Andrea Cavalli's research while affiliated with Istituto Italiano di Tecnologia and other places
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Publications (32)
Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer the presence of protein isoforms. However, the detection and quantification processes are noisy; in particu...
The lanthionine synthetase C-like (LANCL) proteins include LANCL2, which is expressed in the central nervous system (CNS) and in peripheral tissues. LANCL2 exhibits glutathionylation activity and is involved in the neutralization of reactive electrophiles. Several studies explored LANCL2 activation as a validated pharmacological target for diabetes...
Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or progesterone receptor expression, with apocrine differentiation, and with no germline variants i...
![FIG. 4. MSE values using the not regularized [straight line, σ 2 /(n)],...](profile/Giovanni-Ciccotti/publication/369460649/figure/fig2/AS:11431281129518712@1679577043065/MSE-values-using-the-not-regularized-straight-line-s-2-n-ideal-Eq-A17-and_Q320.jpg)
We consider the problem of free energy estimation from the general perspective of regularization and Bayes estimation theory. We try to take advantage of an assumed a priori knowledge of the free energy. We reformulate the original Bennett acceptance ratio method, in this perspective, devise a numerical algorithm to solve it, and give a closed form...
Optimal transport theory is a growing field of mathematics, which has recently found many applications. Here we take advantage of optimal transport for computational free energy estimation. We show analytically, and then via simulation, that this approach is effective in terms of optimizing the barriers of an alchemical transformation.
In recent years the technological limits inherently present in the classical Turing paradigm of computation have sparked the development of innovative solutions based on quantum devices or analog-digital mixed approaches often based on the time evolution of differential equations. Such promising machinery require accurate analysis to understand if...
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on...
Clozapine is one of the most widely used second-generation antipsychotic drugs (SGAs) for the treatment of schizophrenia. Despite advantages over first-generation drugs, clozapine still shows significant side effects and interindividual variations in efficacy. In order to ensure frequent therapeutic drug monitoring (TDM) and improve the compliance...
Cartilage-hair hypoplasia (CHH) is a syndromic immunodeficiency characterized by metaphyseal dysplasia, cancer predisposition, and varying degrees of anemia. It may present as severe combined immunodeficiency in infancy, or slowly progress until fully manifesting in late adolescence/adulthood. No targeted treatment is currently available, and patie...
Advances in next-generation sequencing have provided high-dimensional RNA-seq datasets, allowing the stratification of some tumor patients based on their transcriptomic profiles. Machine learning methods have been used to reduce and cluster high-dimensional data. Recently, uniform manifold approximation and projection (UMAP) was applied to project...
The signal transducer and activator of transcription (STAT) 1 protein plays a key role in the immune response against viruses and other pathogens by transducing, in the nucleus, the signal from type I, type II and type III IFNs. STAT1 activates the transcription of hundreds of genes, some of which have been well characterized for their antiviral pr...
Glycogen synthase kinase 3 beta (GSK-3β) is an evolutionarily conserved serine-threonine kinase dysregulated in numerous pathologies, such as Alzheimer’s disease and cancer. Even though GSK-3β is a validated pharmacological target most of its inhibitors have two main limitations: the lack of selectivity due to the high homology that characterizes t...
Rare diseases (RDs) are complicated health conditions that are difficult to be managed at several levels. The scarcity of available data chiefly determines an intricate scenario even for experts and specialized clinicians, which in turn leads to the so called “diagnostic odyssey” for the patient. This situation calls for innovative solutions to sup...
Protein kinases (PKs) have been recognized as central nervous system (CNS)-disease-relevant targets due to their master regulatory role in different signal transduction cascades in the neuroscience space. Among them, GSK-3β, FYN, and DYRK1A play a crucial role in the neurodegeneration context, and the deregulation of all three PKs has been linked t...
RAS-associated autoimmune leukoproliferative disease (RALD) is a rare immune dysregulation syndrome caused by somatic gain-of-function mutations of either NRAS or KRAS gene in hematopoietic cells. We describe a 27-year-old patient presenting at 5 months of age with recurrent infections and generalized lymphadenopathy who developed a complex multi-o...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) pandemic has been the subject of a large number of studies in recent times. Here, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria in the early 1900'...
