Federico Iacovelli

New COVID-19 pre-print

Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: in vivo, in silico and in vitro preliminary evidences

Elena Campione, Caterina Lanna, Terenzio Cosio, Luigi Rosa, Maria Pia Conte, Federico Iacovelli, Alice Romeo, Mattia Falconi, Claudia Del Vecchio, Elisa Franchin, Maria Stella Lia, Marilena Minieri, Carlo Chiaramonte, Marco Ciotti, Marzia Nuccetelli, Alessandro Terrinoni, Ilaria Iannuzzi, Luca Coppeda, Andrea Magrini, Nicola Moricca, Stefano Sabatini, Felice Rosapepe, Pier Luigi Bartoletti, Sergio Bernardini, Massimo Andreoni, Piera Valenti, Luca Bianchi

The current treatments against SARS-CoV-2 have proved so far inadequate. A potent antiviral drug is yet to be discovered. Lactoferrin, a multifunctional glycoprotein, secreted by exocrine glands and neutrophils, possesses an antiviral activity extendable to SARS-Cov-2. We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. Lactoferrin induced an early viral clearance and a fast clinical symptoms recovery in addition to a statistically significant reduction of D-Dimer, Interleukin-6 and ferritin blood levels. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. Lactoferrin can be used as a safe and efficacious natural agent to prevent and treat COVID-19 infection.

doi: https://doi.org/10.1101/2020.08.11.244996

Antonino Buccheri

Structural bioinformatics

Structural bioinformatics

 

Structural bioinformatics represents a section of bioinformatics dealing with analysis and prediction of three-dimensional (3D) structures of biological macromolecules such as proteins, RNA, and DNA. Through skilled simulative techniques, involving the use of 3D structures, it is possible to compare overall folds or local motifs, to study the principles of folding and evolution, to analyze binding interactions, molecular recognition and structure/function relationships of large macromolecules. Structural bioinformatics requires the use of experimentally determined structures or specially made computational models, and can be seen as a part of computational structural biology.

 

In our group various structural bioinformatics tools are used to plan experiments, to organize and verify experimental data and to control the systematic design of protein mutants with altered functional properties.

 

In details our research area concerns:

 

  • Investigation of the dynamical features of proteins and nucleic acids through classical molecular dynamics simulation or enhanced sampling simulation techniques. These simulative techniques are used to compare time evolutions of structural properties of wild-type and mutated enzymes, to correlate their structure-dynamics-functions relationship in order to obtain a complete picture of the acquired altered functionality from an atomistic point of view.

 

  • Structural characterization, design and construction of large DNA assemblies molecular models, experimentally obtained through covalently linked DNA oligonucleotides or origami techniques, to be used for cargo delivery of active molecules for biomedical purposes. We use large computational facilities to carry out hundred of nanoseconds simulations of this nano-biomaterial systems that include millions of atoms. 

 

  • Investigation of electrostatic interactions in proteins through simulative methods. Through the calculation of the electrostatic potential distribution around macromolecules we study protein-ligand or protein-protein interaction mechanisms.

 

  • Investigation of proteins-ligand and protein-protein molecular recognition through molecular docking simulations. Various programs and algorithms are used to detect information on the way ligands interact with receptors, for biochemical or pharmacological purposes.

 

  • Structure-based virtual screening, using computer-based methods and extended virtual compounds databases, to discover new ligands on the basis of biological structures. This procedure can be performed at low resolution, using millions of compounds, and then translated into a better definition of the obtained results through higher resolution methodologies.

 

  • Creation of novel inhibitory compounds obtained on the basis of previous biochemical data.

 

  • Prediction of protein tertiary structures through homology-based approaches, protein threading and refined combined approaches. The structural models can provide valuable indications in the absence of structures obtained through experimental methods.

 

We are open to any form of collaboration with non-profit institutions or private companies.

