THE PURPOSING OF NEW COMPOUNDS OR THE RE-PURPOSING OF OLD DRUGS BY MEANS OF MULTIVARIATE ANATYSIS ON MOLECULAR DESCRIPTORS

Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors

Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a pu…

Studi di Modellistica Molecolare e Sintesi di Sistemi Indolotriazolopirimidinici

A multivariate analysis on HIV-1 protease inhibitors and resistance induced by mutation

Principal Component Analysis on molecular descriptors as alternative point of view in the search of new Hsp90 inhibitors

Molecular modelling studies on new series of DNA-interactive annelated pyrrolo-pyrimidines

A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model

Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, causes neuropathy. Knowledge is scarce on the impact of this and other mutations upon the chaperone's structure and functions. To make progress, experimental models must be developed. We used an archaeal mutant homolog and demonstrated that the His147Arg mutant has impaired oligomeric assembly, ATPase activity, and defective protein homeostasis functions. These results establish for the first time that a human chaperonin gene defect can be reproduced and studied at the molecular level with an archaeal homolog. The major…

The Interaction of Small Molecules with Biomolecules

The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental dat…

Pirrolo[3,4-h]chinolinoni: Potenziali Agenti Fotochemioterapici

A3 adenosine receptor: Homology modeling and 3D-QSAR studies

Adenosine receptors (AR) belong to the superfamily of G-protein-coupled receptors (GPCRs). They are divided into four subtypes (A1, A2A, A2B, and A3) [1], and can be distinguished on the basis of their distinct molecular structures, distinct tissues distribution, and selectivity for adenosine analogs [2,3]. The hA3R, the most recently identified adenosine receptor, is involved in a variety of intracellular signaling pathways and physiological functions [4]. Expression of A3R was reported to be elevated in cancerous tissues [5], and A3 antagonists have been proposed for therapeutic treatments of cancer. The recent literature availability of crystal structure of hA2A adenosine receptor (PDB c…

Design of antitumor drugs targeting c-kit receptor by a new mixed ligand-structure based method

An important challenge, in the medicinal chemistry field, is the research of novel forceful drugs to overcome tumor-acquired resistance. The c-Kit tyrosine kinase receptor (TKR) represents a suitable target for the carcinogenesis control of gastro-intestinal stromal (GIST), leukemia, and mastocytosis tumors; nevertheless, several hotspot mutations of the protein limit the efficacy of a few clinical administered TKRs inhibitors. In this study, a new in silico protocol based on ligand and structure-based combined method is proposed, with the aim to identify a set of new c-Kit inhibitors able to complex c-Kit mutated proteins. A recent and freely available web-server DRUDIT is used for the lig…

Study of Reactivity in the 1,3-Dipolar Cycloaddition Reactions Leading to New Triazolopyrrolopyrazine Ring Systems

The influence of the structural symmetry of the 2-pi double-reactive-sites component in the 1,3-dipolar cycloaddition reactions, involving nitrilimines as dipoles, was investigated. the experimental data showed that the loss of the symmetry leads to the formation of the monocycloadduct in good yields.

Nuovi inibitori di Aurora chinasi A come target biologico coinvolto nei processi carcinogenici

Identificando Aurora chinasi A come target elettivo per l’inibizione dell’espansione tumorale è stato sfruttato l’approccio computazionale per effettuare un virtual screening su una libreria “in house” di strutture molecolari. L’analisi dei dati computazionali ha permesso di identificare nei derivati della serie pirido[3’,2’:4,5]furo[3,2-d]-1,2,3-triazin-4(3H)one di tipo 3 nuovi composti a potenziale attività inibitoria sul sito ATP-asico di Aurora chinasi A. La sintesi del sistema triciclico-eteroaromatico 3 prevede la diazotazione della 3-amino-furopiridina 1 e conseguente reazione di copulazione con una serie di ammine primarie opportunamente scelte, permettendo l’isolamento delle 3-tria…

G-quadruplex vs. duplex-DNA binding of nickel(II) and zinc(II) Schiff base complexes

Novel nickel(II) (1) and zinc(II) (2) complexes of a Salen-like ligand, carrying a pyrimidine ring on the N,N' bridge, were synthesized and characterized. Their interaction with duplex and G-quadruplex DNA was investigated in aqueous solution through UV-visible absorption, circular dichroism and viscometry measurements. The results obtained point out that, while the zinc(II) complex does not interact with both duplex and G-quadruplex DNA, the nickel(II) complex 1 binds preferentially to G-quadruplex respect to duplex-DNA, with values of the DNA-binding constants, Kb, 2.6×10(5)M(-1) and 3.5×10(4)M(-1), respectively. Molecular dynamics simulations provided an atomic level model of the top-sta…

New imidazo[1,2-c]pyrrolo[3,2-e]pyrimidinone derivatives as potential DNA-binders

Pyrrolo[3,4-e][1,2,3]triazolo[1,5-a]pyrimidine and pyrrolo[3,4-d] [1,2,3]triazolo[1,5-a]pyrimidine. New tricyclic ring systems of biological interest

Derivatives of the new ring system pyrrolo[3,4-e][1,2,3] triazolo[1,5-a]pyrimidine 6 were prepared in high yields in one step by reaction of 3-azidopyrrole 3 and substituted acetonitriles. Compound 6b rearranged, upon heating in dimethyl sulfoxide in the presence of water, to pyrrolo[3,4-d][1,2,3]triazolo-[1,5-a]pyrimidine 7.

In silico identification of small molecules as new cdc25 inhibitors through the correlation between chemosensitivity and protein expression pattern

The cell division cycle 25 (Cdc25) protein family plays a crucial role in controlling cell proliferation, making it an excellent target for cancer therapy. In this work, a set of small molecules were identified as Cdc25 modulators by applying a mixed ligand-structure-based approach and taking advantage of the correlation between the chemosensitivity of selected structures and the protein expression pattern of the proposed target. In the first step of the in silico protocol, a set of molecules acting as Cdc25 inhibitors were identified through a new ligand-based protocol and the evaluation of a large database of molecular structures. Subsequently, induced-fit docking (IFD) studies allowed us…

The Role of 1,3-Dipolar Cycloaddition Reactions in the Design and Synthesis of Complex Heterocyclic Scaffolds with Anti-tumor/Anti-infective Activity

1,3-Dipolar cycloaddition in the synthesis of a new potential DNA-intercalating agent: indolo[3,2-e]pyrrolo[1,2-c]triazolo[1,5-a]pyrimidine

“QSPR, Sintesi ed Attività Biologica di Nuovi Derivati del Sistema Tetraciclico Indolo[3,2-e][1,2,3]triazolo[1,5-a]pirimidinico.”

DRUDIT: Web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets

Abstract Motivation New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tool…

Synthesis and antiproliferative activity of Naphtalenyl substituted 1,2-dihydropyrazol-5-one and related fused tetrazine

In recent years, besides the main field of nonsteroidal anti-inflammatory agents, the interest towards pyrazolone derivatives has been renewed because of their wide biological and pharmacological applications [1]. Currently, particular attention is focused on such a class of compounds due to the affinity with sigma receptor and their relationship with cancer [2].To these purposes we planned to design, synthesize and evaluate the antiproliferative activity (MTS assays) of a new series of 3-methyl-2-(1-R-naphthalen-2-yl)-1,2-dihydropyrazol-3-one derivatives 1 against HeLa, MCF-7, LAN-5, Caco2 in order to explore their anticancer potential. Additionally, further elaboration of the amino deriva…

Computational methodologies in the discovery of inhibitors of HIV-1

Does Ligand Symmetry Play a Role in the Stabilization of DNA G-Quadruplex Host-Guest Complexes?

In efforts to find agents with improved biological activity against cancer cells, recent years have seen an increased interest in the study of small molecules able to bind the deoxyribonucleic acid (DNA) when it assumes secondary structures known as G-quadruplexes (G4s) preferring them over the B form. Currently, several compounds reported in literature have already shown to be good candidates as G4s DNA stabilizers. Even though some specific features for the G4s affinity are known, such as a π-delocalized system able to stack at the top/end of a G-tetrad and positively charged substituents able to interact with the grooves, it is not clear yet what kind of structural features affect more t…

In vitro and in silico studies of polycondensed diazine systems as anti-parasitic agents

Abstract Parasitic diseases caused by protozoarian agents are still relevant today more than ever. Recently, we synthesized several polycondensed diazine derivatives by means 1,3-dipolar cycloaddition reactions. A broad selection of these compounds were submitted to in vitro biological screening against Plasmodium falciparum , Leishmania infantum , Trypanosoma brucei , and Trypanosoma cruzi , resulting active at micromolar level. Induced Fit Docking/MM-GBSA studies were performed giving interesting indications about the probable mechanism of action of the most active compounds

Inside the Hsp90 inhibitors binding mode through induced fit docking

Abstract During the last few decades, the development of new anticancer strategies had to face the instability of many tumors, occurring when the genetic plasticity of cells produces new drug-resistant cancers. It has been shown that a chaperone protein, heat shock protein 90 (Hsp90), is one of the fundamental factors involved in the cell response to stresses, and its role in many biochemical pathways has been demonstrated. Thus, the inhibition of Hsp90 represents a new target of antitumor therapy, since it may influence many specific signaling pathways. The natural antibiotic Geldanamycin is the first Hsp90 inhibitor that has been identified. Nevertheless, more potent and water-soluble sma…

Studi di dinamica molecolare su Mdm2 legata a due differenti inibitori

Docking of Indolo- and Pyrrolo-pyrimidines to DNA New DNA-interactive Polycycles from 2-Amino-indoles/pyrroles and BMMA

Identification of biological targets through the correlation between cell line chemosensitivity and protein expression pattern.

