Computational tools for the study of the structure-property relationship and design of new biologically active compounds

The aim of this PhD course was to explore a broad overview on the topic of the Structure-Property Relationship (SPR) with a strong emphasis on the pratical aspects. Data in chemical research, and in particular in drug discovery, is varied and oftentimes very complex. In drug discovery one has to make sense of different type of data such as structural, biological, physico-chemical, pharmacological, toxicological and so on, which, ultimately have to be associated to a single molecular structure. In order to sort out these data and extract appropriate information, a number of tools have been devised on computers and workstations in the form of different programs; the reader will find that many of these tools and methods have been used during this PhD course. More in details in Chapter 1 the homology modeling of the adenosine receptors was explored and accompanied to the pharmacophoric analysis and synthesis of new compounds. In Chapter 2 the analysis of the MMP-inhibitor interaction led us to implement the Amber Forcefield, and the following docking analysis allowed the design of new selective inhibitors. The modeling of the activate form of the cannabinoid receptors (Chapter 3) corresponded to an attempt for going away from the homology modeling procedures; together with the goal of obtaining a quantitative model from an automated docking study. In Chapter 4 the study of ligand-estrogen receptor interaction was developed exploring the free energy calculation, while finally in the last Chapter the angiotensin receptor AT1 construction led us to propose a new binding orientation for the non-peptide antagonists, using the 3D-QSAR approach as validation and predictive method

α/β-Hydrolase Domain (ABHD) Inhibitors as New Potential Therapeutic Options against Lipid-Related Diseases

Much of the experimental evidence in the literature has linked altered lipid metabolism to severe diseases such as cancer, obesity, cardiovascular pathologies, diabetes, and neurodegenerative diseases. Therefore, targeting key effectors of the dysregulated lipid metabolism may represent an effective strategy to counteract these pathological conditions. In this context, α/β-hydrolase domain (ABHD) enzymes represent an important and diversified family of proteins, which are involved in the complex environment of lipid signaling, metabolism, and regulation. Moreover, some members of the ABHD family play an important role in the endocannabinoid system, being designated to terminate the signaling of the key endocannabinoid regulator 2-arachidonoylglycerol. This Perspective summarizes the research progress in the development of ABHD inhibitors and modulators: design strategies, structure-activity relationships, action mechanisms, and biological studies of the main ABHD ligands will be highlighted

Development of a Fingerprint-Based Scoring Function for the Prediction of the Binding Mode of Carbonic Anhydrase II Inhibitors

Carbonic anhydrase II (CAII) is a zinc-containing metalloenzyme whose aberrant activity is associated with various diseases such as glaucoma, osteoporosis, and different types of tumors; therefore, the development of CAII inhibitors, which can represent promising therapeutic agents for the treatment of these pathologies, is a current topic in medicinal chemistry. Molecular docking is a commonly used tool in structure-based drug design of enzyme inhibitors. However, there is still a need for improving docking reliability, especially in terms of scoring functions, since the complex pattern of energetic contributions driving ligand⁻protein binding cannot be properly described by mathematical functions only including approximated energetic terms. Here we report a novel CAII-specific fingerprint-based (IFP) scoring function developed according to the ligand⁻protein interactions detected in the CAII-inhibitor co-crystal structures of the most potent CAII ligands. Our IFP scoring function outperformed the ability of Autodock4 scoring function to identify native-like docking poses of CAII inhibitors and thus allowed a considerable improvement of docking reliability. Moreover, the ligand⁻protein interaction fingerprints showed a useful application in the binding mode analysis of structurally diverse CAII ligands

Discovery and optimization of benzoylpiperidine derivatives as new reversible, potent and selective MAGL inhibitors

The serine hydrolase monoacylglycerol lipase (MAGL) is the main responsible of the degradation of 2-arachidonoylglycerol, an endocannabinoid implicated in several physiological processes. Moreover, MAGL is involved in the formation of pro-tumorigenic signaling molecules. MAGL inhibition is considered a valid therapeutic approach to treat several pathological conditions, including several types of cancer.[1] So far, only a limited number of MAGL inhibitors have been discovered and most of them are characterized by an irreversible mechanism of action, determining the occurrence of undesired effects. In this study we identified a reversible MAGL inhibitor by a structure-based virtual screening analysis. With the aim of identifying more potent and selective MAGL inhibitors, chemical modifications were introduced to the original compound to improve both potency and selectivity.[2] The structural optimization led to the obtainment of nanomolar inhibitors (Figure 1), which are selective over other hydrolases and cannabinoid receptors. These new inhibitors exert an appreciable antiproliferative activity in cancer cells and are able to inhibit MAGL in in vivo assays. [1] Mulvihill MM, Nomura DK, Life Sci. 2013; 92(8-9):492-497. [2] Granchi C, Rizzolio F, Palazzolo S, Carmignani S, Macchia M, Saccomanni G, Manera C, Martinelli A, Minutolo F, Tuccinardi T, J Med Chem. 2016; 59(22):10299-10314

Receptor-based virtual screening evaluation for the identification of estrogen receptor β ligands.

