Oxidation-labile linkers for controlled drug delivery.

The continuous symbiosis throughout chemical biology and drug discovery has led to the design of innovative bifunctional molecules for targeted and controlled drug delivery. Among the different tools, protein-drug and peptide-drug conjugates are trend approaches to achieve targeted delivery, selectivity and efficacy. To meet the main goals of these bioconjugates, the selection of the appropriate payloads and linkers is crucial, as they must provide in vivo stability, while they may also help to achieve the therapeutic target and action. In neurodegenerative diseases or some cancer types, where oxidative stress plays an important role, linkers sensitive to oxidative conditions may be able to release the drug once the conjugate achieves the target. Considering specially this specific application, this mini-review covers the most relevant publications on oxidation-labile linkers.

Structure-Based Optimization of Coumarin hA3 Adenosine Receptor Antagonists.

Adenosine receptors participate in many physiological functions. Molecules that may selectively interact with one of the receptors are favorable multifunctional chemical entities to treat or decelerate the evolution of different diseases. 3-Arylcoumarins have already been studied as neuroprotective agents by our group. Here, differently 8-substituted 3-arylcoumarins are complementarily studied as ligands of adenosine receptors, performing radioligand binding assays. Among the synthesized compounds, selective A3 receptor antagonists were found. 3-(4-Bromophenyl)-8-hydroxycoumarin (compound 4) displayed the highest potency and selectivity as A3 receptor antagonist (Ki = 258 nM). An analysis of its X-ray diffraction provided detailed information on its structure. Further evaluation of a selected series of compounds indicated that it is the nature and position of the substituents that determine their activity and selectivity. Theoretical modeling calculations corroborate and explain the experimental data, suggesting this novel scaffold can be involved in the generation of candidates as multitarget drugs.

Coumarin derivatives as promising xanthine oxidase inhibitors.

Xanthine oxidase (XO) is an interesting target for the synergic treatment of several diseases. Coumarin scaffold plays an important role in the design of efficient and potent inhibitors. In the current work, twenty 3-arylcoumarins and eight 3-heteroarylcoumarins were evaluated for their ability to inhibit XO. Among all the candidates, 5,7-dihydroxy-3-(3'-hydroxyphenyl)coumarin (compound 20) proved to be the best inhibitor with an IC50 of 2.13 µM, being 7-fold better than the reference compound, allopurinol (IC50 = 14.75 µM). To deeply understand the potential of this compound, the inhibition mode was also evaluated. Compound 20 showed an uncompetitive profile of inhibition. Molecular docking studies were carried out to analyze the interaction of compound 20 with the studied enzyme. The binding mode involving residues different from the catalytic site of the binding pocket, is compatible to the observed uncompetitive inhibition. Compound 20 was not cytotoxic at its IC50 value, as demonstrated by the viability of 99.1% in 3 T3 cells. Furthermore, pharmacokinetics and physicochemical properties were also calculated, which corroborated with the potential of the studied compounds as promising XO inhibitors.

New insights into highly potent tyrosinase inhibitors based on 3-heteroarylcoumarins: Anti-melanogenesis and antioxidant activities, and computational molecular modeling studies.

Melanogenesis is a physiological pathway for the formation of melanin. Tyrosinase catalyzes the first step of this process and down-regulation of its activity is responsible for the inhibition of melanogenesis. The search for molecules capable of controlling hyperpigmentation is a trend topic in health and cosmetics. A series of heteroarylcoumarins have been synthesized and evaluated. Compounds 4 and 8 exhibited higher tyrosinase inhibitory activities (IC50=0.15 and 0.38µM, respectively), than the reference compound, kojic acid (IC50=17.9µM). Compound 4 acts as competitive, while compound 8 as uncompetitive inhibitor of mushroom tyrosinase. Furthermore, compounds 2 and 8 inhibited tyrosinase activity and melanin production in B16F10 cells. In addition, compounds 2-4 and 8 proved to have an interesting antioxidant profile in both ABTS and DPPH radicals scavenging assays. Docking experiments were carried out in order to study the interactions between these heteroarylcoumarins and mushroom tyrosinase.

Synthesis and pharmacological activities of non-flavonoid chromones: a patent review (from 2005 to 2015).