Matching biological data sequences is one of the most interesting ways to discover new bioactive compounds. In particular, matching cell chemosensitivity with a protein expression profile can be a useful approach to predict the activity of compounds against definite biological targets. In this review, we discuss this correlation. First, we analyze case studies in which some known drugs, acting on known targets, show a good correlation between their antiproliferative activities and protein expression when a large panel of tumor cells is considered. Then, we highlight how the application of in silico methods based on the correlation between cell line chemosensitivity and gene/protein expressi…

MADoSPRO: a new approach to molecular modelling studies on a series of DNA minor groove binders

The aim of this work was devoted to develop a method to predict Delta G values for a series of minor groove binders. Starting from a matrix of docking dataset for 10 minor groove binders (known and not) to 20 DNA fragments, with various sequences, it was possible to analyze the interaction modes and to calculate the Delta G value for new derivatives through MADoSPRO procedure. The method allowed, through the QSPR analysis, to characterize the type of interactions in such complexes, that was demonstrated to be related to quantum chemical and electrostatic descriptors, in agreement with the information available in literature on the structural requirements of specific minor groove ligands. Mo…

Evaluation of matrix effect on the GC/MS response of eighteen pesticides by multivariate approach

Docking and synthesis of pyrrolopyrimidodiazepinone derivatives (PPDs) and their precursors: New scaffolds for DNA-interacting agents

New classes of pyrrolopyrimidodiazepinone derivatives (PPDs) and their precursors were studied in silico for their ability to form stable complex with DNA fragment. In the docking studies two binding modes can be envisaged: groove mode and intercalating mode. In the case of the best ligands the docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs whereas the side chain lies close to the minor groove. Synthetic approach to the PPD ring systems is discussed.

TECNICHE DI MODELLISTICA MOLECOLARE NELLA PROGETTAZIONE DI INIBITORI DELL'ATTIVITÀ TRASCRIZIONALE DI HIF-1

The influence of acidic pH environment in regulating the activity of novel HIF-1 inhibitors

NOVEL ANTAGONISTS FOR AN Hsp60-BASED ANTICANCER CHAPERONOTHERAPY

The Heat shock proteins (Hsps) are nowadays considered the most important cell chaperones, which result overexpressed in response to a number of cell stress stimuli.In tumor cells, when Hsp60 accumulates in the cytosol, without mitochondrial release, it exerts an anti-apoptotic effect, by inhibiting pro-caspase-3 (pC3) activation. In this context, our study aims to elucidate the structural details of the interaction between Hsp60 and pC3 and to design novel antagonists able to specifically block this interaction. The analysis of virtual screening results highlights the 4-(3-chloro-4-fluorophenylamino)- 6-[(1H-imidazol-4-yl-methyl)-3-carbonitrile-quinolines of type 1 and the N-{5-[1H-imidazo…

Drugs Polypharmacology by in Silico Methods: New Opportunities in Drug Discovery

Background Polypharmacology, defined as the modulation of multiple proteins rather than a single target to achieve a desired therapeutic effect, has been gaining increasing attention since 1990s, when industries had to withdraw several drugs due to their adverse effects, leading to permanent injuries or death, with multi-billiondollar legal damages. Therefore, if up to then the "one drug one target" paradigm had seen many researchers interest focused on the identification of selective drugs, with the strong expectation to avoid adverse drug reactions (ADRs), very recently new research strategies resulted more appealing even as attempts to overcome the decline in productivity of the drug dis…

Molecular Docking and QSPR approach on NCI Anti-Cancer Agents Mechanism Database Topoisomerase I inhibitors

Virtual lock and key approach: the revival of Fischer model

Molecular Docking approach on the Topoisomerase I inhibitors series included in the NCI anti-cancer agents mechanism database

Topoisomerase I (Top1) is an essential enzyme participating to all those processes associated with separation of DNA strands. It manages superhelical tensions through the transient breakage of one strand of duplex DNA, followed by the unwinding of supercoiled DNA. Camptothecins, a class of alkaloids extracted from the wood of a Chinese tree, were found to be potent inhibitors of Topoisomerase I. The National Cancer Institute (NCI) Anti-cancer Agents Mechanism Database contains several camptothecins derivatives, classified as selective Top1 inhibitors. In this work we performed molecular docking studies on 24 camptothecin-like inhibitors present in this database (using Autodock 3.0.5). In or…

Analisi Multivariata e Docking nello Studio degli Inibitori di HIV-1 Integrasi

1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, through 1,3-Dipolar Cycloadditions

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…

New triazolo-pyrrolopyrazine systems by 1,3-dipolar cycloaddition

LOOKING FOR NEW HSP-90 INHIBITORS THROUGH A MOLECULAR DOCKING/PHARMACOPHORE APPROACH

Synthesis, characterization and DNA binding studies of potential G4 stabilizer metal complexes

Investigation of flap motions in wild type and M46I/G51D Mutant HIV-1 Protease by molecular dynamics studies

DNA minor groove binders: an overview on molecular modeling and QSAR approaches

Molecular recognition of DNA by small molecules and proteins is a fundamental problem in structural biology and drug design. Understanding of recognition in both sequence-selective and sequence neutral ways at the level of successful prediction of binding modes and site selectivity will be instrumental for improvements in the design and synthesis of new molecules as potent and selective gene-regulatory drugs. Minor groove is the target of a large number of non-covalent binding agents. DNA binding with specific sequences, mostly AT, takes place by means of a combination of directed hydrogen bonding to base pair edges, van der Waals interactions with the minor groove walls and generalized ele…

A convenient synthesis of cycloadduct bis-1,2,4-triazolo[4,3-a:3’,4’-c]quinoxalines by 1,3-dipolar cycloaddition

Molecular Modeling and Dynamics of the transcriptionfactor NF-kB complexed with IkB

THE DISCOVERY OF NEW HIF-1 INHIBITORS THROUGH MOLECULAR MODELING STUDIES

Curcumin-like compounds designed to modify amyloid beta peptide aggregation patterns

International audience; Curcumin is a natural polyphenol able to bind the amyloid beta peptide, which is related to Alzheimer's disease, and modify its self-assembly pathway. This paper focuses on a multi-disciplinary study that starts from the design of curcumin-like compounds with the key chemical features required for inhibiting amyloid beta aggregation, and reports the effects of these compounds on the in vitro aggregation of amyloid beta peptides. Chemoinformatic screening was performed through the calculation of molecular descriptors that were able to highlight the drug-like profile, followed by docking studies with an amyloid beta peptide fibril. The computational design underlined t…

Targeted synthesis of pyrrolo tricycles for selective biomolecules overexpressed in cancer cells

BINDING MODES OF HSP90 INHIBITORS INVESTIGATED THROUGH INDUCED FIT DOCKING: IMPORTANCE OF ACTIVE SITE FLEXIBILITY

One pot-like regiospecific access to 1-aryl-1H-pyrazol-3(2H)-one derivatives and evaluation of the anticancer activity

A set of variously substituted 1-arylpyrazol-3-one derivatives, including the di-ortho-aryl substituted ones, was synthesized as new potential anticancer compounds. To fulfill this aim, herein a regiospecific synthesis was proposed utilizing a new revisited one pot procedure, starting from commercial anilines and easily accessible 2,5-dimethyl-furan-3-one. In the course of the sequential ordered steps, in some cases, a nitro group displacement by chlorine took place to a minor extent. The in vitro screening against the full panel of ~60 human cancer cell lines (NCI) showed a moderate, but promising selective antiproliferative activity against the UO31 renal tumor cell line, only in compound…

La chemiometria ed il molecular modeling in ausilio alla scoperta ed all’ottimizzazione di lead compounds

Theoretical Determination Of The pKas Of Betalamic Acid Related To The Free-Radical Scavenger Capacity: Comparison Between Semi-Empirical And Ab Initio Methods

Apoptotic induction on HeLa tumor cell line. A comparison of activity between pyrazolo[1,2-a]benzo[1,2,3,4]tetrazinone derivatives and their synthetic precursors

Pyrrolo[1,2-f]phenanthridines and related non-rigid analogues as antiviral agents.

Abstract The pyrrolo[1,2- f ]phenanthridines 8 – 22 and the corresponding non-rigid analogues 23 – 41 were synthesised and their ability to inhibit the replication of HIV-1 was tested. Only the polycyclic derivatives 10 , 11 , and 13 showed a weak anti -HIV activity, whereas several pyrrolo-phenanthridines ( 8 , 10 , 16 – 18 ) were found to stimulate the multiplication of MT-4 cells at low concentrations. Derivative 10 demonstrated to possess the unique property of stimulating the multiplication of lymphocytes joined to HIV inhibition.

Reattività di diazine benzocondensate asimmetriche nelle reazioni di cicloaddizione 1,3-dipolare con dipoli nitriliminici

Phytochemical Profile and Antioxidant, Antiproliferative, and Antimicrobial Properties of Rubus idaeus Seed Powder

In the context of the contemporary research on sustainable development and circular economy, the quest for effective strategies aimed at revaluation of waste and by-products generated in industrial and agricultural production becomes important. In this work, an ethanolic extract from red raspberry (Rubus idaeus) seed waste (WRSP) was evaluated for its phytochemical composition and functional properties in term of antioxidative, antiproliferative, and antimicrobial activities. Chemical composition of the extract was determined by both HPLC-ESI-MS/MS and spectrophotometric methods. Phytochemical analysis revealed that flavan-3-ols and flavonols were the major phenolic compounds contained in W…

Studi spettroscopici su complessi indolotriazolopirimidina-DNA nativo.

Docking of indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from amino-indoles/pyrroles and BMMA

New indolo- and pyrrolo-pyrimidines of type 1-4 were studied for their ability to form stable complexes with DNA fragments. The calculated free energies of binding were found in the range -8.39 ÷ -16.72 Kcal/mol. The docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs whereas the side chain lies along the minor groove.

Protocollo chemiometrico per la predizione del meccanismo di azione di derivati a potenziale attività antitumorale

Bis-1,2,4-triazolo[4,3-a:3′,4′-c]quinoxalines of pharmaceutical interest from 1,3-dipolar cycloaddition

Abstract Various derivatives of the heterocyclic system 1,12,12a,12b-tetrahydrobis-1,2,4-triazolo[4,3-a:3′,4′-c]quinoxaline of pharmaceutical interest have been obtained by double site- and regio-selective 1,3-dipolar cycloaddition of arylnitrilimines to quinoxalines. No evidence for the formation of mono-adducts was obtained, at variance with literature reports. Specific studies to establish the exact stereochemistry of the bis-cycloadducts were undertaken.

Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: the investigation of p53-MDM2 interaction and its inhibition by small molecules.

The mdm2 oncogene product, MDM2, is an ubiquitin protein ligase that inhibits the transcriptional activity of the tumor suppressor p53 and promotes its degradation. About 50% of all human cancers present mutations or deletions in the TP53 gene. In the remaining half of all human neoplasias that express the wild-type protein, aberrations of p53 regula- tors, such as MDM2, account for p53 inhibition. For this reason, designing small-molecule inhibitors of the p53-MDM2 protein-protein interaction is a promising strategy for the treatment of cancers retaining wild-type p53. The development of inhibitors has been challenging. Although many small-molecule MDM2 inhibitors have shown potent in vitr…

Potenziali agenti DNA-interattivi: Benzotieno[2,3-e][1,2,3]triazolo[1,5-a]pirimidine

Design of new DNA-interactive agents by molecular docking and QSPR approach

The design of new series of pyrrolo-pyrimidine derivatives, further annelated with a third heterocycle of different size, which also present several chain shape moieties of variable length and with different physico-chemical character, is reported. In this contribution we showed that the combination of docking-based and QSPR-based methods could lead to good models for ligand-DNA interaction prediction. By means of these computational approaches on 360 proposed inhibitors, we were able to select the most promising candidates as DNA-interactive drugs potentially endowed with antitumor activity.

Identificazione e sintesi di nuovi potenziali inibitori di Heat Shock Protein 90

Vaccinium macrocarpon (Cranberry)-Based Dietary Supplements: Variation in Mass Uniformity, Proanthocyanidin Dosage and Anthocyanin Profile Demonstrates Quality Control Standard Needed

Vaccinium macrocarpon (syn. American Cranberry) is employed in dietary supplements (DS) with the aim to improve urinary tract well-being. This property is linked to the antiadhesion-activity of proanthocyanidins (PACs) against uropathogenic-bacteria. However, the current European legislation has been criticized for being weak and ineffective. Indeed, recent scientific works report mislabeled, contaminated, and adulterated supplements containing dangerous or unknown compounds, or sold at toxic doses. In this work, we analysed 24 DS that claim to contain cranberry, and to have a specific dosage of PACs. Our tests included the control of the good manufacturing practice according to the Europea…

Annelated pyrrolo-pyrimidines from amino-cyanopyrroles and BMMAs as leads for new DNA-interactive ring systems.

The efficient one-pot synthesis of several new tricyclic systems of type 1 and 2, obtained from the reaction of substituted 2-amino-3-cyanopyrroles and 3-amino-4-cyanopyrroles with BMMAs, is reported. The duration and yields of the reaction strongly depend on the reactivity of the starting pyrrole and on the size of the ring to be formed. Mechanist features of the reaction were investigated and proposed by studying also the reactivity of a 3-aminopyrrole-2,4-dicyano substituted. The method reported represents the first example of the use of BMMA reagents in combination with pyrrole derivatives and allows an easy and versatile entry to a large number of hitherto unknown pyrrolo-pyrimidines f…

Heterocyclic Scaffolds for the Treatment of Alzheimer's Disease

Background: The treatment and diagnosis of Alzheimer’s Disease (AD) are two of the most urgent goals for research around the world. The cognitive decline is generally associated with the elevated levels of extracellular senile plaques, intracellular neurofibril- lary tangles (NFTs), and with a progressive shutdown of the cholinergic basal forebrain neurons transmission. Even if several key targets are under fervent investigation in the cure of AD, till now, the only approved therapeutic strategy is the treatment of symptoms by using cholinesterases inhibitors. It has been demonstrated that both acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes are not only responsible of…

Studio del ruolo delle mutazioni “gatekeeper” V654A e T670I di c-kit kinase nell’interazione con inibitori attraverso un approccio misto Dinamica Molecolare/Docking

La sovraespressione del proto-oncogene c-kit è stata riscontrata nelle cellule ematopoietiche, nel cancro a piccole cellule del polmone e nei tumori stromali gastrointestinali1-3. L’importanza clinica dell’espressione di c-kit nei tumori ha indirizzato la ricerca verso inibitori di questa tirosina chinasi. Imatinib (Gleevec®) (in figura) è stato il primo farmaco utilizzato in terapia, ma la comparsa di mutazioni su c-kit ha portato ad una riduzione dell’efficacia o a completa resistenza a questo trattamento. In alternativa, altri composti si sono mostrati attivi anche nei confronti dei mutanti come ad esempio Sunitinib (Sutent®)4, ma la necessità di nuovi e più efficaci inibitori contro i m…

Pirazolo[3,4-d][1,2,3]triazolo[1,5-a]pirimidina: accesso sintetico tramite cicloaddizioni 1,3-dipolari e riarrangiamento di Dimroth

Pyrrolo[2,3-h]quinolinones: synthesis and photochemotherapic activity.

A series of derivatives of the new ring system pyrrolo[2,3-h]quinoline-2-one was synthesized and evaluated as photoreagents toward cultured human tumor cells. Remarkable phototoxycity resulted for some derivatives, especially those bearing the phenyl group at the 7-position.

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives

The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mech…

In silico, spectroscopic, and biological insights on annelated pyrrolo[3,2-e]pyrimidines with antiproliferative activity

The in silico COMPARE analysis was performed on 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one, a compound with promising antiproliferative activity, previously synthetized and screened against a panel of 60 human tumor cell lines. The results evidenced that this compound matches the biological properties of Chromomycin A3 and Actinomycin D, known drugs with high DNA binding affinity. Prompted by such results, a thorough spectroscopic investigation of its DNA aqueous solutions was performed, with the aim to verify its DNA-binding properties. DNA groove-binding interaction was assigned by UV-vis spectrophotometri…

Double chained naphthalenes as G4 binders

DERIVATI TIENO[3,2-d]-1,2,3-TRIAZIN-4(3H)ONI ANELLATI:UNA NUOVA CLASSE DI INIBITORI DI AURORA CHINASI A

A QSAR study investigating the potential anti-HIV-1 effect of some acyclovir and ganciclovir analogs

A QSAR study, involving the use of calculated physical-chemical properties (TSAR TM ), and the use of a neural network approach (TSAR TM ), has been performed on the potential anti-HIV-1 activity of a series of Acyclovir and Ganciclovir analogs. Model obtained allows reliable predictions for the anti-HIV-1 activity of these derivatives, and showed that the presence of the Ganciclovir chain in triazolopyrrolopyrimidine and pyrimidopyrrolopyrimidine series seems to increase the antiviral effect.

Molecular Modelling on Leptin and the Ob Receptor as anti-obesity target

Obesity is a chronic pathology with multi-factorial aetiology, characterized by extreme body weight due to storing of fat in the adipose tissue, caused by an increase of caloric income, decrease of energetic intake, or both. The body weight control is a mechanism finely regulated by several hormonal, metabolic, and nervous pathways. Recessive homozygous mutations in the ob/ob and db/db mouse strain cause extreme obesity. The products of the ob and db genes are leptin and its receptor, respectively (1,2). The leptin receptor is critical for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream. Under normal circ…

Quinoline anticancer agents active on DNA and DNA-interacting proteins: From classical to emerging therapeutic targets.

Quinoline is one of the most important and versatile nitrogen heterocycles embodied in several biologically active molecules. Within the numerous quinolines developed as antiproliferative agents, this review is focused on compounds interfering with DNA structure or with proteins/enzymes involved in the regulation of double helix functional processes. In this light, a special focus is given to the quinoline compounds, acting with classical/well-known mechanisms of action (DNA intercalators or Topoisomerase inhibitors). In particular, the quinoline drugs amsacrine and camptothecin (CPT) have been studied as key lead compounds for the development of new agents with improved PK and tolerability…

Pyrrolo[2,1-d][1,2,3,5]tetrazine-4(3H)-ones, a new class of azolotetrazines with potent antitumor activity.

Pyrrolo[2,1-d][1,2,3,5]tetrazinones 10a-o, compounds that hold the deaza skeleton of the antitumor drug temozolomide, were prepared by reaction of 2-diazopyrroles 9 and isocyanates. Such a synthetic route represents, among those leading to azolotetrazinones reported so far, the only possible one since attempts to cyclize to the title ring system 2-amino-1-carbamoylpyrroles 11 or the mono substituted 2-triazenopyrrole 12 failed. Compounds 10 were screened at the National Cancer Institute (NCI) for their activity against a panel of about 60 human tumor cell lines. Most of them possess remarkable antineoplastic activity having GI(50) values in the low micromolar or sub-micromolar range and rea…

SYNTHESIS OF 3,5-BIS(3'-INDOLYL)PYRAZOLES, ANALOGUES OF NORTOPSENTIN

G4-DNA vs. B-DNA binding of Schiff base transition metal complexes

The competitive binding of nickel(II), copper(II) and zinc(II) complexes toward B- and G4-DNA was addressed through spectroscopic titrations and rationalized by computational investigations, consisting of molecular dynamics simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations [1]. The experimental DNA binding studies clearly highlight the selectivity of the compounds, in particular the nickel(II) complex, toward G4-DNA from both h-Telo and c-myc. Moreover, the compounds show biological activity against HeLa and MCF-7 cancer cell lines. Remarkably, the experimental DNA-binding affinity trend of the three metal complexes, obtained from the DNA-binding co…

Isoindolo[1,2-a]quinoxaline derivatives with potent antitumor activity.

New benzothieno[3,2-d]-1,2,3-triazines with antiproliferative activity: synthesis, spectroscopic studies, and biological activity.

