Nunes, Josué Carvalho, Daniela Alexandre, et al.
    Biochemical Pharmacology, 2021
  • Aptamer-based approaches to detect nucleolin in prostate cancer
    André Miranda, Tiago Santos, Josué Carvalho, Daniela Alexandre, Andreia Jardim, et al.
    Talanta, 2021
  • Locking up the as1411 aptamer with a flanking duplex: Towards an improved nucleolin-targeting
    André Miranda, Tiago Santos, Eric Largy, Carla Cruz
    Pharmaceuticals, 2021

RECENT SCHOLAR PUBLICATIONS

  • Therapeutic Applications of Nucleic Acid Aptamers
    P Lourenço, D Moreira, D Alexandre, I Maocha, J Lopes-Nunes, ...
    Springer Handbook of Medical Biotechnology, 395-427 , 2025
    2025
  • Cellular modulation of a G-quadruplex structure found in the lung cancer-related microRNA-3196
    D Alexandre, J Polido, A Miranda, RHE Hudson, D Monchaud, ...
    International Journal of Biological Macromolecules 318, 145263 , 2025
    2025
    Citations: 9
  • The Potential of B-myb G-quadruplex in Cancer Therapy: Insights into Formation, Small Molecule Binding and Biological Outcomes
    A Miranda, A Cucchiarinni, CEC Esnault, JC Andrau, P Oliveira, ...
    EUROPEAN BIOPHYSICS JOURNAL 54, S152-S152 , 2025
    2025
  • Sensitive fluorescent detection of SARS-CoV-2 RNA using an enzymatic-based method
    A Miranda, B Baptista, M Figueira, F Sousa, CJ Maia, S Socorro, C Cruz
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 331, 125766 , 2025
    2025
  • Exploring the G-quadruplex formation of AS1411 derivatives
    P Lourenço, D Moreira, A Miranda, J Lopes-Nunes, I Maocha, T Santos, ...
    Molecules 30 (8), 1673 , 2025
    2025
    Citations: 6
  • I-motif formation in the promoter region of the B-MYB proto-oncogene
    A Alves, A Miranda, I Zanin, SN Richter, JL Mergny, C Cruz
    International Journal of Biological Macromolecules 296, 139582 , 2025
    2025
    Citations: 4
  • Detecting mir-155-3p through a Molecular Beacon Bead-Based Assay
    D Moreira, D Alexandre, A Miranda, P Lourenco, PV Baptista, C Tomaz, ...
    Molecules 29 (13), 3182 , 2024
    2024
    Citations: 3
  • G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene
    A Miranda, A Cucchiarini, C Esnault, JC Andrau, PA Oliveira, JL Mergny, ...
    International Journal of Biological Macromolecules 270, 132244 , 2024
    2024
    Citations: 3
  • Targeting proto-oncogene B-MYB G-quadruplex with a nucleic acid–based fluorescent probe
    P Lourenco, A Miranda, MPC Campello, A Paulo, J Louis-Mergny, C Cruz
    International Journal of Biological Macromolecules 266, 131055 , 2024
    2024
    Citations: 5
  • Targeting of G‐quadruplex DNA with 99m Tc(I)/Re(I) Tricarbonyl Complexes Carrying Pyridostatin Derivatives
    E Palma, C Içhedef, C Fernandes, A Belchior, P Raposinho, L Gano, ...
    Chemistry–A European Journal 30 (22), e202400285 , 2024
    2024
    Citations: 4
  • Synthesis of 1, 10‐phenanthroline‐2, 9‐bistriazoles: Evaluation as G‐quadruplex binders and anti‐tumor activity
    J Figueiredo, I Carreira-Barral, P Lourenço, A Miranda, J Lopes Nunes, ...
    ChemMedChem, e202400591 , 2024
    2024
    Citations: 1
  • Gallic acid–triethylene glycol aptadendrimers synthesis, biophysical characterization and cellular evaluation
    A Miranda, R Lopez-Blanco, J Lopes-Nunes, AM Melo, MPC Campello, ...