INTRODUCTION: Chromones are one of the major classes of naturally occurring compounds. Their chemistry has been widely explored and extensively reviewed. The following review intends to give a broad overview of the patented chromones. Particular attention has been given to their synthesis, uses and applications in last 10 years. AREAS COVERED: The authors provide an overview of the recent scientific reports describing the obtaining and study of new chromones. The review emphasizes the rationale behind natural sources, synthesis, biological activities and structure-activity relationships of the new chromone derivatives. The article is based on the literature published from 2005 to 2015 related to the development of this family of compounds. The patents presented in this review have been collected from multiple electronic databases including SciFinder, Espacenet and Mendeley. EXPERT OPINION: Although a great number of chromones have been published in bibliographic sources in the last years, there is little innovation in the synthetic methodologies. Some natural sources and isolation techniques were described. Different pharmacological applications have also been claimed. Two of the most studied applications have been the use of these compounds as therapeutic agents for cancer and skin diseases. Some safety requirements need to be developed in order to find new chemical entities as new drugs.

Development of novel adenosine receptor ligands based on the 3-amidocoumarin scaffold.

With the aim of finding new adenosine receptor (AR) ligands presenting the 3-amidocoumarin scaffold, a study focusing on the discovery of new chemical entities was carried out. The synthesized compounds 1-8 were evaluated in radioligand binding (A1, A2A and A3) and adenylyl cyclase activity (A2B) assays in order to determine their affinity for human AR subtypes. The 3-benzamide derivative 4 showed the highest affinity of the whole series and was more than 30-fold selective for the A3 AR (Ki=3.24 µM). The current study supported that small structural changes in this scaffold allowed modulating the affinity resulting in novel promising classes of A1, A2A, and/or A3 AR ligands. We also performed docking calculations in hA2A and hA3 to identify the hypothetical binding mode for the most active compounds. In addition, some ADME properties were calculated in order to better understand the potential of these compounds as drug candidates.

Bioactive Coumarins from Marine Sources: Origin, Structural Features and Pharmacological Properties.

Nature is an ancient pharmacy that is largely used as an inspiring source for drug discovery processes for the early eras. Several drugs used nowadays are of natural product origin or inspired on the basis of natural product structures and approximately half of the 20 best-selling non-protein drugs are related to natural products. However, a largely unexplored marine world that presumably harbors the most biodiversity may be the vastest resource to discover compounds with remarkable biological properties. Marine based drug discovery research has been mainly focused on crude extracts. The purpose of this review is to summarize the findings reported in this area, particularly focuses on marine-derived coumarincontaining compounds.

Oxidative stress and neurodegenerative diseases: looking for a therapeutic solution inspired on benzopyran chemistry.

Reactive species are continuously produced in vivo by all body tissues. However, when an imbalance between the reactive species production and the endogenous pool of antioxidants occurs, the resulting oxidative stress can somehow intensify the pathophysiological mechanisms of several diseases, such as neurodegenerative diseases. Although the aetiology of Parkinson's and Alzheimer's diseases is not yet completely understood, it is accepted by the scientific community that the oxidative stress can act as a trigger or can be involved in the course of both diseases. Therefore, the development of an antioxidant-based therapy could be a helpful approach to ameliorate the deleterious effects of oxidative stress in neurodegenerative diseases. Coumarins and chromones are natural or synthetic chemical entities described as privileged structures with diverse biological activities that have been used to design new drugs with potential anti-Alzheimer and anti-Parkinson profiles. Since some of these compounds also displayed potent antioxidant activity, the rationale approach to developing new drugs based on the benzopyran scaffold, as therapeutic alternatives for neurodegenerative diseases, is a valid and compelling topic. This review provides a medicinal chemistry overview on the discovery and development of benzopyran-based compounds endowed with antioxidant, neuroprotective and anti-Alzheimer or anti-Parkinson activities.

Study of coumarin-resveratrol hybrids as potent antioxidant compounds.

In the present work we synthesized a selected series of hydroxylated 3-phenylcoumarins 5-8, with the aim of evaluating in detail their antioxidant properties. From an in depth study of the antioxidant capacity data (ORAC-FL, ESR, CV and ROS inhibition) it was concluded that these derivatives are very good antioxidants, with very interesting profiles in all the performed assays. The study of the effect of the number and position of the hydroxyl groups on the antioxidant activity was the principal aim of this study. In particular, 7-hydroxy-3-(3'-hydroxy)phenylcoumarin (8) proved to be the most active and effective antioxidant of the selected series in four of the performed assays (ORAC-FL = 11.8, capacity of scavenging hydroxyl radicals = 54%, Trolox index = 2.33 and AI30 index = 0.18). However, the presence of two hydroxyl groups on this molecule did not increase greatly the activity profile. Theoretical evaluation of ADME properties of all the derivatives was also carried out. All the compounds can act as potential candidates for preventing or minimizing the free radical overproduction in oxidative-stress related diseases. These preliminary findings encourage us to perform a future structural optimization of this family of compounds.