New benzothieno[3,2-d]-1,2,3-triazines, together with precursors triazenylbenzo[b]thiophenes, were designed, synthesized and screened as anticancer agents. The structural features of these compounds prompted us to investigate their DNA binding capability through UV–vis absorption titrations, circular dichroism, and viscometry, pointing out the occurrence of groove-binding. The derivative 3-(4-methoxy-phenyl)benzothieno[3,2-d]-1,2,3-triazin-4(3H)-one showed the highest antiproliferative effect against HeLa cells and was also tested in cell cycle perturbation experiments. The obtained results assessed for the first time the anticancer activity of benzothieno[3,2-d]-1,2,3-triazine nucleus, and…

SYNTHESIS AND PHOTOCHEMIOTHERAPEUTIC ACTIVITY OF THIOPYRANO[2,3-E]INDOL-2-ONES

A series of derivatives of the new ring system thiopyrano[2,3-e]indol-2-one was prepared with the aim of obtaining new photochemotherapeutic drugs. Biological screenings were performed on this new class of photoactivable drugs and a strong antiproliferative effect was observed upon irradiation with UVA light. The compound bearing a methyl substituent at the pyrrole nitrogen resulted as the most interesting showing IC50 in the nanomolar range.

Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis

In this paper we describe a comparative analysis between multivariate and docking methods in the study of the drug resistance to the reverse transcriptase and the protease inhibitors. In our early papers we developed a simple but efficient method to evaluate the features of compounds that are less likely to trigger resistance or are effective against mutant HIV strains, using the multivariate statistical procedures PCA and DA. In the attempt to create a more solid background for the prediction of susceptibility or resistance, we carried out a comparative analysis between our previous multivariate approach and molecular docking study. The intent of this paper is not only to find further supp…

A synthetic approach to new polycyclic ring system of biological interest through domino reaction: indolo[2,3-e][1,2,3]triazolo[1,5-a]pyrimidine

Abstract The title indolo-triazolo-pyrimidines were obtained from 3-azidoindoles and can be used as models for the design of DNA-interactive compounds. Hetero-domino reaction of azidoindoles/pyrroles and acetonitriles constitutes the synthetic entry to annelated 1,2,3-triazolo[1,5- a ]pyrimidines.

Benzothieno-triazolo-pyrimidine: a new class of potential DNA-binders

Isoindolo[2,1-c]benzo[1,2,4]triazines: a new ring system with antiproliferative activity.

Abstract A series of isoindolo-benzo-triazines of type 4 was obtained by diazotization of 2-(2-aminoaryl)-1-cyanoisoindoles 3a – j . All the synthesized derivatives were screened by the National Cancer Institute (NCI, Bethesda, USA), for in vitro antitumor activity against a 3-human cancer cell line panel consisting of MCF7 (breast), NCI-H460 (lung), and SF-268 (CNS). Derivatives 4a , f , i , j were selected to be evaluated in the full panel of about 50 human tumor cell lines derived from nine human cancer cell types and showed antiproliferative activity generally in the micromolar range. The most sensitive cell lines were: MOLT-4 and SR of the leukemia subpanel, A549/ATCC and EKVX of the n…

New annelated thieno[2,3-e][1,2,3]triazolo[1,5-a]pyrimidines, with potent anticancer activity, designed through VLAK protocol

Drug design was performed through the Virtual Lock-and-Key (VLAK) protocol. This in silico approach allowed to select new annelated thienotriazolopyrimidine derivatives, potentially antitumor drugs. Starting from benzothieno[2,3-e][1,2,3]triazolo[1,5-a]pyrimidine and Pyrido[3',2':4,5]thieno[2,3-e][1,2,3]triazolo[1,5-a]pyrimidine core structures, new derivatives of these nuclei were designed and synthesized. Three of them were selected by the Development Therapeutical Program (DTP) of the National Cancer Institute (NCI) for the anticancer screening against a panel of 60 human tumor cell lines. The biological results showed that the new derivatives exhibited an excellent antiproliferative act…

Design, synthesis, and biological evaluation of a new class of benzo[b]furan derivatives as antiproliferative agents, with in silico predicted antitubulin activity

A new series of 3-benzoylamino-5-(1H-imidazol-4-yl)methylaminobenzo[b]furans were synthesized and screened as antitumor agents. As a general trend, tested compounds showed concentration-dependent antiproliferative activity against HeLa and MCF-7 cancer cell lines, exhibiting GI50 values in the low micromolar range. In most cases, insertion of a methyl substituent on the imidazole moiety improved the antiproliferative activity. Therefore, methyl-imidazolyl-benzo[b]furans compounds were tested in cell cycle perturbation experiments, producing cell cycle arrest with proapoptotic effects. Their core similarity to known colchicine binding site binders led us to further study the structure featur…

SELECTIVE G-QUADRUPLEX STABILIZERS: SALPHEN-LIKE COMPLEXES WITH ANTIPROLIFERATIVE ACTIVITY

Schiff base complexes derived from N,N!-bridged tetradentate ligands involving N2O2 donor atoms present very favourable features to act as G4 binders. Thus, a series of square-planar and square pyramidal metal complexes, ML2+ (M = Ni, Cu, and Zn), have been synthesized and characterized.

The discovery of new inhibitors of HIF-1 transcriptional activity by virtual screening

Nuovi derivati 3,5-diaril-4,5-diidropirazolici come inibitori di HSP90

Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target.

Body weight control is a mechanism finely regulated by several hormonal, metabolic, and nervous pathways. The leptin receptor (Ob-R) is crucial for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream, and under normal circumstances, circulating levels are proportionate to the fat body mass. Sensing of elevated leptin levels by the hypothalamic neurocircutry activates a negative feedback loop resulting in reduced food intake and increased energy expenditure. Decreased concentrations lead to opposite effects. Therefore rational design of leptin agonists constitute an appealing challenge in the battle against ob…

Hsp60, a Novel Target for Antitumor Therapy: Structure-Function Features and Prospective Drugs Design

Heat shock protein 60 kDa (Hsp60) is a chaperone classically believed to be involved in assisting the correct folding of other mitochondrial proteins. Hsp60 also plays a role in cytoprotection against cell stressors, displaying for example, antiapoptotic potential. Despite the plethora of studies devoted to the mechanism of Hsp60's function, especially in prokaryotes, fundamental issues still remain unexplored, including the definition of its role in cancer. Key questions still unanswered pertain to the differences in structure-function features that might exist between the well-studied prokaryotic GroEL and the largely unexplored eukaryotic Hsp60 proteins. In this article we discuss these …

Sintesi di Oligopeptidi Pirrolici Isomeri della Distamicina e della Netropsina

Kinase Inhibitors in Multitargeted Cancer Therapy

The old-fashioned anticancer approaches, aiming in arresting cancer cell proliferation interfering with non-specific targets (e.g. DNA), have been replaced, in the last decades, by more specific target oriented ones. Nonetheless, single-target approaches have not always led to optimal outcomes because, for its complexity, cancer needs to be tackled at various levels by modulation of several targets. Although at present, combinations of individual single-target drugs represent the most clinically practiced therapeutic approaches, the modulation of multiple proteins by a single drug, in accordance with the polypharmacological strategy, has become more and more appealing. In the perspective of…

Identification of an LPS-Induced Chemo-Attractive Peptide from Ciona robusta

Background: Previously published work has demonstrated that the LPS injection of Ciona robusta leads to the overexpression of a truncated form of an immune-related mRNA (C8short) by means of Ciona robusta (CR) alternative polyadenylation (APA) (CR-APA). Methods: The 3D structure of the C8short-derived Ciona robusta chemo-attractive peptide (CrCP) was evaluated by homology modeling. The biological activity of the CrCP was studied in vitro using a primary human dermal cell line (HuDe). Real-Time PCR was used to investigate the expression levels of genes involved in cell motility. NF-&kappa

Sintesi di derivati triazolo-chinossalinici e triazolo-pirrolopirazinici di interesse farmaceutico mediante cicloaddizioni 1,3-dipolari

IN THE SEARCH OF LEPTIN AGONISTS AS ANTI-OBESITY DRUGS: PROTEIN/PROTEIN DOCKING, MOLECULAR DYNAMICS, AND VIRTUAL SCREENING

The body weight control is a mechanism thinly regulated by several hormonal, metabolic, and nervous pathways (1). Recessive homozygous mutations in the ob/ob and db/db mouse strain cause extreme obesity. The products of the ob and db genes are leptin and its receptor, respectively. The leptin receptor is crucial for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream. Under normal circumstances, circulating leptin levels are proportionate to the fat body mass. Sensing of elevated leptin levels by the hypothalamic neurocircutry activates a negative feedback loop resulting in reduced food intake and increased e…

Studi di Docking su Isomeri della Distamicina e della Netropsina

Design and synthesis of high affinity compounds for the Hsp60 expression control in carcinogenic processes

First observed in cells exposed to high temperatures, Heat shock proteins (Hsps) are nowadays considered the most important cell “chaperone” complexes over-­expressed in response to a number of cell stress stimuli.1 The chaperone activity is the main function of the eukaryotic Heat shock protein 60 kDa (Hsp60), involved in the capture and refold of unfolded or misfolded proteins. Additional roles in signal transduction,2 senescence activation3 and apoptosis4 have been ascribed to cytosolic Hsp60. During the carcinogenIc process, in vivo studies demonstrated increased levels of human Hsp60 in several organs, such as uterine exocervix,5 large bowel,6 and prostate.6 In this context, our study …

In Silico Design of New Dual Inhibitors of SARS-CoV-2 MPRO through Ligand- and Structure-Based Methods

The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series’ of small molecules with a significant affinity for SARS-CoV-2 MPRO, by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The B…

IKK-β inhibitors: An analysis of drug–receptor interaction by using Molecular Docking and Pharmacophore 3D-QSAR approaches

Abstract The IKK kinases family represents a thrilling area of research because of its importance in regulating the activity of NF-kB transcription factors. The discovery of the central role played by IKK-β in the activation of transcription in response to apoptotic or inflammatory stimuli allowed to considerate its modulation as a promising tool for the treatment of chronic inflammation and cancer. To date, several IKK-β inhibitors have been discovered and tested. In this work, an analysis of the interactions between different classes of inhibitors and their biological target was performed, through the application of Molecular Docking and Pharmacophore/3D-QSAR approaches to a set of 141 in…

Molecular dynamics studies on Mdm2 complexes: An analysis of the inhibitor influence

p53 is a powerful anti-tumoral molecule frequently inactivated by mutations or deletions in cancer. However, half of all human tumors expresses wild-type p53, and its activation, by antagonizing its negative regulator Mdm2, might offer a new strategy for therapeutic protocol. In this work, we present a molecular dynamics study on Mdm2 structure bound to two different known inhibitors with the aim to investigate the structural transitions between apo-Mdm2 and Mdm2-inhibitor complexes. We tried to gain information about conformational changes binding a benzodiazepine derivative inhibitor with respect the known nutlin and the apo form. The conformational changes alter the size of the cleft and…

SYNTHESIS AND EVALUATION OF CURCUMIN ANALOGUES AS NEURO-PROTECTIVE AGENTS FOR THE ALZHEIMER'S DISEASE

The Alzheimer's disease (AD) is the most common form of senile dementia.1 The most important role in AD is played by the aggregation process of beta-amyloid peptide (Aß), responsible for the cytotoxic effects.2 In this context, the purpose of this study was to synthesize new dicarbonyl compounds 1 structurally related to curcumin3, with anti-aggregation activity against Aß.Parallel studies involve the synthesis of heterocyclic-based curcumin-like molecules that are currently under investigation by means of in silico protocols in order to rationalize the ligand-biological target interactions.

