Francesco Bonì | Università degli Studi di Milano - State University of Milan (Italy) (original) (raw)

Papers by Francesco Bonì

Viruses

Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, th... more Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, the mode of action of these compounds remains poorly understood. The HeE1-17Y derivative has already been shown to be a potent compound against a variety of flaviviruses of global relevance. In this work, the mode of action of HeE1-17Y has been studied for West Nile virus taking advantage of reporter replication particles (RRPs). Viral infectivity was drastically reduced by incubating the compound with the virus before infection, thus suggesting a direct interaction with the viral particles. Indeed, RRPs incubated with the inhibitor appeared to be severely compromised in electron microscopy analysis. HeE1-17Y is active against other enveloped viruses, including SARS-CoV-2, but not against two non-enveloped viruses, suggesting a virucidal mechanism that involves the alteration of the viral membrane.

Antiviral Research, 2021

The current emergency of the novel coronavirus SARS-CoV2 urged the need for broad-spectrum antivi... more The current emergency of the novel coronavirus SARS-CoV2 urged the need for broad-spectrum antiviral drugs as the first line of treatment. Coronaviruses are a large family of viruses that already challenged humanity in at least two other previous outbreaks and are likely to be a constant threat for the future. In this work we developed a pipeline based on in silico docking of known drugs on SARS-CoV1/2 RNA-dependent RNA polymerase combined with in vitro antiviral assays on both SARS-CoV2 and the common cold human coronavirus HCoV-OC43. Results showed that certain drugs displayed activity for both viruses at a similar inhibitory concentration, while others were specific. In particular, the antipsychotic drug lurasidone and the antiviral drug elbasvir showed promising activity in the low micromolar range against both viruses with good selectivity index.

The current emergency of the novel coronavirus SARS-CoV-2 urged the need for broad-spectrum antiv... more The current emergency of the novel coronavirus SARS-CoV-2 urged the need for broad-spectrum antiviral drugs as the first line of treatment. Coronaviruses are a large family of viruses that already challenged humanity in at least two other previous outbreaks and are likely to be a constant threat for the future. In this work we developed a pipeline based on in silico docking of known drugs on SARS-CoV RNA-dependent RNA polymerase combined with in vitro antiviral assays on both SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Results showed that certain drugs displayed activity for both viruses at a similar inhibitory concentration, while others were specific. In particular, the antipsychotic drug lurasidone and the antiviral drug elbasvir showed promising activity in the low micromolar range against both viruses with good selective index.

Neuronal calcium sensors play a crucial role in different pathways of Ca2+-mediated neurotransmis... more Neuronal calcium sensors play a crucial role in different pathways of Ca2+-mediated neurotransmission. Among them guanylate cyclase-activating protein 1 (GCAP1) is expressed only in photoreceptors and activates or inhibits retinal guanylate cyclase 1 (retGC1) depending on cellular Ca2+ concentrations during phototransduction. To date, 22 pathogenic mutations responsible for retinal dystrophy have been associated to GCAP1, but a complete picture of the molecular determinants of the disease is still missing. The only crystal structure available so far is the wt Ca2+-bound monomeric homologue from chicken and no cure exists for retinal dystrophy. In this work I report for the first time that the recombinant human GCAP1 is characterized by a highly dynamic monomer-dimer equilibrium, whose dissociation constant is influenced by salt concentration and by the nature of the divalent ion bound. Surprisingly, I discovered that also the chicken protein shows a similar mechanism, suggesting tha...

Biomolecules

The guanylyl cyclase-activating protein 1, GCAP1, activates or inhibits retinal guanylyl cyclase ... more The guanylyl cyclase-activating protein 1, GCAP1, activates or inhibits retinal guanylyl cyclase (retGC) depending on cellular Ca2+ concentrations. Several point mutations of GCAP1 have been associated with impaired calcium sensitivity that eventually triggers progressive retinal degeneration. In this work, we demonstrate that the recombinant human protein presents a highly dynamic monomer-dimer equilibrium, whose dissociation constant is influenced by salt concentration and, more importantly, by protein binding to Ca2+ or Mg2+. Based on small-angle X-ray scattering data, protein-protein docking, and molecular dynamics simulations we propose two novel three-dimensional models of Ca2+-bound GCAP1 dimer. The different propensity of human GCAP1 to dimerize suggests structural differences induced by cation binding potentially involved in the regulation of retGC activity.