Oxidative Stress and Neurodegenerative Diseases: Looking for a Therapeutic Solution Inspired on Benzopyran Chemistry.

Reactive species are continuously produced in vivo by all body tissues. However, when an imbalance between the reactive species production and the endogenous pool of antioxidants occurs, the resulting oxidative stress can somehow intensify the pathophysiological mechanisms of several diseases, such as neurodegenerative diseases. Although the aetiology of Parkinson's and Alzheimer's diseases is not yet completely understood, it is accepted by the scientific community that the oxidative stress can act as a trigger or can be involved in the course of both diseases. Therefore, the development of an antioxidant-based therapy could be a helpful approach to ameliorate the deleterious effects of oxidative stress in neurodegenerative diseases. Coumarins and chromones are natural or synthetic chemical entities described as privileged structures with diverse biological activities that have been used to design new drugs with potential anti-Alzheimer and anti-Parkinson profiles. Since some of these compounds also displayed potent antioxidant activity, the rationale approach to developing new drugs based on the benzopyran scaffold, as therapeutic alternatives for neurodegenerative diseases, is a valid and compelling topic. This review provides a medicinal chemistry overview on the discovery and development of benzopyran-based compounds endowed with antioxidant, neuroprotective and anti-Alzheimer or anti-Parkinson activities.

Insight into the interactions between novel coumarin derivatives and human A3 adenosine receptors.

A study focused on the discovery of new chemical entities based on the 3-arylcoumarin scaffold was performed with the aim of finding new adenosine receptor (AR) ligands. Thirteen synthesized compounds were evaluated by radioligand binding (A1, A2A, and A3) and adenylyl cyclase activity (A2B) assays in order to study their affinity for the four human AR (hAR) subtypes. Seven of the studied compounds proved to be selective A3 AR ligands, with 3-(4'-methylphenyl)-8-(2-oxopropoxy)coumarin (12) being the most potent (Ki =634 nM). None of the compounds showed affinity for the A2B receptor, while four compounds were found to be nonselective AR ligands for the other three subtypes. Docking simulations were carried out to identify the hypothetical binding mode and to rationalize the interaction of these types of coumarin derivatives with the binding site of the three ARs to which binding was observed. The results allowed us to conclude that the 3-arylcoumarin scaffold composes a novel and promising class of A3 AR ligands. ADME properties were also calculated, with the results suggesting that these compounds are promising leads for the identification of new drug candidates.

Synthesis and adenosine receptors binding affinities of a series of 3-arylcoumarins.

OBJECTIVES: In the present communication, we report the synthesis, pharmacological evaluation, theoretical evaluation of absorption, distribution, metabolism and excretion properties and structure-activity relationship study of a selected series of 3-arylcoumarins (compounds 1-9). Adenosine receptors (ARs) binding activity and selectivity of the synthesized compounds 1-9 were evaluated in this study. Different substituents were introduced in both benzene rings of the evaluated scaffold, at positions 6 and 3' or 4' of the moiety. The lack of data on the 3-arylcoumarin scaffold encouraged us to explore the ARs' binding activity of a selected series of derivatives. METHODS: A new series of coumarins (compounds 1-9) were synthesized and evaluated by radioligand binding studies towards ARs. KEY FINDINGS: Analysing the experimental data, it can be observed that neither the simple 3-arylcoumarin nor the 4'-nitro derivatives presented detectable binding affinity for the evaluated receptors, although most of the other substituted derivatives have good binding affinity profiles, especially against the hA1 /hA3 or only hA3 AR. CONCLUSIONS: The most remarkable derivative is compound 2, presenting the best affinity for hA3 AR (Ki = 2680 nM) and significant selectivity for this subtype.

Chalcone-based derivatives as new scaffolds for hA3 adenosine receptor antagonists.

