Simone Brogi

Simone Brogi
Verified
Simone verified their affiliation via an institutional email.
Verified
Simone verified their affiliation via an institutional email.
  • Ph.D.
  • Professor (Associate) at University of Pisa

About

215
Publications
72,135
Reads
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4,591
Citations
Current institution
University of Pisa
Current position
  • Professor (Associate)
Additional affiliations
March 2023 - December 2024
Isfahan University of Medical Sciences
Position
  • Visiting Professor
February 2019 - January 2022
University of Pisa
Position
  • Professor (Assistant)
Description
  • Head of in silico pharmacology and toxicology Unit at Department of Pharmacy at University of Pisa
January 2009 - January 2019
University of Siena
Position
  • Fellow
Education
October 2007 - October 2010
University of Siena
Field of study
  • Computational Chemistry
January 2007 - December 2007
University of Siena
Field of study
  • Computational Chemistry
October 1996 - April 2005
University of Siena
Field of study
  • Molecular Biology

Publications

Publications (215)
Article
Full-text available
Prokineticins are angiogenic hormones that activate two G protein-coupled receptors: PKR1 and PKR2. PKR1 has emerged as a critical mediator of cardiovascular homeostasis and cardioprotection. Identification of non-peptide PKR1 agonists that contribute to myocardial repair and collateral vessel growth hold promises for treatment of heart diseases. T...
Article
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The development of a novel comprehensive approach for the prediction of hERG activity is herein presented. Software Phase has been used to derive a 3D-QSAR model, employing as alignment rule a common pharmacophore built on a subset of 22 highly active compounds (threshold Ki: 50 nM) against hERG K⁺ channel. Five features comprised the pharmacophore...
Article
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The rapid and extensive expansion of the new betacoronavirus SARS-Cov-2 (CoVid-19) is responsible for several thousand deaths in a very short time. This fast progression led the world health organization (WHO) to classify it as a pandemic on 11th March 2020. Waiting for the availability of new vaccines, this global emergency has triggered the searc...
Article
In the Central Nervous System (CNS), extra virgin olive oil (EVOO) produces interesting effects against neurodegenerative disorders including Alzheimer’s disease (AD). The valuable properties of EVOO are largely ascribable to oleuropein aglycone (OA), the most abundant phenolic constituent. In particular, it has been demonstrated that in AD, OA pro...
Article
Multitarget approach in drug design is a powerful strategy in tackling the multifactorial nature of Alzheimer's disease (AD). Herein we report a novel strategy in the design of multitargeted therapeutics for AD through dual inhibition of acetylcholinesterase (AChE) and microRNA-15b biogenesis. We performed high-throughput screening (HTS) of a chemi...
Article
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To explore and investigate the potential contribution and impact of Artificial Intelligence (AI), Machine Learning (ML), and in silico methodologies in a particular field of the drug discovery trajectory, such as the evaluation of Absorption, Distribution, Metabolism, Excretion (ADME) properties and toxicological liabilities (i.e., hERG liability,...
Article
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After the success of the Special Issue entitled “Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation” (https://www.mdpi.com/journal/viruses/special_issues/novelantiviral_agents, accessed on 8 April 2025) which closed in June 2023 [1], a second edition of the above mentioned Special Issue was launched in late...
Article
Background Plant species of the genus Daphne clasps a historical background with a potential source of bioactive phytochemicals such as flavonoids and daphnodorins. These compounds manifest a significant chemotaxonomic value in drug discovery. Their flair comprehensive pharmacological, phytochemical, biological, catalytic, and clinical utilities ma...
Article
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This study aimed to provide an inclusive in silico investigation for the identification of novel drug targets that can be exploited to develop drug candidates for treating oral infections caused by S. sputigena. By coupling subtractive genomics with an in silico drug discovery approach, we identified dTDP-4-dehydrorhamnose 3,5-epimerase (UniProt ID...
Article
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In the last few years, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been the cause of a worldwide pandemic, highlighting the need for novel antiviral agents. The main protease (Mpro) of SARS‐CoV‐2 was immediately identified as a crucial enzyme for viral replication and has been validated as a drug target. Here, we present the de...
Article
Background: The rise in the frequency of liver cancer all over the world makes it a prominent area of research in the discovery of new drugs or repurposing of existing drugs. Methods: This article describes the pharmacophore-based structure-activity relationship (3DQSAR) on the secondary metabolites of Alhagi maurorum to inhibit human liver cancer...