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

European Biophysics Journal

Biochemical and Biophysical Research Communications

Human molecular genetics, 2018

AGel amyloidosis is a genetic degenerative disease characterized by the deposition of insoluble g... more AGel amyloidosis is a genetic degenerative disease characterized by the deposition of insoluble gelsolin protein aggregates in different tissues. Until recently, this disease was associated with two mutations of a single residue (Asp187 to Asn/Tyr) in the second domain of the protein. The general opinion is that pathogenic variants are not per se amyloidogenic but rather that the mutations trigger an aberrant proteolytic cascade, which results in the production of aggregation prone fragments. Here, we report the crystal structure of the second domain of gelsolin carrying the recently identified Gly167Arg mutation. This mutant dimerizes through a three-dimensional domain swapping mechanism, forming a tight but flexible assembly, which retains the structural topology of the monomer. To date, such dramatic conformational changes of this type have not been observed. Structural and biophysical characterizations reveal that the Gly167Arg mutation alone is responsible for the monomer to di...

Scientific reports, Sep 16, 2016

Mutations in gelsolin are responsible for a systemic amyloidosis first described in 1969. Until r... more Mutations in gelsolin are responsible for a systemic amyloidosis first described in 1969. Until recently, the disease was associated with two substitutions of the same residue, leading to the loss of the calcium binding site. Novel interest arose in 2014 when the N184K variant of the protein was identified as the etiological agent of a novel kidney-localized amyloidosis. Here we provide a first rationale for N184K pathogenicity. We show that the mutation induces a destabilization of gelsolin second domain, without compromising its calcium binding capacity. X-ray data combined with molecular dynamics simulations demonstrates that the primary source of the destabilization is a loss of connectivity in proximity of the metal. Such rearrangement of the H-bond network does not have a major impact on the overall fold of the domain, nevertheless, it increases the flexibility of a stretch of the protein, which is consequently processed by furin protease. Overall our data suggest that the N18...

Biochemical and Biophysical Research Communications

Viruses

Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, th... more Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, the mode of action of these compounds remains poorly understood. The HeE1-17Y derivative has already been shown to be a potent compound against a variety of flaviviruses of global relevance. In this work, the mode of action of HeE1-17Y has been studied for West Nile virus taking advantage of reporter replication particles (RRPs). Viral infectivity was drastically reduced by incubating the compound with the virus before infection, thus suggesting a direct interaction with the viral particles. Indeed, RRPs incubated with the inhibitor appeared to be severely compromised in electron microscopy analysis. HeE1-17Y is active against other enveloped viruses, including SARS-CoV-2, but not against two non-enveloped viruses, suggesting a virucidal mechanism that involves the alteration of the viral membrane.

Antiviral Research, 2021

The current emergency of the novel coronavirus SARS-CoV2 urged the need for broad-spectrum antivi... more The current emergency of the novel coronavirus SARS-CoV2 urged the need for broad-spectrum antiviral drugs as the first line of treatment. Coronaviruses are a large family of viruses that already challenged humanity in at least two other previous outbreaks and are likely to be a constant threat for the future. In this work we developed a pipeline based on in silico docking of known drugs on SARS-CoV1/2 RNA-dependent RNA polymerase combined with in vitro antiviral assays on both SARS-CoV2 and the common cold human coronavirus HCoV-OC43. Results showed that certain drugs displayed activity for both viruses at a similar inhibitory concentration, while others were specific. In particular, the antipsychotic drug lurasidone and the antiviral drug elbasvir showed promising activity in the low micromolar range against both viruses with good selectivity index.

The current emergency of the novel coronavirus SARS-CoV-2 urged the need for broad-spectrum antiv... more The current emergency of the novel coronavirus SARS-CoV-2 urged the need for broad-spectrum antiviral drugs as the first line of treatment. Coronaviruses are a large family of viruses that already challenged humanity in at least two other previous outbreaks and are likely to be a constant threat for the future. In this work we developed a pipeline based on in silico docking of known drugs on SARS-CoV RNA-dependent RNA polymerase combined with in vitro antiviral assays on both SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Results showed that certain drugs displayed activity for both viruses at a similar inhibitory concentration, while others were specific. In particular, the antipsychotic drug lurasidone and the antiviral drug elbasvir showed promising activity in the low micromolar range against both viruses with good selective index.