OBJECTIVES: With the aim of finding new adenosine receptor (AR) ligands based on the chalcone scaffold, we report the synthesis of a new series of coumarin-chalcone hybrids and the pharmacological characterization of their actions at four subtypes of AR. METHODS: The synthesized compounds 5-10 were characterized in radioligand binding (A1 , A2A and A3 ) and adenylyl cyclase activity assays (A2B ) to determine the affinity of the compounds for the four human AR (hAR) subtypes. KEY FINDINGS: Coumarin-chalcone hybrids were found to be ligands with a novel structure, not reported thus far, that showed varying affinity and selectivity for AR subtypes. CONCLUSIONS: The coumarin-chalcone hybrids in which ring B of the chalcone scaffold was a thiophene (compounds 5 and 9) were found to be the most potent compounds of the series. Compound 9, in which ring A of the chalcone moiety was the phenyl ring of the coumarin, showed similar activity against hA1 , hA2A and hA3 ARs, while compound 5, in which ring A of the chalcone was substituted by the benzopyrone ring of the coumarin moiety, showed similar activity only at the hA3 AR and, therefore, was deemed to be selective (Ki (dissociation constant) = 5160 nm).

Targeting adenosine receptors with coumarins: synthesis and binding activities of amide and carbamate derivatives.

OBJECTIVES: With the aim of finding the structural features governing binding activity and selectivity against adenosine receptors (ARs), several 3-subtituted coumarins with amide (compounds 3-6) and carbamate (7-9) functions were synthesized. To study its possible influence on the binding activity and selectivity, a hydroxyl substituent was also introduced at position 4 of the coumarin moiety. METHODS: A new series of coumarins (3-9) were synthesized and evaluated by radioligand binding studies towards ARs. KEY FINDINGS: None of the 4-hydroxy derivatives (4, 8 and 9) showed binding affinity for any of the ARs. None of the compounds interacted with the hA(2B) AR (K(i) > 100,000 nM). Compounds 3, 5, 6 and 7 had different activity profiles with dissimilar binding affinity and selectivity towards human A1, A(2A) and A3 ARs. CONCLUSIONS: The most remarkable derivative is compound 7, which presents the best affinity and selectivity for the A3 adenosine receptor (K(i) = 5500 nM).

Synthesis and cytotoxic activity of non-naturally substituted 4-oxycoumarin derivatives.

Coumarins are a large family of natural and synthetic compounds exerting different pharmacological effects, including cytotoxic, anti-inflammatory or antimicrobial. In the present communication we report the synthesis of a series of 12 diversely substituted 4-oxycoumarin derivatives including methoxy substituted 4-hydroxycoumarins, methyl, methoxy or unsubstituted 3-aryl-4-hydroxycoumarins and 4-benzyloxycoumarins and their anti-proliferative effects on breast adenocarcinoma cells (MCF-7), human promyelocytic leukemia cells (HL-60), human histiocytic lymphoma cells (U937) and mouse neuroblastoma cells (Neuro2a). The most potent bioactive molecule was the 4-hydroxy-5,7-dimethoxycoumarin (compound 1) which showed similar potency (IC(50) 0.2-2 µM) in all cancer cell lines tested. This non-natural product reveals a simple bioactive scaffold which may be exploited in further studies.

A network-QSAR model for prediction of genetic-component biomarkers in human colorectal cancer.

The combination of the network theory and the calculation of topological indices (TIs) allow establishing relationships between the molecular structure of large molecules like the genes and proteins and their properties at a biological level. This type of models can be considered quantitative structure-activity relationships (QSAR) for biopolymers. In the present work a QSAR model is reported for proteins, related to human colorectal cancer (HCC) and codified by different genes that have been identified experimentally by Sjöblom et al. [2006. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268-274] among more than 10000 human genes. The 69 proteins related to human colorectal cancer (HCCp) and a control group of 200 proteins not related to HCC (no-HCCp) were represented through an HP Lattice type Network. Starting from the generated graphs we calculate a set of descriptors of electrostatic potential type (xi(k)) that allow to establish, through a linear discriminant analysis (LDA), a QSAR model of relatively high percentage of good classification (higher than 80%) to differentiate between HCCp and no-HCCp proteins. The purpose of this study is helping to predict the possible implication of a certain gene and/or protein (biomarker) in the colorectal cancer. Different procedures of validation of the obtained model have been carried out in order to corroborate its stability, including cross-validation series (CV) and evaluation of an additional series of 200 no-HCCp. This biostatistic methodology could be applied to predict human colorectal cancer biomarkers and to understand much better the biological aspects of this disease.

Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories.

