Maicol Bissaro
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View article: Beyond conventional sequence-based encoding: a generalized Machine Learning pipeline for oligonucleotide property prediction
Beyond conventional sequence-based encoding: a generalized Machine Learning pipeline for oligonucleotide property prediction Open
The development of RNA-based therapeutics has significantly expanded the landscape of drug discovery by enabling precise modulation of gene expression. These approaches offer the potential to target previously "undruggable" genes, overcomi…
View article: Riluzole–Rasagiline Hybrids: Toward the Development of Multi-Target-Directed Ligands for Amyotrophic Lateral Sclerosis
Riluzole–Rasagiline Hybrids: Toward the Development of Multi-Target-Directed Ligands for Amyotrophic Lateral Sclerosis Open
Polypharmacology is a new trend in amyotrophic lateral sclerosis (ALS) therapy and an effective way of addressing a multifactorial etiology involving excitotoxicity, mitochondrial dysfunction, oxidative stress, and microglial activation. I…
View article: A Computational Workflow for the Identification of Novel Fragments Acting as Inhibitors of the Activity of Protein Kinase CK1δ
A Computational Workflow for the Identification of Novel Fragments Acting as Inhibitors of the Activity of Protein Kinase CK1δ Open
Fragment-Based Drug Discovery (FBDD) has become, in recent years, a consolidated approach in the drug discovery process, leading to several drug candidates under investigation in clinical trials and some approved drugs. Among these success…
View article: Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics
Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics Open
Macrocycles are attractive structures for drug development due to their favorable structural features, potential in binding to targets with flat featureless surfaces, and their ability to disrupt protein–protein interactions. Moreover, lar…
View article: Front Cover: Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M<sup>pro</sup> by Using Supervised Molecular Dynamics (SuMD) Simulations (ChemMedChem 13/2021)
Front Cover: Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M<sup>pro</sup> by Using Supervised Molecular Dynamics (SuMD) Simulations (ChemMedChem 13/2021) Open
The Front Cover summarizes the computational pipeline which characterises HT-SuMD, a computational protocol exploiting supervised molecular dynamics simulations to perform the posing of a small fragment library. In this study, HT-SuMD accu…
View article: On the mechanism of tumor cell entry of aloe‐emodin, a natural compound endowed with anticancer activity
On the mechanism of tumor cell entry of aloe‐emodin, a natural compound endowed with anticancer activity Open
Aloe‐emodin (1,8‐dihydroxy‐3‐[hydroxymethyl]‐anthraquinone), AE, is one of the active constituents of a number of plant species used in traditional medicine. We have previously identified, for the first time, AE as a new antitumor agent an…
View article: Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M<sup>pro</sup> by Using Supervised Molecular Dynamics (SuMD) Simulations
Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M<sup>pro</sup> by Using Supervised Molecular Dynamics (SuMD) Simulations Open
Computational approaches supporting the early characterization of fragment molecular recognition mechanism represent a valuable complement to more expansive and low‐throughput experimental techniques. In this retrospective study, we have i…
View article: Developing novel classes of protein kinase CK1δ inhibitors by fusing [1,2,4]triazole with different bicyclic heteroaromatic systems
Developing novel classes of protein kinase CK1δ inhibitors by fusing [1,2,4]triazole with different bicyclic heteroaromatic systems Open
View article: Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir
Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir Open
View article: HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR
HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR Open
Fragment-based lead discovery (FBLD) is one of the most efficient methods to develop new drugs. We present here a new computational protocol called High-Throughput Supervised Molecular Dynamics (HT-SuMD), which makes it possible to automat…
View article: Comparing Fragment Binding Poses Prediction Using HSP90 as a Key Study: When Bound Water Makes the Difference
Comparing Fragment Binding Poses Prediction Using HSP90 as a Key Study: When Bound Water Makes the Difference Open
Fragment-Based Drug Discovery (FBDD) approaches have gained popularity not only in industry but also in academic research institutes. However, the computational prediction of the binding mode adopted by fragment-like molecules within a pro…
View article: HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR
HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR Open
In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments…
View article: HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR
HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR Open
In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments…