Article
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Microbial fermentation is a primary method by which a variety of foods and beverages are produced. The term refers to the use of microbes such as bacteria, yeasts, and molds to transform carbohydrates into different substances. Fermentation is important for preserving, enhancing flavor, and improving the nutritional quality of various perishable fo...
Article
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Five phenolic Schiff bases (7–11) incorporating a fragment of methanesulfonamide were synthesized and evaluated for their efficacy as antitumor agents. Compounds 7 and 8 demonstrated the most potent antitumor action, with a positive cytotoxic effect (PCE) of 54/59 and 59/59 and a mean growth percentage (MG%) of 67.3% and 19.5%, respectively, compar...
Article
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Background/Objectives: This study investigated the potential of green algae-derived carotenoids as natural inhibitors of the proprotein convertase subtilisin/kexin type 9 (PCSK9), a key regulator of cholesterol metabolism. PCSK9 promotes the degradation of low-density lipoprotein receptors (LDLR), thereby increasing blood cholesterol levels and ele...
Article
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A pandemic encompasses both health and economic concerns. Pandemics are not a novel phenomenon in human society. Their nature, severity, and response, however, vary over time
Article
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In the present work, a new set of N‐(2‐((4‐(1,3‐diphenyl‐1H‐pyrazol‐4‐yl)pyridine sulfonamide derivatives was synthesized. Final target compounds were tested against JNK1 and JNK2 isoforms. Compounds 8f and 8d showed the highest activity over both JNK isoforms. They showed submicromolar activity over JNK1 (IC50 0.90 µM and 0.96 µM, respectively). T...
Article
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Because of their unique ability to target specific malignancies, a wide range of natural and synthetic nanomaterials-with diameters typically smaller than a few hundred nanometers-are being used more and more for therapeutic and diagnostic applications.
Article
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Understanding seismic activity patterns is necessary for earthquake behavior and prediction in order to anticipate future earthquakes. Tectonic plate movement and stress buildup along fault lines define seismic behavior. An examination of geological features, historical earthquake data, and seismic activity monitoring are important forecast techniq...
Article
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This study presents a novel approach to understanding microbial differing qualities inside contagious has through single-cell genomic DNA profiling. By confining and sequencing single cells, we capture the genomic scenes of fungal-resident microbial species, advertising uncommon determination of their hereditary cosmetics. This strategy overcomes t...
Cover Page
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About the Cover: This cover art, in part created using the “Leonardo” AI tool, describes how repistat, a new tetrahydro-γ-carboline HDAC inhibitor, rescued vision in the atp6v0e1–/– zebrafish model of blindness and the rd10 mouse model of retinitis pigmentosa. This compound, derived from iterative med chem cycles and endowed with physicochemical pr...
Article
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Edible chitosan coatings enhance food quality and health outcomes by providing significant nutritional and nutraceutical benefits. These coatings, which are made from chitin, offer a natural barrier that decreases microbial contamination and deterioration, prolonging the shelf life and preserving the freshness of food. Its bioactive qualities, whic...
Article
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A phobia is a kind of anxiety condition characterized by a strong, irrational dread of a particular object or situation. Avoidance behavior, in which people will stop at nothing to avoid being around distressing stimuli, is frequently the outcome of this dread. Usually, the level of dread is not commensurate with the danger or danger itself. Common...
Preprint
Full-text available
In the present work, a new set of N-(2-((4-(1,3-diphenyl-1H-pyrazol-4-yl)pyridine sulfonamide derivatives was synthesized. The new set of compounds can be divided into two main series; compounds 7a-g, which contain a 3-methoxy phenyl moiety at position 3 of the pyrazole ring, and compounds 8a-g, which contain 3-hydroxy phenyl at position 3 of the p...
Book
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Because of growing concerns about future outbreaks caused by pathogens, we launched a Research Topic in 2022, namely “Design and Development of new Therapeutics Against Infectious Diseases Using Computational and Experimental Approaches” hosted by the journal Frontiers in Cellular and Infection Microbiology. In this scenario, the most important con...
Article
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Antitumor activity using 59 cancer cell lines and enzyme inhibitory activity of a newly synthesized pyrazoline-linked 4-methylsulfonylphenyl scaffold (compounds 18a–q) were measured and compared with those of standard drugs. Pyrazolines 18b, 18c, 18f, 18g, 18h, and 18n possessed significant antitumor activity, with a positive cytotoxic effect (PCE)...