    Pharmaceutics 14 (11), 2456 , 2022
    2022
    Citations: 8
  • G-quadruplex aptamer-ligand characterization
    D Moreira, D Leitão, J Lopes-Nunes, T Santos, J Figueiredo, A Miranda, ...
    Molecules 27 (20), 6781 , 2022
    2022
    Citations: 14
  • Stabilization of a DNA aptamer by ligand binding
    T Santos, J Lopes-Nunes, D Alexandre, A Miranda, J Figueiredo, ...
    Biochimie 200, 8-18 , 2022
    2022
    Citations: 26
  • Aptamer-based microfluidics for circulating tumor cells
    C Cruz, A Miranda, T Santos
    Aptamers Engineered Nanocarriers for Cancer Therapy 1, 556 , 2022
    2022
    Citations: 3
  • Targeting a G-quadruplex from let-7e pre-miRNA with small molecules and nucleolin
    T Santos, A Miranda, L Imbert, D Monchaud, GF Salgado, EJ Cabrita, ...
    Journal of Pharmaceutical and Biomedical Analysis 215, 114757 , 2022
    2022
    Citations: 15
  • Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin
    T Santos, A Miranda, L Imbert, A Jardim, CRF Caneira, V Chu, JP Conde, ...
    European Journal of Pharmaceutical Sciences 169, 106093 , 2022
    2022
    Citations: 11
  • Molecular Beacon assay development for severe acute respiratory syndrome coronavirus 2 detection
    J Carvalho, J Lopes-Nunes, J Figueiredo, T Santos, A Miranda, ...
    Sensors 21 (21), 7015 , 2021
    2021
    Citations: 11
  • Ligands as stabilizers of G-Quadruplexes in non-coding RNAs
    J Figueiredo, T Santos, A Miranda, D Alexandre, B Teixeira, P Simões, ...
    Molecules 26 (20), 6164 , 2021
    2021
    Citations: 19
  • Recognition of nucleolin through interaction with RNA G-quadruplex
    T Santos, A Miranda, MPC Campello, A Paulo, G Salgado, EJ Cabrita, ...
    Biochemical Pharmacology 189, 114208 , 2021
    2021
    Citations: 38

MOST CITED SCHOLAR PUBLICATIONS

  • Recognition of nucleolin through interaction with RNA G-quadruplex
    T Santos, A Miranda, MPC Campello, A Paulo, G Salgado, EJ Cabrita, ...
    Biochemical Pharmacology 189, 114208 , 2021
    2021
    Citations: 38
  • Locking up the AS1411 aptamer with a flanking duplex: towards an improved nucleolin-targeting
    A Miranda, T Santos, E Largy, C Cruz
    Pharmaceuticals 14 (2), 121 , 2021
    2021
    Citations: 36
  • Targeting Nucleolin By RNA G-Quadruplex-Forming Motif
    J Figueiredo, A Miranda, J Lopes-Nunes, J Carvalho, D Alexandre, ...
    Biochemical Pharmacology, 114418 , 2020
    2020
    Citations: 31
  • Stabilization of a DNA aptamer by ligand binding
    T Santos, J Lopes-Nunes, D Alexandre, A Miranda, J Figueiredo, ...
    Biochimie 200, 8-18 , 2022
    2022
    Citations: 26
  • Aptamer-based approaches to detect nucleolin in prostate cancer
    A Miranda, T Santos, J Carvalho, D Alexandre, A Jardim, CRF Caneira, ...
    Talanta 226, 122037 , 2021
    2021
    Citations: 26
  • Ligands as stabilizers of G-Quadruplexes in non-coding RNAs
    J Figueiredo, T Santos, A Miranda, D Alexandre, B Teixeira, P Simões, ...