Neuronal calcium sensors play a crucial role in different pathways of Ca2+-mediated neurotransmis... more Neuronal calcium sensors play a crucial role in different pathways of Ca2+-mediated neurotransmission. Among them guanylate cyclase-activating protein 1 (GCAP1) is expressed only in photoreceptors and activates or inhibits retinal guanylate cyclase 1 (retGC1) depending on cellular Ca2+ concentrations during phototransduction. To date, 22 pathogenic mutations responsible for retinal dystrophy have been associated to GCAP1, but a complete picture of the molecular determinants of the disease is still missing. The only crystal structure available so far is the wt Ca2+-bound monomeric homologue from chicken and no cure exists for retinal dystrophy. In this work I report for the first time that the recombinant human GCAP1 is characterized by a highly dynamic monomer-dimer equilibrium, whose dissociation constant is influenced by salt concentration and by the nature of the divalent ion bound. Surprisingly, I discovered that also the chicken protein shows a similar mechanism, suggesting tha...

Biomolecules

The guanylyl cyclase-activating protein 1, GCAP1, activates or inhibits retinal guanylyl cyclase ... more The guanylyl cyclase-activating protein 1, GCAP1, activates or inhibits retinal guanylyl cyclase (retGC) depending on cellular Ca2+ concentrations. Several point mutations of GCAP1 have been associated with impaired calcium sensitivity that eventually triggers progressive retinal degeneration. In this work, we demonstrate that the recombinant human protein presents a highly dynamic monomer-dimer equilibrium, whose dissociation constant is influenced by salt concentration and, more importantly, by protein binding to Ca2+ or Mg2+. Based on small-angle X-ray scattering data, protein-protein docking, and molecular dynamics simulations we propose two novel three-dimensional models of Ca2+-bound GCAP1 dimer. The different propensity of human GCAP1 to dimerize suggests structural differences induced by cation binding potentially involved in the regulation of retGC activity.

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

European Biophysics Journal

Biochemical and Biophysical Research Communications

Human molecular genetics, 2018

AGel amyloidosis is a genetic degenerative disease characterized by the deposition of insoluble g... more AGel amyloidosis is a genetic degenerative disease characterized by the deposition of insoluble gelsolin protein aggregates in different tissues. Until recently, this disease was associated with two mutations of a single residue (Asp187 to Asn/Tyr) in the second domain of the protein. The general opinion is that pathogenic variants are not per se amyloidogenic but rather that the mutations trigger an aberrant proteolytic cascade, which results in the production of aggregation prone fragments. Here, we report the crystal structure of the second domain of gelsolin carrying the recently identified Gly167Arg mutation. This mutant dimerizes through a three-dimensional domain swapping mechanism, forming a tight but flexible assembly, which retains the structural topology of the monomer. To date, such dramatic conformational changes of this type have not been observed. Structural and biophysical characterizations reveal that the Gly167Arg mutation alone is responsible for the monomer to di...

Scientific reports, Sep 16, 2016

Mutations in gelsolin are responsible for a systemic amyloidosis first described in 1969. Until r... more Mutations in gelsolin are responsible for a systemic amyloidosis first described in 1969. Until recently, the disease was associated with two substitutions of the same residue, leading to the loss of the calcium binding site. Novel interest arose in 2014 when the N184K variant of the protein was identified as the etiological agent of a novel kidney-localized amyloidosis. Here we provide a first rationale for N184K pathogenicity. We show that the mutation induces a destabilization of gelsolin second domain, without compromising its calcium binding capacity. X-ray data combined with molecular dynamics simulations demonstrates that the primary source of the destabilization is a loss of connectivity in proximity of the metal. Such rearrangement of the H-bond network does not have a major impact on the overall fold of the domain, nevertheless, it increases the flexibility of a stretch of the protein, which is consequently processed by furin protease. Overall our data suggest that the N18...

Biochemical and Biophysical Research Communications