Article
Full-text available
Because of growing concerns about future outbreaks caused by pathogens, we launched a research topic in 2022, namely “Design and Development of new Therapeutics Against Infectious Diseases Using Computational and Experimental Approaches” hosted by the journal Frontiers in Cellular and Infection Microbiology. In this scenario, the most important con...
Article
Inherited retinal diseases, which include retinitis pigmentosa, are a family of genetic disorders characterized by gradual rod-cone degeneration and vision loss, without effective pharmacological treatments. Experimental approaches aim to delay disease progression, supporting cones' survival, crucial for human vision. Histone deacetylases (HDACs) m...
Article
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Nature has an excellent hub to open more therapeutic ways by providing diversity in phytoconstituents. To increase the patient compliance by delivering active elements in a supportive way, a specific scientific path is needed. It is quite challenging to discover a phytochemical constituent for any lead therapeutic purpose.In past, drug discovery to...
Article
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Intermittent fasting (IF) has been indicated as a valuable alternative to the classical caloric restriction dietary regimen for lowering body weight and preventing obesity-related complications, such as metabolic syndrome and type II diabetes. However, is it effective? In this review article, we analyzed over 50 clinical studies in which IF, conduc...
Preprint
Full-text available
Intermittent fasting (IF) has been indicated as a valuable alternative to the classical caloric restriction dietary regimen for lowering body weight and preventing obesity-related complications such as metabolic syndrome and type II diabetes. However, is it effective? In this review article, we analyzed over 50 clinical studies in which IF, conduct...
Article
Full-text available
Candidiasis is considered an emerging public health concern because of the occurrence of drug-resistant Candida strains and the lack of an available structurally diverse antifungal drug armamentarium. The indole alkaloid globospiramine from the anticandidal Philippine medicinal plant Voacanga globosa exhibits a variety of biological activities; how...
Article
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Bisindole alkaloids are a source of inspiration for the design and discovery of new-generation anticancer agents. In this study, we investigated the cytotoxic and antiproliferative activities of three spirobisindole alkaloids from the traditional anticancer Philippine medicinal plant Voacanga globosa, along with their mechanisms of action. Thus, th...
Preprint
Full-text available
Candidiasis is considered an emerging public health concern because of the occurrence of drug-resistant Candida strains and the lack of available structurally diverse antifungal drug armamentariums. The indole alkaloid globospiramine from the anticandidal Philippine medicinal plant Voacanga globosa exhibits a variety of biological activities; howev...
Article
Full-text available
Chronic Lymphocytic Leukemia (CLL) patients have a defective expression of the proapoptotic protein p66Shc and of its transcriptional factor STAT4, which evoke molecular abnormalities, impairing apoptosis and worsening disease prognosis and severity. p66Shc expression is epigenetically controlled and transcriptionally modulated by STAT4; epigenetic...
Article
By controlling several antioxidant and detoxifying genes at the transcriptional level, including NAD(P)H quinone oxidoreductase 1 (NQO1), multidrug resistance-associated proteins (MRPs), UDP-glucuronosyltransferase (UGT), glutamate-cysteine ligase catalytic (GCLC) and modifier (GCLM) subunits, glutathione S-transferase (GST), sulfiredoxin1 (SRXN1),...
Article
Breast cancer is a major issue of investigation in drug discovery due to its rising frequency and global dominance. Plants are significant natural sources for the development of novel medications and therapies. Medicinal mushrooms have many biological response modifiers and are used for the treatment of many physical illnesses. In this research, a...
Book
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This is a reprint of articles from the Special Issue published online in the open access journal Viruses (ISSN 1999-4915) entitled “Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation” (https://www.mdpi.com/journal/viruses/special_issues/novelantiviral_agents).
Book
Full-text available
This is a reprint of articles from the Special Issue published online in the open-access journal Computation (ISSN 2079-3197) titled Computation to Fight SARS-CoV-2 (COVID-19). This reprint contains articles concerning the last pandemic health emergency, considering the period 2020–2023.
Article
New potent, selective monoacylglycerol lipase (MAGL) inhibitors based on the azetidin-2-one scaffold ((±)-5a–v, (±)-6a–j, and (±)-7a–d) were developed as irreversible ligands, as demonstrated by enzymatic and crystallographic studies for (±)-5d, (±)-5l, and (±)-5r. X-ray analyses combined with extensive computational studies allowed us to clarify t...