Receptor-guided 3D-QSAR approach for the discovery of c-kit tyrosine kinase inhibitors

Studies of the the three-dimensional quantitative structure–activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a co-crystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to validate the selected pharmacophore model. The best pharmacophore model consisted of five features: one hydrogen-bond donor and four aromatic rings. Reliable statistics were obtained (R 2 = 0.95, R pred 2  = 0.75), and the model was validated by using it to select c-kit inhibitors from a database; 82.1% of the hits it retrieved were active. Accordingly, our model can be reliably u…

The Repurposing of Old Drugs or Unsuccessful Lead Compounds by in Silico Approaches: New Advances and Perspectives

Have you a compound in your lab, which was not successful against the designed target, or a drug that is no more attractive? The drug repurposing represents the right way to reconsider them. It can be defined as the modern and rationale approach of the traditional methods adopted in drug discovery, based on the knowledge, insight and luck, alias known as serendipity. This repurposing approach can be applied both in silico and in wet. In this review we report the molecular modeling facilities that can be of huge support in the repurposing of drugs and/or unsuccessful lead compounds. In the last decades, different methods were proposed to help the scientists in drug design and in drug repurpo…

Sintesi ed Attivita’ Fotobiologica di Tiopirano[2,3-c]indol-2-oni

2,5-BIS(3'-INDOLYL)THIOPHENES, ANALOGUES OF MARINE ALKALOID NORTOPSENTIN

Pyrimido[5,4-c]pyrrolo[2,1-a]isoquinoline: a new potential DNA-interactive ring system

The acid catalyzed decomposition of the azide 9 failed to give the title compounds, which were however obtained by a Pschorr-type cyclization on reactive 1-(6-aminopyrimidin-5-yl)-pyrroles of type 13. Derivatives of type 14 and 15 were fully characterized by NMR data. Theoretical calculations demonstrated that the new compounds possess properties suitable for DNA- intercalation.

Study on the mechanism of action of antitumor photochemotherapic agents by means of docking and QSPR analysis

Synthesis, antiproliferative activity, and in silico insights of new 3-benzoylamino-benzo[ b ]thiophene derivatives

A new series of 3-benzoylamino-5-imidazol-5-yl-benzo[b]thiophenes and the parent amino derivatives were synthesized and screened as antitumor agents. All tested compounds showed concentration-dependent antiproliferative activity profile against HeLa cell line, exhibiting GI50 values in the low micromolar range. The most active compounds were tested in cell cycle perturbation experiments. A rapid accumulation of cells in the G2/M phase, with a concomitant reduction of cells in both the S and G0/G1 phases, was observed, suggesting that cell exposure to selected derivatives produces mitotic failure. To rationalize the biological results, the 3-benzoylamino-benzo[b]thiophenes were analyzed thro…

The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors

AbstractThe maturation of coronavirus SARS-CoV-2, which is the etiological agent at the origin of the COVID-19 pandemic, requires a main protease Mpro to cleave the virus-encoded polyproteins. Despite a wealth of experimental information already available, there is wide disagreement about the Mpro monomer-dimer equilibrium dissociation constant. Since the functional unit of Mpro is a homodimer, the detailed knowledge of the thermodynamics of this equilibrium is a key piece of information for possible therapeutic intervention, with small molecules interfering with dimerization being potential broad-spectrum antiviral drug leads. In the present study, we exploit Small Angle X-ray Scattering (…

Pyrrolo[2,1-d][1,2,3,5]tetrazinones deaza analogues of temozolomide with potent antitumor activity

The title compounds, that hold the deaza skeleton of temozolomide, exhibited potent in vitro antiproliferative activity. An evaluation of such a biological activity indicates that the mode of action of these compounds differs from that of temozolomide and is also mechanistically unrelated to that of any known antitumor drug.

A Multivariate Analysis of HIV-1 Protease Inhibitors and Resistance Induced by Mutation

This paper describes the use of the multivariate statistical procedure principal component analysis as a tool to explore the inhibitory activity of classes of protease inhibitors (PIs) against HIV-1 viruses (wild type and more-frequent single mutants, V82A, V82F, and I84V) and against protease enzymes. The analysis of correlations between biological activity and molecular descriptors or similarity indexes allowed a reliable classification of the 51 derivatives considered in this study. The best results were obtained in the case of the I84V mutant for which a high number of predictions was achieved. On this basis, this statistical approach is proposed as a reliable method for the prediction …

New Tricyclic System of Biological Interest Thieno[3,2-e][1,2,3]triazolo[1,5-a]pyrimidine Trough Domino Reactions of 2-Azidothiophene.

An unexpected Dimroth rearrangement leading to annelated thieno[3,2-d][1,2,3]triazolo[1,5-a]pyrimidines with potent antitumor activity.

An unusual Dimroth rearrangement occurring in the reaction leading to annelated thieno[2,3-e][1,2,3]triazolo[1,5-a]pyrimidine core allowed the isolation of the linear isomer thieno[3,2-d][1,2,3]triazolo[1,5-a]pyrimidine. By decorating the linear isomer with the same chains that improved the biological activity of the angular isomers, new annelated thieno[3,2-d][1,2,3]triazolo[1,5-a]pyrimidines were designed and synthesized. They were selected by the Developmental Therapeutics Program (DTP) of the National Cancer Institute (NCI) for the anticancer screening against a panel of 60 human tumor cell lines. The biological results showed that the new derivatives exhibited strong antiproliferative …

Leptin and the OB-receptor as anti-obesity target: recent in silico advances in the comprehension of the protein-protein interaction and rational drug design of anti- obesity lead compounds.

The OB-receptor or leptin receptor (LR) is crucial for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream. Under normal circumstances, circulating leptin levels are proportionate to the fat body mass. Sensing of elevated leptin levels by the hypothalamic neuro-circuitry activates a negative feedback loop resulting in reduced food intake and increased energy expenditure. Decreased leptin concentrations lead to opposite effects. Therefore, rational design of leptin agonists/antagonists could be an appealing challenge in the battle against obesity. The Leptin/LR interactions have been studied in several works b…

Synthesis and biological activities of a new class of heat shock protein 90 inhibitors, designed by energy-based pharmacophore virtual screening

The design through energy-based pharmacophore virtual screening has led to aminocyanopyridine derivatives as efficacious new inhibitors of Hsp90. The synthesized compounds showed a good affinity for the Hsp90 ATP binding site in the competitive binding assay. Moreover, they showed an excellent antiproliferative activity against a large number of human tumor cell lines. Further biological studies on the derivative with the higher EC50 confirmed its specific influence on the cellular pathways involving Hsp90.

In Silico Insights into the SARS CoV-2 Main Protease Suggest NADH Endogenous Defences in the Control of the Pandemic Coronavirus Infection

COVID-19 is a pandemic health emergency faced by the entire world. The clinical treatment of the severe acute respiratory syndrome (SARS) CoV-2 is currently based on the experimental administration of HIV antiviral drugs, such as lopinavir, ritonavir, and remdesivir (a nucleotide analogue used for Ebola infection). This work proposes a repurposing process using a database containing approximately 8000 known drugs in synergy structure- and ligand-based studies by means of the molecular docking and descriptor-based protocol. The proposed in silico findings identified new potential SARS CoV-2 main protease (MPRO) inhibitors that fit in the catalytic binding site of SARS CoV-2 MPRO. Several sel…

Isoindolo[2,1-c]benzo[1,2,4]triazine: a New Ring System with Potential Antitumor Activity

Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant

The emergence of drug-resistant mutants of HIV-1 is a tragic effect associated with conventional long-treatment therapies against acquired immunodeficiency syndrome. These mutations frequently involve the aspartic protease encoded by the virus; knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lasting treatment regimes. The flap regions of the protease are the target of a particular type of mutations occurring far from the active site. These mutations modify the affinity for both substrate and ligands, thus conferring resistance. In this work, molecular dynamics simulations were perform…

NCI Anti-cancer agent mechanism database. An analysis by the combined use of molecular docking and QSPR

The interaction of Schiff Base complexes of nickel(II) and zinc(II) with duplex and G-quadruplex DNA

The duplex and G-quadruplex DNA-binding of six nickel(II) and zinc(II) complexes of three salphen-like ligands (salphen = N,N?-bis-salicylidene-1,2-phenylenediaminato) was investigated by UV-visible absorption and circular dichroism spectroscopy. The results obtained, in particular the values of the DNA-binding constants, Kb, point out that the nickel(II) complexes show a higher affinity toward both duplex and G-quadruplex DNA, compared to the analogous zinc(II) complexes. Interestingly, the zinc(II) complexes possess high selectivity toward G-quadruplex DNA, being negligible their binding with duplex DNA. Molecular dynamics (MD) simulations provided atomistic models for the interpretation …

Bioactive triterpenes of protium heptaphyllum gum resin extract display cholesterol-lowering potential