Computational intelligence, particularly deep learning, offers powerful tools for discriminating and generating samples such as images. Deep learning methods have been used in different artistic contexts for neural style transfer, artistic style recognition, and musical genre recognition. Using a constrained manifold analysis protocol, we discuss t...
In the present, proof-of-concept paper, we explore the potential of one common solid support for blood microsampling (dried blood spot, DBS) and a device (volumetric absorptive microsampling, VAMS) developed for the untargeted lipidomic profiling of human whole blood, performed by high-resolution LC-MS/MS. Dried blood microsamples obtained by means...
Personalized medicine and therapies represent the goal of modern medicine, as drug discovery strives to move away from one-cure-for-all and makes use of the various targets and biomarkers within differing disease areas. This approach, especially in oncology, is often undermined when the cells make use of alternative survival pathways. As such, acqu...
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds b...
Therapeutic drug monitoring (TDM) is an important tool for correlating the administered drug dose to drug and metabolite concentrations in the body and to therapeutic and adverse effects. In the case of treatment with drugs active on the central nervous system (CNS), frequent TDM becomes really useful, especially for patient compliance checking and...
p>Molecular dynamics (MD) and enhanced sampling MD was performed for 100 ns on the biological assembly of the COVID-19 protease ( 6LU7 ), and a template of the COVID-19 S-protein:ACE2 receptor interface (99.88% coverage of 6M0J; model03, swissmodel ). Apo-site pharmacophores of the resulting structural clusters were used to mine the FDA database (8...
p>Molecular dynamics (MD) and enhanced sampling MD was performed for 100 ns on the biological assembly of the COVID-19 protease ( 6LU7 ), and a template of the COVID-19 S-protein:ACE2 receptor interface (99.88% coverage of 6M0J; model03, swissmodel ). Apo-site pharmacophores of the resulting structural clusters were used to mine the FDA database (8...
Patients suffering from major depression and related pathologies (feeding and eating disorders, obsessive-compulsive disorder, post-traumatic stress disorder, anxiety disorders, etc.) are usually treated with antidepressant agents belonging to several pharmacological and chemical classes; the most recent of these agents are collectively known as “n...
After the development of “classical” tricyclic antidepressants and monoamine oxidase inhibitors, numerous other classes of antidepressant drugs have been introduced onto the market. The selective serotonin reuptake inhibitor class is the best‐known one, but many others exist, usually identified by their mechanism of activity. In this second part of...
αβ-Tubulin is a validated target for anticancer drug discovery, and molecules binding to this protein are used to treat several types of tumors. Here, we report on a combined X-ray crystallography and molecular dynamics approach to study drug binding within the colchicine site of αβ-tubulin, focusing on plinabulin, an agent currently in phase 3 cli...
Cadherins are a large family of transmembrane calcium-dependent cell adhesion proteins that orchestrate adherens junction formation and are crucially involved in tissue morphogenesis. Due to their important role in cancer development and metastasis, cadherins can be considered attractive targets for drug discovery. A recent crystal structure of the...
Selected members of the large rolipram-related GEBR family of phosphodiesterase-4 (PDE4) inhibitors have been shown to facilitate long term potentiation (LTP) and improve memory functions without causing emetic-like behavior in rodents. Despite their micromolar-range binding affinities and their promising pharmacological and toxicological profiles,...
In BRCA2-defective cells, poly(adenosine diphosphate [ADP]-ribose) polymerase inhibitors can trigger synthetic lethality, as two independent DNA-repairing mechanisms result simultaneously impaired. Here, we have pharmacologically induced synthetic lethality, which was triggered by combining two different small organic molecules. When administered w...
Enteroviruses (EVs) are among the most frequent infectious agents in humans worldwide and represent the leading cause of upper respiratory tract infections. No drugs for the treatment of EV infections are currently available. Recent studies have also linked enterovirus infection with pulmonary exacerbations, especially in cystic fibrosis (CF) patie...