Article
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Retinoic acid receptor-related orphan receptor γt (RORγt) is a nuclear receptor found in various tissues that plays a crucial role in the differentiation and proliferation of T helper 17 (Th17) cells, as well as in their generation of the pro-inflammatory cytokine IL-17A. RORγt represents a promising therapeutic target for autoimmune diseases, meta...
Article
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In this research, natural compounds from Calotropisprocera were screened according to their antimicrobial activity against the pathogenic microbes selected as E. coli, S. aureus, Traypanosomabrucei, Moraxella catarrhalis, and Leishmaniaamazonensis. A 3D‐QSAR study was performed that evaluated the correlation of the structural parameters for the ant...
Article
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Background: Structure–activity relationship (SAR) is considered to be an effective in silico approach when discovering potential antagonists for breast cancer due to gene mutation. Major challenges are faced by conventional SAR in predicting novel antagonists due to the discovery of diverse antagonistic compounds. Methodologyand Results: In predict...
Article
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In this study, we applied a computer-based protocol to identify novel antioxidant agents that can reduce oxidative stress (OxS), which is one of the main hallmarks of several disorders, including cancer, cardiovascular disease, and neurodegenerative disorders. Accordingly, the identification of novel and safe agents, particularly natural products,...
Article
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Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, w...
Article
Full-text available
Representing more than 20% of all deaths occurring worldwide, infectious diseases remain one of the main factors in both human and animal morbidity and mortality. Approximately one-third of these deaths are attributable to viruses. Accordingly, over the past two decades, emerging and re-emerging viral agents, including the most recent SARS-CoV-2 an...
Article
Full-text available
Severe acute respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the etiological virus of Coronavirus Disease 2019 (COVID-19) which has been a public health concern due to its high morbidity and high mortality. Hence, the search for drugs that incapacitate the virus via inhibition of vital proteins in its life cycle is ongoing due to the paucity of...
Article
Full-text available
This paper offers an insightful exploration of the ecological roles played by endophytic bacteria within plants, underscoring their indispensable importance in promoting overall plant growth and health. Endophytic bacteria represent a fascinating group of microorganisms that take up residence within plants during at least a portion of their life cy...
Article
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Article History This paper offers an insightful exploration of the ecological roles played by endophytic bacteria within plants, underscoring their indispensable importance in promoting overall plant growth and health. Endophytic bacteria represent a fascinating group of microorganisms that take up residence within plants during at least a portion...
Article
Full-text available
In April 2020, during the last pandemic health emergency, we launched a Special Issue hosted by Computation—section Computational Biology, entitled “Computation to Fight SARS-CoV-2 (COVID-19)”. The COVID-19 infective condition is caused by the etiological agent SARS-CoV-2 (2019-nCoV), a novel, highly virulent betacoronavirus. Therefore, SARS-CoV-2...
Article
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Pseudomonas aeruginosa (PA), one of the ESKAPE pathogens, is an opportunistic Gram-negative bacterium responsible for nosocomial infections in humans but also for infections in patients affected by AIDS, cancer, or cystic fibrosis (CF). Treatment of PA infections in CF patients is a global healthcare problem due to the ability of PA to gain antibio...
Article
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Alzheimer's disease (AD) is most commonly found in women than men as the risk increases with age. Phytochemicals are in-silico screening from Punica granatum peels for their antioxidant activity to utilized for Alzheimer's disease. Alzheimer's disease is inhibited by the hormone estrogen which protect the brain from the bad effect of amyloid-beta a...
Article
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This review article offers an outlook on the use of opioids as therapeutics for treating several diseases, including cancer and non-cancer pain, and focuses the analysis on the opportunity to target opioid receptors for treating opioid use disorder (OUD), drug withdrawal, and addiction. Unfortunately, as has been well established, the use of opioid...
Article
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Due to the limited availability of antifungal drugs, their relevant side effects and considering the insurgence of drug-resistant strains, novel antifungal agents are urgently needed. To identify such agents, we have developed an integrated computational and biological screening platform. We have considered a promising drug target in antifungal dru...
Article
Plant-derived compounds represent an important source for developing innovative drugs. One of the widely distributed plants, especially in Afghanistan and Pakistan, Seriphidium stenocephalum, was investigated in this study to identify bioactive compounds. The plant extract was subjected to silica gel column chromatography, four phenolic acid deriva...