 

Antonino Buccheri

Metagenomics

 

 

Metagenomics is defined as the study of microbial communities directly in their natural environment. This allows to avoid the problem of sampling and cultivation of micro-organisms in laboratory. Metagenomics is widely applied in ecology, in the field of human health and begins to be applied in the food sector. The advent of Next Generation Sequencing (NGS) has revolutionised the study of genetics and genomics. The main benefits of these technologies consists in the achievement of DNA and RNA sequences at high speed, at low manual work and even at lower cost when compared to Sanger sequencing method.
Data analysis is still the main bottleneck in an NGS experiment, due to the large amount of data produced by these technologies. The development of new pipelines and the integration of pre-existing algorithms are essential to confidently interpret the data from this huge volume of information.
The aim of this project concern the application of NGS technologies in alimentary, clinical and ecological fields. We specialize in bioinformatics analysis of 16S gene metabarcoding and viral metagenomics.

Antonino Buccheri

DNA Nanostructures

DNA Nanostructures

DNA nanotechnology

 

Understanding and exploiting new, complex functional bio-materials is an interdisciplinary effort at the interface between biology, physics, chemistry, material science and engineering. The unique self-recognition properties of DNA defined by the strict rules of Watson-Crick base pairing, makes this material ideal for the self-assembly of predesigned nanostructures in a bottom-up approach.

DNA is an extremely suitable polymer for the generation of nanostructures since:

(1) DNA molecules are highly stable and biocompatible;

(2) molecular recognition between two different strands of DNA is based on a simple four-letter code; 

(3) natural or artificial DNA motifs can be engineered to control nanocage opening/closing mechanisms;

(4) DNA strands provide a safe hydrophilic environment in which useful payloads, such as proteins, can be trapped;

(5) DNA strands can be chemically modified to confer a hydrophobic environment into the nanocages, where small drugs can be trapped;

(6) DNA strands can be modified with cellular recognition signals targeting specific cells or tissues.

 

In our laboratory, we are working on the design and assembly of DNA nanostructures of different geometry, engineered with several DNA motifs that can change conformation upon application of an external stimulus such as pH variation, temperature jump or addition of an external ligand. The conformational changes permit to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The cages are also decorated with specific ligand for selective cell-targeting tasks. The research is aimed to address the fundamental challenges related to the development of new functionally structured materials based on DNA and to gain a deep understanding of the structure and dynamics of the nanostructures using long-time atomistic simulations which can predict the likelihood of successful assembly as well as structural properties of DNA nanostructures before experiments.The final aim is the building of controlled functional DNA nano-devices to be used as selective drug nano-vector for therapeutic purpose targeting specific cell lines such as tumor cells.

Antonino Buccheri

Topoisomerase in Cancer Research

Topoisomerase in Cancer Research

DNA topoisomerases are enzymes that control and modify the topological states of DNA in cells. Human topoisomerase I is composed of 765 aminoacids, and the crystal structure of the N-terminal truncated protein (topo70) together with proteolytic experiments show that the enzyme is composed of four different domains: N-terminal domain (amino acids 1-206), core domain (aminoacid 207-635), linker domain (636-712), and C-terminal domain (amino acids 713-765). The catalytic cycle is composed by five subsequent steps: binding of the enzyme to DNA; DNA cleavage; controlled rotation of the DNA scissile-strand; DNA religation; DNA release. Human topoisomerase I is of significant medical interest being the only target of the antitumor drug camptothecin (CPT). CPT reversibly binds to the covalent intermediate DNA-enzyme, stabilizing the cleavable complex and reducing the rate of religation. The stalled topoisomerase I collides with the progression of the replication fork producing lethal double-strand DNA breaks and cell death.

In our laboratory, we are interested in the characterization of the mechanism of action of this enzyme and in the elucidation of the principles governing the drug interaction in order to develop more efficient drug. In detail at the moment we are studying topoisomerase I mutants displaying drug-resistance correlating their structural dynamical properties with their varied function and their different answer to the drug. We are also involved in the understanding of the fine details of the protein drug interaction through coupled spectroscopic studies and ‘ab initio’ calculations of the drug in solution. Finally, we are working on the description of the structure of the enzyme in its open conformation.