View article: The rise of molecular simulations in fragment-based drug design (FBDD): an overview
The rise of molecular simulations in fragment-based drug design (FBDD): an overview Open
Fragment-based drug discovery (FBDD) is an innovative approach, progressively more applied in the academic and industrial context, to enhance hit identification for previously considered undruggable biological targets. In particular, FBDD …
View article: New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations
New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations Open
Adenosine receptors (ARs), like many otherGprotein-coupledreceptors (GPCRs), are targets of primary interest indrug design. However, one of the main limits for the development of drugs for this class of GPCRs is the complex selectivity pro…
View article: Scaffold Repurposing of in-House Chemical Library toward the Identification of New Casein Kinase 1 δ Inhibitors
Scaffold Repurposing of in-House Chemical Library toward the Identification of New Casein Kinase 1 δ Inhibitors Open
Recent studies have highlighted the key role of Casein kinase 1 δ (CK1δ) in the development of several neurodegenerative pathologies, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). So f…
View article: Targeting the Coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors Lopinavir, Ritonavir, and Nelfinavir
Targeting the Coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors Lopinavir, Ritonavir, and Nelfinavir Open
Coronavirus SARS-CoV-2 is a recently discovered single-stranded RNA (ssRNA) betacoronavirus, responsible for a severe respiratory disease known as coronavirus disease 2019 (COVID-19), which is rapidly spreading. Chinese health authorities,…
View article: Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? Open
Although proteins have represented the molecular target of choice in the development of new drug candidates, the pharmaceutical importance of ribonucleic acids has gradually been growing. The increasing availability of structural informati…
View article: Targeting the Coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors Lopinavir, Ritonavir, and Nelfinavir.
Targeting the Coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors Lopinavir, Ritonavir, and Nelfinavir. Open
This dataset consists of three videos in .mp4 format. The videos were generated using the computational technique of Supervised Molecular Dynamics (SuMD) to provide molecular insight on the whole interaction pathway of lopinavir, ri…
View article: Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach Open
The use and misuse of antibiotics has resulted in critical conditions for drug-resistant bacteria emergency, accelerating the development of antimicrobial resistance (AMR). In this context, the co-administration of an antibiotic with a com…
View article: Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations
Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations Open
One of the most intriguing findings highlighted from G protein-coupled receptor (GPCR) crystallography is the presence, in many members of class A, of a partially hydrated sodium ion in the middle of the seven transmembrane helices (7TM) b…
View article: Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database Open
The number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it has increased tenfold in the last twenty years. The availability of an ever-growing number of structures is having a huge impact on the Structure-B…
View article: Mixed-reversible and covalent kinase inhibition as a possible new strategy to treat neuro-inflammatory/degenerative diseases
Mixed-reversible and covalent kinase inhibition as a possible new strategy to treat neuro-inflammatory/degenerative diseases Open
Dual GSK-3β/CK-1δ inhibition could be a potential strategy to treat neurodegenerative diseases like Parkinson’s disease (PD). In order to validate this hypothesis, an inhibitor able to target both kinases in the submicromolar range was dev…
View article: A Triazolotriazine‐Based Dual GSK‐3β/CK‐1δ Ligand as a Potential Neuroprotective Agent Presenting Two Different Mechanisms of Enzymatic Inhibition
A Triazolotriazine‐Based Dual GSK‐3β/CK‐1δ Ligand as a Potential Neuroprotective Agent Presenting Two Different Mechanisms of Enzymatic Inhibition Open
Glycogen synthase kinase 3β (GSK‐3β) and casein kinase 1δ (CK‐1δ) are emerging targets for the treatment of neuroinflammatory disorders, including Parkinson's disease. An inhibitor able to target these two kinases was developed by docking‐…
View article: Targeting Protein Kinase CK1δ with Riluzole: Could It Be One of the Possible Missing Bricks to Interpret Its Effect in the Treatment of ALS from a Molecular Point of View?
Targeting Protein Kinase CK1δ with Riluzole: Could It Be One of the Possible Missing Bricks to Interpret Its Effect in the Treatment of ALS from a Molecular Point of View? Open
Riluzole, approved by the US Food and Drug Administration (FDA) in 1995, is the most widespread oral treatment for the fatal neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The drug, whose mechanism of action is still obscu…