Hypercholesterolemia is one of the major causes of cardiovascular disease, the risk of which is further increased if other forms of dyslipidemia occur. Current therapeutic strategies include changes in lifestyle coupled with drug administration. Statins represent the most common therapeutic approach, but they may be insufficient due to the onset of resistance mechanisms and side effects. Consequently, patients with mild hypercholesterolemia prefer the use of food supplements since these are perceived to be safer. Here, we investigate the phytochemical profile and cholesterol-lowering potential of Protium heptaphyllum gum resin extract (PHE). Chemical characterization via HPLC-APCI-HRMS2 and…

Virtual lock-and-key approach: The in silico revival of Fischer model by means of molecular descriptors

Abstract In the last years the application of computational methodologies in the medicinal chemistry fields has found an amazing development. All the efforts were focused on the searching of new leads featuring a close affinity on a specific biological target. Thus, different molecular modeling approaches in simulation of molecular behavior for a specific biological target were employed. In spite of the increasing reliability of computational methodologies, not always the designed lead, once synthesized and screened, are suitable for the chosen biological target. To give another chance to these compounds, this work tries to resume the old concept of Fischer lock-and-key model. The same can …

DA-Phen, a new dopamine aminoacid conjugate: in vivo testing and molecular modeling as dopaminergic modulator

Antiproliferative properties and g-quadruplex-binding of symmetrical naphtho[1,2-b:8,7-b’]dithiophene derivatives

Background: G-quadruplex (G4) forming sequences are recurrent in telomeres and promoter regions of several protooncogenes. In normal cells, the transient arrangements of DNA in G-tetrads may regulate replication, transcription, and translation processes. Tumors are characterized by uncontrolled cell growth and tissue invasiveness and some of them are possibly mediated by gene expression involving G-quadruplexes. The stabilization of G-quadruplex sequences with small molecules is considered a promising strategy in anticancer targeted therapy. Methods: Molecular virtual screening allowed us identifying novel symmetric bifunctionalized naphtho[1,2-b:8,7-b’]dithiophene ligands as interesting ca…

PROGETTAZIONE, SINTESI E VALUTAZIONE BIOLOGICA DI NUOVI INIBITORI DI HSP90

The influence of substitution in the quinoxaline nucleus on 1,3-dipolar cycloaddition reactions: A DFT study

Abstract The reaction mechanism of 1,3-dipolar cycloadditions of both symmetric and unsymmetric benzo-condensed diazines with a nitrilimine dipole, to give two different mono- and bis-cycloadducts, in tetrahydrofuran (THF) solution, was studied by DFT calculations. The results obtained show that each 1,3-dipolar cycloaddition reaction always proceeds by a two steps mechanism, in which the first intermediate shows only one covalent bond between the beta carbon of the nitrilimine and the aromatic nitrogen of the diazine molecule. The structure and energy content of the two transition states of the two cycloaddition steps, in the case of the unsymmetric benzo-condensed diazine, nicely explains…

STUDIO DELL'INTERAZIONE DI DNA-NATIVO CON Zn(3-ACETIL-1-(2-NITROFENIL)PENTAN-1,4-DIONATO)2

New Tetracyclic Ring System of Biological Interest Indolo[3,2-e][1,2,3]triazolo[1,5-a]pyrimidine through domino reactions of 2-azidoindole

Studi di Molecular Modelling su Derivati del Nuovo Sistema Eterociclico DNA-interattivo Isoindolo[2,1-c]benzo[1,2,4]triazina

ChemInform Abstract: Pyrrolo[3,4-e][1,2,3]triazolo[1,5-a]pyrimidine and Pyrrolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine. New Tricyclic Ring Systems of Biological Interest.

Derivatives of the new ring system pyrrolo[3,4-e][1,2,3] triazolo[1,5-a]pyrimidine 6 were prepared in high yields in one step by reaction of 3-azidopyrrole 3 and substituted acetonitriles. Compound 6b rearranged, upon heating in dimethyl sulfoxide in the presence of water, to pyrrolo[3,4-d][1,2,3]triazolo-[1,5-a]pyrimidine 7.

Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity

The affinity of three square-planar nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff-base complexes for wild-type human telomeric (h-Telo) and protooncogene c-myc G-quadruplex (G4) DNA was investigated by UV-visible absorption spectroscopy and circular dichroism. DNA-binding constants (Kb) were determined by spectrophotometric titrations for both G4-DNA and B-DNA. The results obtained point out that the three metal complexes selectively bind G4-DNA with higher affinity, up to two orders of magnitude, with respect to B-DNA. The nickel(II) complex 1 was found to be the most effective G4-DNA stabilizer and the Kb values decrease in the order 1 > 2 ≈ 3. Innovative computational investigat…

2-OXO-[1,4]OXAZINO[3,2-E]INDOLE: A NEW RING SYSTEM WITH POTENTIAL PHOTOBIOLOGICAL PROPERTIES

Reactivity of asymmetric benzo-condensed diazines with nitrilimine dipoles in the 1,3-dipolar cycloaddition reactions

The reactivity of asymmetric benzo-condensed diazines in the 1,3-dipolar cycloaddition reactions with nitrilimines was investigated. The results demonstrated that, at variance with the symmetric quinoxaline, a certain grade of diastereoselectivity emerged. Moreover in the case of the 5-methylquinoxaline and quinazoline a mono-cycloadduct was obtained.

Bcl-2 come target di farmaci antitumorali modulatori dell'apoptosi

Lead optimization through VLAK protocol: New annelated pyrrolo-pyrimidine derivatives as antitumor agents

Abstract The chemometric protocol VLAK was applied to predict improvement of the biological activity of pyrrolo-pyrimidine derivatives as anticancer agents, by using the NCI ACAM Database as depository of antitumor drugs with a known mechanism of action. Among the selected compounds two of these showed a good increase in the antitumor activity. These new pyrrolo-pyrimidine compounds were demonstrated effective against the full panels of NCI DTP tumour human cell lines. The derivative 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one reveled efficacious against the leukemia subpanel, in particular the RPMI cell line…

1,2-Dihydropyrazole[1,2-a]benzo[1,2,4]triazine-3-one: deaza analogue tricyclic scaffold with valuable antiproliferative activity

MOLECULAR DYNAMICS AND DOCKING IN THE STUDY OF NEW INHIBITORS OF MDM2-p53 INTERACTION

In-silico screening of new potential Bcl-2/Bcl-xl inhibitors as apoptosis modulators

One of the major problems in the fight against cancer is drug-resistance, which, at a molecular level, can be acquired through mutations able to deactivate apoptosis. In particular, proteins in the Bcl-2 family are central regulators of programmed cell death, and members that inhibit apoptosis, such as Bcl-xl and Bcl-2, are overexpressed in many tumours. The development of new inhibitors of these proteins as potential anticancer therapeutics represents a new frontier. In this work, we carried out an in-silico screening of compounds from a free database of more than 2 million structures (ZINC database), which allowed us to identify 17 sulfonamide derivatives as new potential inhibitors; thes…

Phytochemical profile and antioxidant properties of the edible and non-edible portions of black sapote (Diospyros digyna Jacq.)

This study evaluated the phytochemical profile and antioxidative properties of the edible and non-edible portions of black sapote. The phytochemical analysis highlighted the presence of several bioactive compounds, differently distributed among peel, pulp and seeds. In particular, the peel resulted rich of flavan-3-ols and proanthocyanidins, whereas seeds contained high amount of organic acids, including ferulic, citric and sinapic acids. Concerning functional properties, both edible and non-edible portions showed a significant prevention of lipid peroxidation in a cell-based model. Moreover, the results suggested that the antioxidant protection involved both redox active properties and gen…

HIV-1 Protease Inhibitors and Resistance Induced by Mutation. Correlation between Multivariate Analysis and Molecular Docking.

Inside c-kit tyrosine kinase: molecular modeling and QSAR in the search of new inhibitors

Protective effects of melatonin in inflamed intestinal epithelium are associated with reduced NF-κB activation and changes in DNA methylation status

Melatonin is the main product of the pineal gland but is also released in the gastrointestinal tract (GIT). Production of melatonin at GIT is independent of the photoperiod and contributes almost completely to plasma melatonin concentration during daylight hours. The physiological role of melatonin at GIT is poorly characterized but recently anti-inflammatory effects have been reported. In this study, we evaluated the effect of Melatonin in intestinal epithelial cells (IEC) stimulated by Interleukin-1β. Our results clearly show that melatonin at micromolar concentrations inhibits the inflammatory response in IEC. The protective effect is expressed through a marked decrease in release and ex…

Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors

The approval of the first HIV-1 protease inhibitors (HIV-1 PRIs) marked a fundamental step in the control of AIDS, and this class of agents still represents the mainstay therapy for this illness. Despite the undisputed benefits, the necessary lifelong treatment led to numerous severe side-effects (metabolic syndrome, hepatotoxicity, diabetes, etc.). The HIV-1 PRIs are capable of interacting with “secondary” targets (off-targets) characterized by different biological activities from that of HIV-1 protease. In this scenario, the in-silico techniques undoubtedly contributed to the design of new small molecules with well-fitting selectivity against the main target, analyzing possible undesirabl…

ChemInform Abstract: Pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine: A New Ring System Through Dimroth Rearrangement.

Abstract Derivatives of the new ring system pyrazolo[3,4- d ][1,2,3]triazolo[1,5- a ]pyrimidine were synthesized from the corresponding angular isomers, through a Dimroth rearrangement, in quantitative yields. Preliminary computational studies demonstrated that this class of compounds could be a good candidate as DNA intercalating agents.

Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation

We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-d…

Synthesis and antiproliferative activity of [1,2,3,5]tetrazino[5,4-a]indoles, a new class of azolo-tetrazinones.

Eight derivatives of the new ring system [1,2,3,5]tetrazino[5,4-a]indole-4-one 7, were synthesised in good yields by reaction of 2-diazoindoles with alkyl or aryl isocyanates. Compounds 7 were screened at National Cancer Institute (NCI) for their activity against a panel of approximately 60 human tumour cell lines. Some of them showed antiproliferative activity having generally GI50 in the micromolar range. The most sensitive cell lines were SF-295, SNB-75 and SF-539 of the CNS cancer sub-panel, SR of the leukaemia sub-panel, UACC-62 of the melanoma sub-panel and OVCAR-4 of the ovarian cancer sub-panel. 2004 Elsevier Ltd. All rights reserved.