Article
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Hypoxia-inducible factors (HIFs) are the main regulatory factors implicated in the adaptation of cancer cells to hypoxic stress, which has provoked much interest as an attractive target for the design of promising chemotherapeutic agents. Since indirect HIF inhibitors (HIFIs) lead to the occurrence of various side effects, the need of the hour is t...
Article
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In this paper, we present the development of a computer-based repurposing approach to identify FDA-approved drugs that are potentially able to interfere with irisin dimerization. It has been established that altered levels of irisin dimers are a pure hallmark of lipodystrophy (LD) syndromes. Accordingly, the identification of compounds capable of s...
Article
Full-text available
In July 2021 we announced a Frontiers Research Topic, hosted by Frontiers in Chemistry, entitled “Advances in Green Synthesis for Drug Discovery”, as a part of the Green and Sustainable Chemistry section of the journal. The topic related to the green synthesis methods aimed to highlight novel environmentally safe approaches for synthesizing novel c...
Article
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A novel series of 12 antipyrine derivatives containing 1,3,4-oxadiazoles (4a-d), 1,3,4-thiadiazoles (6a-d), and pyrimidines (8a-d), was preparedand assessed for its potential in vitro COX-2 inhibitors. Compared to Celecoxib, compounds 4b-d and 8d were the most potent derivatives c with a half-maximal inhibitory concentration range of 53–69 nM. Cons...
Cover Page
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The Front Cover shows the sustainable approach used to develop new unsymmetrical squaramides acting as allosteric GSK3β inhibitors, promoting TCF‐LEF transcription in retinal pigment epithelial ARPE‐19 cells. This work highlights how green chemistry coupled with computational and biological studies could be a valuable strategy for developing intere...
Article
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The severity of the COVID-19 pandemic has necessitated the search for drugs against SARS-CoV-2. In this study, we explored via in silico approaches myxobacterial secondary metabolites against various receptor-binding regions of SARS-CoV-2 spike which are responsible in recognition and attachment to host cell receptors mechanisms, namely ACE2, GRP78...
Article
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The sirtuin 1 (SIRT1) activator resveratrol has emerged as a promising candidate for the prevention of vascular oxidative stress, which is a trigger for endothelial dysfunction. However, its clinical use is limited by low oral bioavailability. In this work, we have applied a previously developed computational protocol to identify the most promising...
Article
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Macroautophagy (autophagy) has been a highly conserved process throughout evolution and allows cells to degrade aggregated/misfolded proteins, dysfunctional or superfluous organelles and damaged macromolecules, in order to recycle them for biosynthetic and/or energetic purposes to preserve cellular homeostasis and health. Changes in autophagy are i...
Article
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Macroautophagy (autophagy) has been a highly conserved process throughout evolution and allows cells to degrade aggregated/misfolded proteins, dysfunctional or superfluous organelles and damaged macromolecules, in order to recycle them for biosynthetic and/or energetic purposes to preserve cellular homeostasis and health. Changes in autophagy are i...
Article
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The glycogen synthase kinase 3β (GSK‐3β) is a ubiquitous enzyme that is a validated target for the development of potential therapeutics useful in several diseases including retinal degeneration. Aiming at developing an innovative class of allosteric inhibitors of GSK‐3β potentially useful for retinal degeneration, we explored the class of squarami...
Article
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Luteolin (LUT) is a well-known flavonoid that exhibits a number of beneficial properties. Among these, it shows cardioprotective effects, as confirmed by numerous studies. However, its effect on mitochondrial potassium channels, the activation of which is related to cytoprotection, as well as on heart ischemia/reperfusion (I/R) damage prevention, h...
Article
Since the inception of COVID-19 pandemic in December 2019, socio-economic crisis begins to rise globally and SARS-CoV-2 was responsible for this outbreak. With this outbreak, currently, world is in need of effective and safe eradication of COVID-19. Hence, in this study anti-SAR-Co-2 potential of FDA approved marine drugs (Biological macromolecules...
Article
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The sustainable use of resources is essential in all production areas, including pharmaceuticals. However, the aspect of sustainability needs to be taken into consideration not only in the production phase, but during the whole medicinal chemistry drug discovery trajectory. The continuous progress in the fields of green chemistry and the use of art...
Article
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Arginase is a metalloenzyme that plays a central role in Leishmania infections. Previously, rosmarinic and caffeic acids were described as antileishmanial agents and as Leishmania amazonensis arginase inhibitors. Here, we describe the inhibition of arginase in L. amazonensis by rosmarinic acid analogs (1–7) and new caffeic acid-derived amides (8–10...
