Domenico Raimondo

Associate Professor of Bioinformatics, Dept. Molecular Medicine – Sapienza University of Rome

domenico.raimondo@uniroma1.it

Academic Appointments:

  • Since 2019: Associate Professor of Bioinformatics, Sapienza University of Rome
  • 2018-2023: Junior Research Fellow, Sapienza School for Advanced Studies (SSAS)
  • Since 2024: Board Member, PhD in “Bioinformatics and Computational Biology”, Sapienza  University of Rome
  • Since 2017: Board Member, PhD in “Genetics and Molecular Biology”, Sapienza University of Rome
  • 2017-2023: Faculty member of the “Stem cell and gene editing – U-stem” Second Level Master School at Sapienza University of Rome

Scientific interests

I have 20 years of experience in Protein Structure Bioinformatics and Computational Biology. My research focuses on the computational investigation of macromolecules of biomedical relevance, with particular emphasis on their structure, dynamics, and interactions, including the analysis of protein–protein and protein–ligand systems in both health and disease. I am actively involved in the rational design and in silico optimization of molecules with potential therapeutic applications. Additionally, I integrate bioinformatics and computational biology tools to analyze clinical datasets, with a specific focus on cancer biology, the mechanisms underlying rare diseases and immune-mediated disorders.

Contribution to Science:

– Therapeutic Targets in Multiple Myeloma: CD38–cGAMP and Gadd45β–MKK7 Interactions

Using computational modeling integrated with experimental data, I contributed to characterizing CD38 as a direct binder and inhibitor of extracellular cGAMP, revealing a novel immunoregulatory function. I also supported the design of D-peptides targeting the Gadd45β–MKK7 interaction to induce apoptosis in multiple myeloma cells, uncovering new therapeutic strategies.

– Computational Investigation of Chemerin–CCRL2 Recognition and Antibody-Related Projects

I employ advanced molecular dynamics simulations to study receptor–ligand interactions, particularly in immune-related targets. My research on the CCRL2–Chemerin complex, using a multiscale computational strategy that combines coarse-grained and all-atom MD simulations, provided mechanistic insights into ligand recognition and binding. I am also involved in projects related to antibodies and immune-mediated pathologies.

– Structural Modeling of hNOX2 for Drug Discovery

I contributed to developing a dynamic structural model of hNOX2, a key enzyme in ROS production, using advanced simulations of membrane protein complexes and molecular docking experiments. This model is now being used as a platform for in silico screening of potential NOX2 inhibitors.

– Pin1–Notch3 Interaction in Ovarian Cancer Chemoresistance

Using molecular dynamics approch and advanced structural bioinformatics tools, I analyzed the Pin1–Notch3 interface and identified a motif on Notch3 essential for stable binding. These findings provide molecular insights into platinum resistance in high-grade serous ovarian cancer and may support targeted therapy development.