We introduce here a new class of invariants for MD trajectories based on the spectral moments pi(k)(L) of the Markov matrix associated to lattice network-like (LN) graph representations of Molecular Dynamics (MD) trajectories. The procedure embeds the MD energy profiles on a 2D Cartesian coordinates system using simple heuristic rules. At the same time, we associate the LN with a Markov matrix that describes the probabilities of passing from one state to other in the new 2D space. We construct this type of LNs for 422 MD trajectories obtained in DNA-drug docking experiments of 57 furocoumarins. The combined use of psoralens+ultraviolet light (UVA) radiation is known as PUVA therapy. PUVA is effective in the treatment of skin diseases such as psoriasis and mycosis fungoides. PUVA is also useful to treat human platelet (PTL) concentrates in order to eliminate Leishmania spp. and Trypanosoma cruzi. Both are parasites that cause Leishmaniosis (a dangerous skin and visceral disease) and Chagas disease, respectively; and may circulate in blood products collected from infected donors. We included in this study both lineal (psoralens) and angular (angelicins) furocoumarins. In the study, we grouped the LNs on two sets; set1: DNA-drug complex MD trajectories for active compounds and set2: MD trajectories of non-active compounds or no-optimal MD trajectories of active compounds. We calculated the respective pi(k)(L) values for all these LNs and used them as inputs to train a new classifier that discriminate set1 from set2 cases. In training series the model correctly classifies 79 out of 80 (specificity=98.75%) set1 and 226 out of 238 (Sensitivity=94.96%) set2 trajectories. In independent validation series the model correctly classifies 26 out of 26 (specificity=100%) set1 and 75 out of 78 (sensitivity=96.15%) set2 trajectories. We propose this new model as a scoring function to guide DNA-docking studies in the drug design of new coumarins for anticancer or antiparasitic PUVA therapy.

A new psoralen derivative with enlarged antiproliferative properties.

Following our results with benzopsoralens as potent photochemotherapeutic agents, we report the antiproliferative evaluation of nitrogenated isoster upon and without UVA irradiation. The evaluated pyridazinopsoralen showed a higher photochemotherapeutic activity with respect to the well-known drug, 8-MOP, and a significant cytotoxicity, also in the dark. This result enlarges the interest in this tetracyclic psoralen derivative skeleton in the search of new anticancer agents.

QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks.

Network theory allows relationships to be established between numerical parameters that describe the molecular structure of genes and proteins and their biological properties. These models can be considered as quantitative structure-activity relationships (QSAR) for biopolymers. The work described here concerns the first QSAR model for 122 proteins that are associated with human breast cancer (HBC), as identified experimentally by Sjöblom et al. (Science 2006, 314, 268) from over 10,000 human proteins. In this study, the 122 proteins related to HBC (HBCp) and a control group of 200 proteins that are not related to HBC (non-HBCp) were forced to fold in an HP lattice network. From these networks a series of electrostatic potential parameters (xi(k)) was calculated to describe each protein numerically. The use of xi(k) as an entry point to linear discriminant analysis led to a QSAR model to discriminate between HBCp and non-HBCp, and this model could help to predict the involvement of a certain gene and/or protein in HBC. In addition, validation procedures were carried out on the model and these included an external prediction series and evaluation of an additional series of 1000 non-HBCp. In all cases good levels of classification were obtained with values above 80%. This study represents the first example of a QSAR model for the computational chemistry inspired search of potential HBC protein biomarkers.

Proteomics, networks and connectivity indices.

Describing the connectivity of chemical and/or biological systems using networks is a straight gate for the introduction of mathematical tools in proteomics. Networks, in some cases even very large ones, are simple objects that are composed at least by nodes and edges. The nodes represent the parts of the system and the edges geometric and/or functional relationships between parts. In proteomics, amino acids, proteins, electrophoresis spots, polypeptidic fragments, or more complex objects can play the role of nodes. All of these networks can be numerically described using the so-called Connectivity Indices (CIs). The transformation of graphs (a picture) into CIs (numbers) facilitates the manipulation of information and the search for structure-function relationships in Proteomics. In this work, we review and comment on the challenges and new trends in the definition and applications of CIs in Proteomics. Emphasis is placed on 1-D-CIs for DNA and protein sequences, 2-D-CIs for RNA secondary structures, 3-D-topographic indices (TPGIs) for protein function annotation without alignment, 2-D-CIs and 3-D-TPGIs for the study of drug-protein or drug-RNA quantitative structure-binding relationships, and pseudo 3-D-CIs for protein surface molecular recognition. We also focus on CIs to describe Protein Interaction Networks or RNA co-expression networks. 2-D-CIs for patient blood proteome 2-DE maps or mass spectra are also covered.