    Molecules 26 (20), 6164 , 2021
    2021
    Citations: 19
  • Targeting a G-quadruplex from let-7e pre-miRNA with small molecules and nucleolin
    T Santos, A Miranda, L Imbert, D Monchaud, GF Salgado, EJ Cabrita, ...
    Journal of Pharmaceutical and Biomedical Analysis 215, 114757 , 2022
    2022
    Citations: 15
  • G-quadruplex aptamer-ligand characterization
    D Moreira, D Leitão, J Lopes-Nunes, T Santos, J Figueiredo, A Miranda, ...
    Molecules 27 (20), 6781 , 2022
    2022
    Citations: 14
  • Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin
    T Santos, A Miranda, L Imbert, A Jardim, CRF Caneira, V Chu, JP Conde, ...
    European Journal of Pharmaceutical Sciences 169, 106093 , 2022
    2022
    Citations: 11
  • Molecular Beacon assay development for severe acute respiratory syndrome coronavirus 2 detection
    J Carvalho, J Lopes-Nunes, J Figueiredo, T Santos, A Miranda, ...
    Sensors 21 (21), 7015 , 2021
    2021
    Citations: 11
  • Cellular modulation of a G-quadruplex structure found in the lung cancer-related microRNA-3196
    D Alexandre, J Polido, A Miranda, RHE Hudson, D Monchaud, ...
    International Journal of Biological Macromolecules 318, 145263 , 2025
    2025
    Citations: 9
  • Gallic acid–triethylene glycol aptadendrimers synthesis, biophysical characterization and cellular evaluation
    A Miranda, R Lopez-Blanco, J Lopes-Nunes, AM Melo, MPC Campello, ...
    Pharmaceutics 14 (11), 2456 , 2022
    2022
    Citations: 8
  • Exploring the G-quadruplex formation of AS1411 derivatives
    P Lourenço, D Moreira, A Miranda, J Lopes-Nunes, I Maocha, T Santos, ...
    Molecules 30 (8), 1673 , 2025
    2025
    Citations: 6
  • Targeting proto-oncogene B-MYB G-quadruplex with a nucleic acid–based fluorescent probe
    P Lourenco, A Miranda, MPC Campello, A Paulo, J Louis-Mergny, C Cruz
    International Journal of Biological Macromolecules 266, 131055 , 2024
    2024
    Citations: 5
  • I-motif formation in the promoter region of the B-MYB proto-oncogene
    A Alves, A Miranda, I Zanin, SN Richter, JL Mergny, C Cruz
    International Journal of Biological Macromolecules 296, 139582 , 2025
    2025
    Citations: 4
  • Targeting of G‐quadruplex DNA with 99m Tc(I)/Re(I) Tricarbonyl Complexes Carrying Pyridostatin Derivatives
    E Palma, C Içhedef, C Fernandes, A Belchior, P Raposinho, L Gano, ...
    Chemistry–A European Journal 30 (22), e202400285 , 2024
    2024
    Citations: 4
  • Detecting mir-155-3p through a Molecular Beacon Bead-Based Assay
    D Moreira, D Alexandre, A Miranda, P Lourenco, PV Baptista, C Tomaz, ...
    Molecules 29 (13), 3182 , 2024
    2024
    Citations: 3
  • G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene
    A Miranda, A Cucchiarini, C Esnault, JC Andrau, PA Oliveira, JL Mergny, ...
    International Journal of Biological Macromolecules 270, 132244 , 2024
    2024
    Citations: 3
  • Aptamer-based microfluidics for circulating tumor cells
    C Cruz, A Miranda, T Santos
    Aptamers Engineered Nanocarriers for Cancer Therapy 1, 556 , 2022
    2022
    Citations: 3
  • Synthesis of 1, 10‐phenanthroline‐2, 9‐bistriazoles: Evaluation as G‐quadruplex binders and anti‐tumor activity
    J Figueiredo, I Carreira-Barral, P Lourenço, A Miranda, J Lopes Nunes, ...
    ChemMedChem, e202400591 , 2024
    2024
    Citations: 1