5 Selected publications:

  • 1: Romagnoli A, Rexha J, Perta N, Di Cristofano S, Borgognoni N, Venturini G, Pignotti F, Raimondo D, Borsello T, Di Marino D. Peptidomimetics design and characterization: Bridging experimental and computer-based approaches. Prog Mol Biol Transl Sci. 2025;212:279-327. doi: 10.1016/bs.pmbts.2024.07.002. Epub 2024
    Jul 25. PMID: 40122649.
  • 2: Cuollo L, Di Cristofano S, Sandomenico A, Iaccarino E, Oliver A, Zingoni A, Cippitelli M, Fionda C, Petillo S, Kosta A, Tassinari V, Petrucci MT, Fazio F, Ruvo M, Santoni A, Raimondo D, Soriani A. CD38 restrains the activity of extracellular cGAMP in a model of multiple myeloma. iScience. 2024 Apr 25;27(5):109814. doi: 10.1016/j.isci.2024.109814. PMID: 38746669; PMCID: PMC11091702.
  • 3: Turco EM, Giovenale AMG, Sireno L, Mazzoni M, Cammareri A, Marchioretti C, Goracci L, Di Veroli A, Marchesan E, D’Andrea D, Falconieri A, Torres B, Bernardini L, Magnifico MC, Paone A, Rinaldo S, Della Monica M, D’Arrigo S, Postorivo D, Nardone AM, Zampino G, Onesimo R, Leoni C, Caicci F, Raimondo D, Binda E, Trobiani L, De Jaco A, Tata AM, Ferrari D, Cutruzzolà F, Mazzoccoli G, Ziviani E, Pennuto M, Vescovi AL, Rosati J. Retinoic acid-induced 1 gene haploinsufficiency alters lipid metabolism and causes autophagy defects in Smith-Magenis syndrome. Cell Death Dis. 2022 Nov 21;13(11):981. doi: 10.1038/s41419-022-05410-7. PMID: 36411275; PMCID: PMC9678881.
  • 4: Tornatore L, Capece D, D’Andrea D, Begalli F, Verzella D, Bennett J, Acton G, Campbell EA, Kelly J, Tarbit M, Adams N, Bannoo S, Leonardi A, Sandomenico A, Raimondo D, Ruvo M, Chambery A, Oblak M, Al-Obaidi MJ, Kaczmarski RS, Gabriel I, Oakervee HE, Kaiser MF, Wechalekar A, Benjamin R, Apperley JF, Auner HW, Franzoso G. Preclinical toxicology and safety pharmacology of the first-in-class GADD45β/MKK7 inhibitor and clinical candidate, DTP3. Toxicol Rep. 2019 Apr 19;6:369-379. doi: 10.1016/j.toxrep.2019.04.006. PMID: 31080744; PMCID: PMC6502747.
  • 5: Tornatore L, Sandomenico A, Raimondo D, Low C, Rocci A, Tralau-Stewart C, Capece D, D’Andrea D, Bua M, Boyle E, van Duin M, Zoppoli P, Jaxa-Chamiec A, Thotakura AK, Dyson J, Walker BA, Leonardi A, Chambery A, Driessen C, Sonneveld P, Morgan G, Palumbo A, Tramontano A, Rahemtulla A, Ruvo M, Franzoso G. Cancer- Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors.Cancer Cell. 2014 Dec 8;26(6):938. doi: 10.1016/j.ccell.2014.11.021. Epub 2014 Dec 8. Cancer Cell. 2014 Oct 13;26(4):495-508. doi: 10.1016/j.ccr.2014.07.027. PMID: 28898681; PMCID: PMC5629036.

On-going Grants

Project Title Funding source Amount (Euros) Period Role of the PI
Computational design of ultrashort peptides as protein surface binders ISTITUTO PASTEUR ITALIA - FOND. CENCI BOLOGNETTI 40.000 Marzo 2025 Febbraio 2027 Principal Investigator
Development of CES1 inhibitors to treat advanced colorectal carcinoma (CRC) SAPIENZA UNIVERSITÀ DI ROMA 35.800 Gennaio 2025 Dicembre 2027 Principal Investigator
AC-CURATE: Antiviral Compounds against Coronavirus Using pRotAcs TEchnology MINISTERO UNIVERSITA' RICERCA (MUR - PRIN 2022) 41.700 Ottobre 2023 Settembre 2025 Principal Investigator of the Sapienza University research unit

Complete list of published work in MyBibliography:

https://www.ncbi.nlm.nih.gov/myncbi/domenico.raimondo.1/bibliography/public/

SCOPUS ID: 7004022334

ORCID ID: 0000-0002-1780-7295

 KEYWORDS:

Bioinformatics, Computational Structural Biology, Biomedical macromolecules and pharmacologically active compounds, Drug design and optimization, Computational Immunology, Multiscale molecular simulations and modelling, Protein–protein and protein–ligand interactions

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