Article
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Natural products have been included in our dietary supplements and have been shown to have numerous therapeutic properties. With the looming danger of many zoonotic agents and novel emerging pathogens mainly of viral origin, many researchers are launching various clinical trials, testing these compounds for their antiviral activity. The present wor...
Article
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Parasitic diseases cause significant global morbidity and mortality particularly in the poorest regions of the world. Schistosomiasis, one of the most widespread neglected tropical diseases, affects more than 200 million people worldwide. Histone deacetylase (HDAC) inhibitors are prominent epigenetic drugs that are being investigated in the treatme...
Article
Leishmania spp. are responsible for up to 1 million new cases each year. The current therapeutic arsenal against Leishmania is largely inadequate, and there is an urgent need for better drugs. Trypanothione reductase (TR) represents a druggable target since it is essential for the parasite and not shared by the human host. Here, we report the optim...
Article
The design of compounds able to combine the selective inhibition of cyclooxygenase-2 (COX-2) with the release of nitric oxide (NO) is a promising strategy to achieve potent anti-inflammatory agents endowed with an overall safer profile and reduced toxicity upon gastrointestinal and cardiovascular systems. With the aim of generating novel and select...
Article
Introduction In this article, authors report an inclusive discussion about the combinatorial approach for the treatment of cardiovascular diseases (CVDs) and for counteracting the cardiovascular risk factors. The mentioned strategy was demonstrated to be useful for improving the efficacy of pharmacological treatments and in CVDs showed superior eff...
Article
Full-text available
The natural environment represents an important source of drugs that originates from the terrestrial and, in minority, marine organisms. Indeed, the marine environment represents a largely untapped source in the process of drug discovery. Among all marine organisms, sponges with algae represent the richest source of compounds showing anticancer act...
Cover Page
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Cover Story (https://www.mdpi.com/2079-3197/10/5): The Mpro enzyme is a validated target for developing SARS-CoV-2 antiviral drugs. A number of Mpro enzyme inhibitors, currently discovered, bear an electrophilic warhead, able to form a covalent bond with the active site cysteine residue, linked to a peptidic/peptidomimetic structure interacting wit...
Article
Full-text available
Despite the progress of therapeutic approaches for treating COVID-19 infection, the interest in developing effective antiviral agents is still high, due to the possibility of the insurgence of viable SARS-CoV-2-resistant strains. Accordingly, in this article, we describe a computational protocol for identifying possible SARS-CoV-2 Mpro covalent inh...
Article
The search of new therapeutic tools for the treatment of cancer is being a challenge for medicinal chemists. Due to their role in different pathological conditions, histone deacetylase (HDAC) enzymes are considered valuable therapeutic targets. HDAC6 is a well-investigated HDAC-class IIb enzyme mainly characterized by a cytoplasmic localization; HD...
Article
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Pin1 catalyzes the cis‐trans isomerization of pThr‐Pro or pSer‐Pro amide bonds of various proteins involved in several physio/pathological processes. In this framework, recent research activity is directed toward the identification of new selective Pin1 inhibitors. Here, we developed a set of peptide‐based Pin1 inhibitors. Direct‐binding experiment...
Article
Full-text available
In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to it...
Article
Autophagy is a lysosome dependent cell survival mechanism and is central to the maintenance of organismal homeostasis in both physiological and pathological situations. Targeting autophagy in cancer therapy attracted considerable attention in the past as stress-induced autophagy has been demonstrated to contribute to both drug resistance and malign...
Article
Full-text available
The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest in discovering novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study wherein, using a virtual screening campaign, we id...
Preprint
Full-text available
The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest to discover novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study in which, by a virtual screening campaign, we identif...
Article
Full-text available
The huge advancement in Internet web facilities as well as the progress in computing and algorithm development, along with current innovations regarding high-throughput techniques, enable the scientific community to gain access to biological datasets, clinical data and several databases containing billions of pieces of information concerning scient...
Preprint
Full-text available
The huge advancement of Internet web facilities as well as the progress in computing and algorithm development, along with current innovations regarding high-throughput techniques enables the scientific community to gain access to biological datasets, clinical data, and several databases containing billions of information concerning scientific know...