NiII, and ZnII Schiff Base Complexes: Telomeric G-quadruplex Stabilizers

Recently, NiII and ZnII metal complexes of the ligand Salpyrim have been synthesized and characterized. Their affinity for wild-type h-Telo G-quadruplex DNA and for calf thymus DNA was investigated by UV absorption spectroscopy, circular dichroism and viscometry. The data collectively suggest that both complexes bind effectively to G-quadruplexes by direct end-stacking, stabilizing the oligonucleotide secondary structure. The two complexes are also typical B-DNA intercalators. Remarkably, their binding constants, Kb, with the G4s structures are about 10 fold higher than those with B-DNA, highlighting the selectivity. Experiments to evaluate the biological activity of the two complexes again…

Sintesi di Nuovi Derivati del Sistema Triciclico Pirazolo[3,4-d][1,2,3]triazolo[1,5-a]pirimidinico DNA interattivi

Combined use of PCA and QSAR/QSPR to predict the drugs mechanism of action. An application to the NCI ACAM Database

During the years the National Cancer Institute (NCI) accumulated an enormous amount of information through the application of a complex protocol of drugs screening involving several tumor cell lines, grouped into panels according to the disease class. The Anti-cancer Agent Mechanism (ACAM) database is a set of 122 compounds with anti-cancer activity and a reasonably well known mechanism of action, for which are available drug screening data that measure their ability to inhibit growth of a panel of 60 human tumor lines, explicitly designed as a training set for neural network and multivariate analysis. The aim of this work is to adapt a methodology (previously developed for the analysis of …

Antiproliferative activity of Pyrrolo[3,2-c]quinoline derivatives

The pyrrolo[3,2-c]quinoline scaffold has been known as a core structure of a wide number of bioactive molecules. Several derivatives of such a tricyclic angular heterocycle have shown a wide spectrum of biological activities, such as hypotensive, anti-inflammatory properties, gastric (H)ATPase inhibition effect, and remarkable antitumor activity (1). The high therapeutic potentiality of such a skeleton along with our interest in targets featuring aza-polycondensed aromatic structures, attracted us to develop an alternative synthetic strategy, in order to reach a series of pyrrolo[3,2-c]quinolines in quantitative yields (2). The reaction of 3-acetyl-1,4-dione 1 with selected amines allowed th…

Multivariate analysis in the identification of biological targets for designed molecular structures: The BIOTA protocol

In this work the new protocol BIOlogical Target Assignation (BIOTA) for the prediction of the biological target from molecular structures is proposed. BIOTA is based on the Principal Components Analysis (PCA) application on a matrix of ligands versus molecular descriptors. The application of BIOTA could allow to hypothesize the mechanism of action of a candidate drug prior to its biological evaluation or to repurpose old drugs. The protocol can be fine-tuned by choosing opportune targets (biological or not) and molecular descriptors, and it can be useful in every fields in with it is possible to collect set of compounds with known properties. The robustness of the protocol depends from diff…

In House Methodology to Assign the Mechanism of Action of New Annelated Triazolopyrimidine Derivatives with Anticancer Activity

Principal Component Analysis (PCA) of the Solubility

PCA and QSAR/QSPR used in combination to predict the drugs mechanism of action. An application to the NCI ACAM Database

Zinc complexes as fluorescent chemosensors for nucleic acids: new perspectives for a “boring” element

Zinc(ii) complexes are effective and selective nucleic acid-binders and strongly fluorescent molecules in the low energy range, from the visible to the near infrared. These two properties have often been exploited to quantitatively detect nucleic acids in biological samples, in both in vitro and in vivo models. In particular, the fluorescent emission of several zinc(ii) complexes is drastically enhanced or quenched by the binding to nucleic acids and/or upon visible light exposure, in a different fashion in bulk solution and when bound to DNA. The twofold objective of this perspective is (1) to review recent utilisations of zinc(ii) complexes as selective fluorescent probes for nucleic acid…

Exploring the anticancer potential of pyrazolo[1,2-a]benzo[1,2,3,4] tetrazin-3-one derivatives: The effect on apoptosis induction, cell cycle and proliferation

In order to investigate their anticancer potential, four new pyrazolo[1,2-a]benzo[1,2,3,4]-tetrazinone derivatives, designed through the chemometric protocol VLAK, and three of the most active compounds of the previous series have been evaluated on some cellular events including proliferation, apoptosis induction, and cell cycle. The NCI one dose (10 mu M) screening revealed that the 8,9-di-methyl derivative showed activity against Leukemia (CCRF-CEM) and Colon cancer cell line (COLO 205), reaching 81% and 45% of growth inhibition (GI), respectively. Replacement of the two methyl groups with two chlorine atoms maintained the activity toward Leukemia cell (CCRF-CEM, GI 77%) and selectively e…

Molecular modelling and QSAR in the discovery of HIV-1 integrase inhibitors

The treatment regimens for the HIV-1 have mainly included reverse transcriptase or protease inhibitors but their long-term clinical utility is limited by severe side effects and viral drug resistance. A new attractive target for chemotherapeutic intervention can be the Integrase enzyme, that mediates the integration of HIV-1 DNA into a host chromosome, for which there is no known counterparts in the host cell. A number of derivatives have been found to inhibit IN in in vitro assays, but no successful drug based on them has emerged so far, although many compounds have been proposed. Moreover most of the inhibitors do not belong to a very precise structural class: this fact makes these compou…

DNA-binding of nickel(II), copper(II) and zinc(II) complexes: structure-affinity relationships

Abstract Nickel(II), copper(II) and zinc(II) complexes with the same ligands normally display analogous coordination geometry and binding mode toward DNA. However, although qualitatively alike in structure and properties, different DNA-binding ability has often been observed. This review surveys the most recent examples of binding of the three metal ions complexed with monodentate and chelating bidentate to tetradentate ligands to DNA. An attempt has also been made to rationalize the observed trend in the values of the intrinsic DNA-binding constant, Kb, in terms of structural and chemical features.

In vitro and in silico studies of polycondensed diazine systems as anti-infective agents

Infective diseases caused by protozoarian agents are still relevant today more than ever. In fact, they represent the first cause of death all over the world with seventeen millions victims every year. The development of drug resistance and the broad diffusion of these pathologies make actual the research of new molecules able to act as selective and effective anti-infective chemotherapics.[1] Recently several polycondensed diazine derivatives, by means 1,3-dipolar cycloaddition, reactions [2, 3] were synthesized. A broad selection of these compounds chosen with a wide pattern of substitutions were submitted to biological in vitro screening against Plasmodium falciparum, Leishmania Infantum…

1-methil-3H-pyrazolo[1-2-a]benzo[1-2-3-4]tetrazin-3-ones, design synthesis and biological activity of new antitumoral agents

1-Methylpyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-ones 4, synthesized in good to excellent yields, were designed as novel alkylating agents because of their peculiar chemical behavior. All derivatives showed antiproliferative activity against more than 50 types of tumor cell lines with GI50 reaching sub-micromolar values. SAR studies revealed that the presence of a chlorine atom is well-tolerated in both positions 8 and 9, whereas in the case of the methyl group, switching from the 8 to the 9 position gives rise to the most active compound of the series, 4g, either for the number of cell lines inhibited and for selectivity against leukaemia and renal cancer subpanels. COMPARE and 3D-MIND comp…

Pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine: a new ring system through Dimroth rearrangement

Abstract Derivatives of the new ring system pyrazolo[3,4- d ][1,2,3]triazolo[1,5- a ]pyrimidine were synthesized from the corresponding angular isomers, through a Dimroth rearrangement, in quantitative yields. Preliminary computational studies demonstrated that this class of compounds could be a good candidate as DNA intercalating agents.

3D-QSAR pharmacophore modeling and in silico screening of new Bcl-xl inhibitors.

Bcl-2 proteins family members play several roles in tumoral proliferation: they inhibit proapoptotic activity during oncogenesis, support tumor cells survival, induce chemoresistance. The discovery of new small inhibitors of Bcl-xl represents a new frontier for cancer treatment. In this study, a 3D-QSAR pharmacophore model was developed, based on 42 biarylacylsulfonamides, and used to understand the structural factors affecting the inhibitory potency of these derivatives. Aromatic, negative charge, and hydrogen bond acceptor effects contribute to the inhibitory activity. The model was then employed as 3D search query to screen ZINC drug-like database in order to select new scaffolds. Finall…

Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug

We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalater daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is c…

Pharmacophore modeling e screening in silico di nuovi inibitori della proteina antiapoptotica Bcl-xl

DNA-Binding of NiII, CuII and ZnII Complexes of Salen Derivatives

Nickel(II), copper(II) and zinc(II) complexes of N2O2 tetradentate Schiff base ligands strongly interact with B-DNA, usually by groove-binding and/or by intercalation [1]. It has been also shown that the presence of aromatic substituents on the N,N’ bridge make them suitable G-quadruplex binders [2]. In this context, we have recently investigated the binding toward duplex and G-quadruplex DNA of nickel(II), copper(II) and zinc(II) complexes of N,N’-bis-5-(triethyl ammonium methyl)-salicylidene-2,3-naphthalendiiminato) (see Figure), by spectroscopic and computational methods [3,4]. The compounds show also biological activity against human cancer cell lines. Different substituents are present…

1,3-Dipolar cycloadditions in the synthesis of annelated diazines: design of new scaffolds for anticancer and antimicrobial agents

Study of the role of “gatekeeper” mutations V654A and T670I of c-kit kinase in the interaction with inhibitors by means mixed molecular dynamics/docking approach

The over-expression of c-kit proto-oncogene has been reported in hematopoietic cells, small cell lung cancer, and gastrointestinal stromal tumors. The clinical importance of c-kit expression in tumors focused the research towards inhibitors of this tyrosine kinase. Imatinib (Gleevec®) was the first compound used in therapy, but mutations on c-kit led to reduced effectiveness or ineffectiveness of this treatment. Other compounds are likely to be effective against mutants, such as Sunitinib (Sutent®), but the need for new and most effective inhibitors against mutants is still critical. We report mixed Molecular Dynamics/Docking study with the aim to unveil the molecular mechanism involved in …

Theoretical Determination of the pK a Values of Betalamic Acid Related to the Free Radical Scavenger Capacity: Comparison Between Empirical and Quantum Chemical Methods

Health benefits of dietary phytochemicals have been suggested in recent years. Among 1000s of different compounds, Betalains, which occur in vegetables of the Cariophyllalae order (cactus pear fruits and red beet), have been considered because of reducing power and potential to affect redox-modulated cellular processes. The antioxidant power of Betalains is strictly due to the dissociation rate of the acid moieties present in all the molecules of this family of phytochemicals. Experimentally, only the pK a values of betanin were determined. Recently, it was evidenced it was evidenced as the acid dissociation, at different environmental pHs, affects on its electron-donating capacity, and fur…

Synthesis and antiproliferative activity of [1,2,4] triazino[4,3-a]indoles

A series of [1, 2, 4triazino[4,3-a]indoles was prepared in good yield by reacting 2-diazo-3-ethoxycarbonylindole with methylene active compounds. Derivatives of the title ring system were tested against a panel of 60 human tumor cell lines, and showed inhibitory activity against a wide range of cancer cell lines at micromolar concentration.