Citations
... • The ABA/LANCL1-2 hormone/receptor system emerges as a new controller of ERRα expression levels and transcriptional activity via the AMPK/SIRT1/PGC-1α axis. • A reciprocal feed-forward transcriptional relationship exists between the LANCL proteins and transcriptional coactivators ERRα/PGC-1α, which could be exploited with natural or synthetic LANCL agonists [118] to improve mitochondrial function in multiple clinical settings. ...
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... Each VEP is usually specialized in annotating one or a few categories of variants, such as single nucleotide variations (SNVs), indels, missense variants, or structural variants (SVs) (Geoffroy et al. 2018;Pagel et al. 2019;Rentzsch et al. 2019;Vaser et al. 2016). The variety of VEPs and their functionalities poses the challenge of choosing the appropriate tool for a specific task, a topic that has been addressed in non-systematic reviews (Katsonis et al. 2022;Tabarini et al. 2022). Some reviews summarize VEPs for one type of variant only (Abramowicz and Gos 2018;Glusman et al. 2017). ...
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... Compared with traditional venous blood collection, it allows low capillary blood volume collection through a less painful and invasive fingerprick, enabling individuals to self-collect blood drops, anywhere, with minimal instructions [4,5]. Volumetric absorptive microsampling (VAMS) is one of the microsampling techniques increasingly employed for TDM of a wide class of drugs [6][7][8][9][10][11]. VAMS-based devices are made with plastic handlers with a hydrophilic polymer tip to collect a fixed blood volume (10 μL), potentially allowing accurate blood collection directly from a fingerprick. ...
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... The pathogenesis of anemia in CHH remains unclear, but recent study suggests immune dysregulation as a possible explanation. 34 Autoimmunity was uncommon in our cohort, represented by 1 child who developed autoimmune hemolytic anemia. ...
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... In the case of FDC, the clusters can be extracted both from the intermediate dimensions and the final two-dimensional embedding. In machine learning over the years, numerous clustering approaches have been proposed (Bollon et al., 2022;Li & Wong, 2019), among which FDC uses the DB-SCAN algorithm. In our experiments we used three different clustering algorithms, namely -means which is a centroid-based algorithm, agglomerative which is a hierarchical algorithm and a DBSCAN which is a density based algorithm. ...
... In other words, the newly produced IFN-b mediates the induction of ISG56 by autocrine or paracrine signaling. STAT1 plays a key role in the immune response against pathogens such as viruses and microbes by transmitting signals from IFNs [19]. In the present study, fludarabine, an inhibitor of STAT1 activation, scarcely affected ISG56 and CXCL10 expression induced by poly IC. ...
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... Compounds 159 forms a fourth H-bond with Asp200 while also interacting with the catalytic amino acid Lys85 through bad interaction (Lys85, Glu97 are highly conserved catalytic residues that enhance ATP interactions) [53]. Again, all of the observed interactions suggest that compound 159 could be a potential GSK-3β inhibitor [48,54]. Compound 157 on the other hand (Figure 5b), acted as a H-bond acceptor as well as a donor with Val135 forming two H-bonds. ...
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... Such methods could help identify clusters of patients based on the graph representation. In order to make these change happen, the rare disease community will have to overcome the challenges related with the scarcity of the data [54,66], utilize not only dedicated databases and registries but all data collected during routine healthcare processes -structured, narrative reports, genetic, etc. and favor new digital models able to combine expert knowledge and machine learning approaches. ...
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... Indeed, SLE has been seen infrequently in RALD and a recent study found an interferon signature in RALD similar to that in SLE. 10,11 Therefore, it is likely that cases of RALD are missed due to the overlap with more common disorders and the lack of a diagnostic test. ...
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... It is a phenylaminothiazole derivative that was initially created as an inhibitor of the C-Kit receptor to treat tumors in animals, and it is presently being evaluated to treat cancer in humans [116]. With respect to CNS therapeutics, masitinib is being repurposed as a potential anti-AD drug with nano-molar inhibitory efficacy against Fyn (IC 50 = 240 nM), which can reduce tau hyperphosphorylation and prevent the development of NFTs. ...