Article
Full-text available
Curcumin possesses a plethora of interesting pharmacological effects. Unfortunately, it is also characterized by problematic drug delivery and scarce bioavailability, representing the main problem related to the use of this compound. Poor absorption, fast metabolism, and rapid systemic clearance are the most important factors contributing to low cu...
Article
Histone deacetylases (HDACs) as an important family of epigenetic regulatory enzymes are implicated in the onset and progression of carcinomas. As a result, HDAC inhibition has been proven as a compelling strategy for reversing the aberrant epigenetic changes associated with cancer. However, non-selective profile of most developed HDAC inhibitors (...
Article
Drugs targeting epigenetic mechanisms are attracting the attention of scientists since it was observed that the modulation of this post-translational apparatus, could help to identify innovative therapeutic strategies. Among the epigenetic druggable targets, the positive modulation of SIRT1 has also been related to significant cardioprotective effe...
Article
The continued sustained threat of the SARS-CoV-2 virus world-wide, urgently calls for far-reaching effective therapeutic strategies for treating this emerging infection. Accordingly, this study explores mode of action and therapeutic potential of existing antiviral drugs. Multiple sequence alignment and phylogenetic analyses indicate that the RNA-d...
Article
Full-text available
Introduction Hydrogen sulfide (H2S) is a fundamental biological endogenous gas-mediator in the respiratory system. It regulates pivotal patho-physiological processes such as oxidative stress, pulmonary circulation, airway tone and inflammation. Objectives We herein describe the design and synthesis of molecular hybrids obtained by the condensation...
Article
Temporal lobe epilepsy is the most common form of epilepsy, and current antiepileptic drugs are ineffective in many patients. The endocannabinoid system has been associated with an on-demand protective response to seizures. Blocking endocanna-binoid catabolism would elicit antiepileptic effects, devoid of psychotropic effects. We herein report the...
Article
Full-text available
The development of novel and safe compounds is a challenging task in the drug discovery trajectory. Accordingly, the individuation of promising core molecules with biological activities could pave the way to develop effective drugs to treat a given disease. The use of a computational approach can reduce the time for identifying promising core molec...
Article
Full-text available
Caffeic acid and related natural compounds were previously described as Leishmania amazonensis arginase (L-ARG) inhibitors, and against the whole parasite in vitro. In this study, we tested cinnamides that were previously synthesized to target human arginase. The compound caffeic acid phenethyl amide (CAPA), a weak inhibitor of human arginase (IC50...
Article
In this work we describe the synthesis of potent and selective quinolone-based histone deacetylase 6 (HDAC6) inhibitors. The quinolone moiety has been exploited as an innovative bioactive cap-group for HDAC6 inhibition; its synthesis was achieved by applying a multicomponent reaction. The optimization of potency and selectivity of these products wa...
Preprint
Full-text available
Arginase is a metalloenzyme that plays a central role in Leishmania infection. Previously, rosmarinic and caffeic acids were described as antileishmanial and as a Leishmania amazonensis arginase inhibitor and now, we describe the inhibition of arginase in L. amazonensis by rosmarinic acid analogs (1-7) and new caffeic acids derived amides (8-10). C...

Questions

Question (1)
Question
Dear Colleagues,
The occurrence of a new, extremely pathogenic betacoronavirus, SARS-CoV-2 (2019-nCoV), is responsible for the CoVid-19 pandemic health emergency. Accordingly, SARS-CoV-2 represents a serious global health warning characterized by high mortality, a high contagion rate, and a lack of clinically approved drugs and vaccines. In order to find safe and effective therapeutic options to treat this infectious disease, computer science could play an extremely relevant role to better understand the virus pathogenic mechanism as well as to propose novel therapeutic strategies. Accordingly, due to progress in computer science, in silico methodologies in medicinal chemistry, pharmacology, biology, genetics, and virology cover relevant tasks in modern research in these fields. Furthermore, due to the current global health warning, such computational techniques could speed up research in order to provide innovative and targeted approaches to fight the coronavirus emergency. In light of this, this Special Issue will highlight progress in terms of drug discovery, virus biology, and epidemiology to provide researchers with the most innovative computer-driven methodologies for fighting SARS-CoV-2.
For this Special Issue of Computation, we invite researchers in the fields of computational drug discovery (including drug repurposing approaches), computational biology/genetics, virology, bioinformatics, and epidemiology to submit original research, short communications, and review articles related to the use of computation to fight SARS-CoV-2.
Dr. Simone Brogi Prof. Vincenzo Calderone Guest Editors

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