New insights into the mechanism of action of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives endowed with anticancer potential

Due to the scarce biological profile, the pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one scaffold (PBT) has been recently explored as promising core for potential anticancer candidates. Several suitably decorated derivatives (PBTs) exhibited antiproliferative activity in the low-micromolar range associated with apoptosis induction and cell cycle arrest on S phase. Herein, we selected the most active derivatives and submitted them to further biological explorations to deepen the mechanism of action. At first, a DNA targeting is approached by means of flow Linear Dichroism experiments so as to evaluate how small planar molecules might interact with DNA, including the interference with the catal…

1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, through 1,3-Dipolar Cycloadditions

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…

A Multivariate Analysis on Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors and Resistance Induced by Mutation

This paper describes the use of multivariate statistical procedure PCA as a tool to explore the inhibitory activity of classes of NNRTIs against HIV-1 viruses (wild type and more frequent mutants, Y181C, V106A, K103N, L100I) and against RT enzyme. The analysis of correlations between biological activity and molecular descriptors or similarity indexes allowed a reliable classification of the fifty five derivatives considered in this study. The best results were obtained in the case of L100I and K103N mutants for which the higher number of assignments was found when the principal components derived from the descriptors were used. On this basis this statistical approach is proposed as a reliab…

ChemInform Abstract: Exploring the Anticancer Potential of Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one Derivatives: The Effect on Apoptosis Induction, Cell Cycle and Proliferation.

Abstract In order to investigate their anticancer potential, four new pyrazolo[1,2-a]benzo[1,2,3,4]tetrazinone derivatives, designed through the chemometric protocol VLAK, and three of the most active compounds of the previous series have been evaluated on some cellular events including proliferation, apoptosis induction, and cell cycle. The NCI one dose (10 μM) screening revealed that the 8,9-di-methyl derivative showed activity against Leukemia (CCRF-CEM) and Colon cancer cell line (COLO 205), reaching 81% and 45% of growth inhibition (GI), respectively. Replacement of the two methyl groups with two chlorine atoms maintained the activity toward Leukemia cell (CCRF-CEM, GI 77%) and selecti…

Pharmacophore modelling as useful tool in the lead compounds identification and optimization

The goal of computer-aided molecular design methods in modern medicinal chemistry is to reduce the overall cost and time associated to the discovery and development of a new drug by identifying the most promising candidates to focus the experimental efforts on. Very often, many drug discovery projects have reached already a well-advanced stage before detailed structural data on the protein target have become available. A possible consequence is that often, medicinal chemists develop novel compounds for a target using preliminary structure–activity information, together with the theoretical models of interactions. Only responses that are consistent with the working hypothesis contribute to a…

Design, synthesis, and biological evaluation of pyridothienotriazolopyrimidine derivatives as new HSP90 inhibitors

Design and Synthesis of 4-Substituted Indolo[3,2-e][1,2,3]triazolo[1,5-a]pyrimidine Derivatives with Antitumor Activity

New derivatives of the indolo[3,2- e][1,2,3]triazolo[1,5- a]pyrimidine system, substituted in the 4 position, were designed as novel antitumor agents because of their theoretical capability to form stable complexes with DNA fragments. The calculated free energies of binding were found in the range -12.76 --> -39.68 Kcal/mol. The docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs, whereas the side chain lies along the minor groove. Compounds, selected on the basis of the docking studies and suitably synthesized, showed antiproliferative activity against each type of tumor cell line investigated, generally in the low micromolar range. The mo…

Glycosidopyrroles. Part 4. 1-β-D-ribofuranosyl-pyrroles and indoles as potential antiviral agents

The preparation of new 1-β-D-ribofuranosylpyrroles of type 8 and a new method of synthesis of 1-β-D-ribofuranosylindoles of type 10, according to the scheme, is reported. All these new derivatives showed promising chemical and physical analogies with bioactive molecules but did not show any antiviral activity againstHIV1.

A new Approach to Molecular Modelling Studies on a Series of DNA Minor Groove Binders

The role of side chains in Substituted Pyrrole derivatives towards antiproliferative activity

In the last years, the introduction of side chains in different molecular compounds takes increasing importance. As recently reported in literature, heterocyclic scaffolds with poor biological activity , if properly decorated with selected side chains, can improve their anticancer activity against a large spectrum of human tumor cell lines. For example, the annelated Pyrrolo[3,4-e]Pyrimidines and Pyrrolo[3,2-e]Pyrimidines, opportunely functionalized with a large number of side chains, showed a good increase in the antitumor activity with respect to the starting core structure. New compound thus obtained showed antiproliferative activity against all the human tumor cells, generally in the lo…

SCREENING APOPTOTICI SU NUOVI DERIVATI PIRAZOLO[1,2-A]BENZO[1,2,3,4]TETRAZINONI

Antiproliferative Activity Predictor: A New Reliable In Silico Tool for Drug Response Prediction against NCI60 Panel.

In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute Developmental Therapeutics Program) undoubtedly represents the most famous project aimed at rapidly testing thousands of compounds against multiple tumor cell lines (NCI60). The large amount of biological data stored in the National Cancer Institute (NCI) database and many other databases has led researchers in the fields of computational biology and medicinal chemistry to develop tools to predict the anticancer properties of new agents in advan…

Melatonin reduces inflammatory response in human intestinal epithelial cells stimulated by interleukin‐1β

Melatonin is the main secretory product of the pineal gland, and it is involved in the regulation of periodic events. A melatonin production independent of the photoperiod is typical of the gut. However, the local physiological role of melatonin at the intestinal tract is poorly characterized. In this study, we evaluated the anti-inflammatory activities of melatonin in an in vitro model of inflamed intestinal epithelium. To this purpose, we assessed different parameters usually associated with intestinal inflammation using IL-1 beta-stimulated Caco-2 cells. Differentiated monolayers of Caco-2 cells were preincubated with melatonin (1 nmol/L-50 mu mol/L) and then exposed to IL-1 beta. After …

Synthesis, biological evaluation, and: In silico studies of novel chalcone: In pyrazoline-based 1,3,5-triazines as potential anticancer agents

A novel series of triazin-chalcones (7,8)a-g and triazin-N-(3,5-dichlorophenyl)pyrazolines (9,10)a-g were synthesized and evaluated for their anticancer activity against nine different cancer strains. Triazine ketones 5 and 6 were synthesized from the cyanuric chloride 1 by using stepwise nucleophilic substitution of the chlorine atom. These ketones were subsequently subjected to a Claisen-Schmidt condensation reaction with aromatic aldehydes affording chalcones (7,8)a-g. Then, N-(3,5-dichlorophenyl)pyrazolines (9,10)a-g were obtained by cyclocondensation reactions of the respective chalcones (7,8)a-g with 3,5-dichlorophenylhydrazine. Among all the evaluated compounds, chalcones 7d,g and 8g…

Sintesi di derivati tetraidrobis-triazolochinossalinici e di nuovi sistemi triazolopirrolopirazinici di interesse biologico mediante cicloaddizioni 1,3-dipolari

Bis-1,2,4-triazolo[4,3-a:3’,4’-c]quinoxalines of pharmaceutical interest from 1,3-dipolar cycloaddition

Sintesi di Nuovi Derivati 2,5-bis(3’Indolil)tiofeni, Analoghi dell’Alcaloide Marino Nortopsentina.

ChemInform Abstract: 1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, Through 1,3-Dipolar Cycloadditions

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…

Quinoline-Based Molecules Targeting c-Met, EGF, and VEGF Receptors and the Proteins Involved in Related Carcinogenic Pathways

The quinoline ring system has long been known as a versatile nucleus in the design and synthesis of biologically active compounds. Currently, more than one hundred quinoline compounds have been approved in therapy as antimicrobial, local anaesthetic, antipsychotic, and anticancer drugs. In drug discovery, indeed, over the last few years, an increase in the publication of papers and patents about quinoline derivatives possessing antiproliferative properties has been observed. This trend can be justified by the versatility and accessibility of the quinoline scaffold, from which new derivatives can be easily designed and synthesized. Within the numerous quinoline small molecules developed as a…

The influence of substitution in the quinoxaline nucleus on 1,3-dipolar cycloaddition reactions

The reaction mechanism of 1,3-dipolar cycloadditions of both symmetric and unsymmetric benzo-condensed diazines with a nitrilimine dipole, to give two different mono- and bis-cycloadducts, in tetrahydrofuran (THF) solution, was studied by DFT calculatio ns. The results obtained show that each 1,3-dipolar cycloaddition reaction always proceeds by a two steps mechanism, in which the first intermediate shows only one covalent bond between the beta carbon of the nitrilimine and the aromatic nitrogen of the diazine molecule. The structure and energy content of the two transition states of the two cycloaddition steps, in the case of the unsymmetric benzo-condensed diazine, nicely explains why the…

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