In this paper, a receptor-based virtual screening study for the identification of estrogen receptor β (ERβ) ligands was developed. Starting from a commercial database of 400,000 molecules, only six compounds resulted to be potential active ligands of ERβ. Interestingly, all the six molecules possess scaffolds that had already been reported in known ERβ ligands. Therefore, the results obtained herein confirm the reliability of our virtual screening procedure, thus encouraging the application of this protocol to larger commercial databases in order to identify new ERβ ligands

Identification of Lactate Dehydrogenase 5 Inhibitors using Pharmacophore- Driven Consensus Docking

Background: Human lactate dehydrogenase 5 (hLDH5) represents a promising anticancer target, particularly for the treatment of hypoxic tumors, where it is often hyperexpressed. In fact, by catalyzing the reduction of pyruvate to lactate, hLDH5 allows the survival of tumor cells under hypoxic conditions by means of glycolysis. Despite the efforts dedicated to the identification and development of hLDH5 inhibitors, only few compounds showing promising activity in cancer cell lines have been reported. Objective: In the present study, we developed a virtual screening (VS) protocol aimed at identifying new small molecule inhibitors of hLDH5. Method: The VS strategy consisted in a pharmacophore-driven consensus docking (CD) approach, combining a structure-based pharmacophore screening and CD protocol employing three different docking methods. Results: The VS protocol was applied to filter the Enamine commercial database and allowed the selection of three candidate ligands to be subjected to hLDH5 inhibition assays. One of the selected compounds showed a promising activity, compared to its low molecular weight, with an IC50 of 180.7 ± 16.5 μM. Conclusion: We identified a new small-molecule inhibitor of hLDH5 that can be considered as a new lead for the development of potent hLDH5 inhibitors. Moreover, these results demonstrate the reliability of the VS protocol developed

Natural compounds as inhibitors of lactate dehydrogenase

Lactate dehydrogenase (LDH) catalyses the conversion of pyruvate to lactate, utilizing NADH as co-factor. It’s a tetrameric enzyme composed of two subunits, M and H, whose association can generate five isoforms. One of this, the human isoform 5, hLDH5 has the highest activity in converting pyruvate to lactate under anaerobic conditions, such as those found in hypoxic tumors and for this reason it’s up-regulated in tumor tissues where cells glycolytic rate is up to 200 times higher than that of the normal tissue. hLDH5 inhibition should cause cancer cell death by starvation, without interfering with healthy cells that normally use oxidative phosphorylation for ATP generation (1). Inhibition of LDH is so considered as a promising target in cancer treatment, and natural compounds could serve as useful scaffold to study new anticancer agents. Among the few plant derived hLDH5 inhibitors already investigated there are mainly phenolic derivatives such as gossypol, morin, and galloflavin (2,3). In the last decade our research group successfully detected a good number of compounds obtained from Mediterranean plants with anticancer effect, and for this reason start a research program aimed to discover new classes of natural products having hLDH5 inhibitory activity. In a first study, since some species of Phlomis (Lamiaceae) proved to possess anti-cancer properties, the crude extract of P. kurdica aerial parts was selected as the starting material. Two new flavonoids and one new phenylpropanoid, together with eleven known phenolic compounds, including flavonoids and phenylpropanoids were isolated and assayed for their hLDH5 inhibitory activity. Luteolin 7-O-β-D-glucopyranoside showed an IC50 value similar to that of reference compound galloflavin (4). Then, since Polygala genus (Polygalaceae) is well known to contain phenolic oligosaccharides, xanthones, lignans, and triterpenic saponins and it’s largely used in the traditional medicine, an Italian species P. flavescens subsp. flavescens was chosen. Ten new compounds were isolated from the methanol residue of the aerial parts through Sephadex and RP-HPLC separations, including four flavonol glycosides, two oligosaccharides, one α-ionone, and three triterpenoidic saponins, together with two known oligosaccharides and two flavonol glycosides. The isolates were assayed for their inhibitory activity against hLDH5 and 3,6'-di-O-sinapoylsucrose showed an inhibition potency comparable or even slightly better than reference inhibitor galloflavin. Docking studies were carried out to hypothesize the interaction mode of active compounds in the enzyme active site

Inhibitors of lactate dehydrogenase (hLDH5) from Polygala flavescens subsp. flavescens

The human isoform 5 of lactate dehydrogenase (hLDH5) is an enzyme up-regulated in tumor tissues since cancer cells depend mainly on anaerobic respiration and their glycolytic rate is up to 200 times higher than that of the normal tissue. hLDH5 inhibition should cause cancer cell death by starvation, without interfering with healthy cells that normally use oxidative phosphorylation for ATP generation. Inhibition of LDH is so considered as a promising target in cancer treatment, since it is possible to cause a starving of cancerous cells by reducing glycolysis or by inhibiting the conversion of glucose to lactate. In the course of our research program on the hLDH5 inhibitory activity of natural products [1], a chemical study of P. flavescens subsp. flavescens was carried out. Polygala L. genus (Polygalaceae) is well known to contain phenolic oligosaccharides, xanthones, lignans, and triterpenic saponins and it’s largely used in the traditional medicine [2]. Ten new compounds were isolated from the n-BuOH residue of the aerial parts through Sephadex and RP-HPLC separations, including four flavonol glycosides, two oligosaccharides, one α-ionone, and three triterpenoidic saponins, together with two known oligosaccharides and two flavonol glycosides. All structures were elucidated on the basis of their spectroscopic and spectrometric data. The isolates were assayed for their inhibitory activity against hLDH5 and 3,6'-di-O-sinapoylsucrose showed an IC50 value of 90.4 µM. Modeling studies were carried out to suggest the putative interaction mode of this compound in the enzyme active site. This analysis highlighted that 3,6'-di-O-sinapoylsucrose shows a high number of H-bonds and interacts with enzyme regions rarely explored by the known hLDH5 inhibitors

Interaction of anticancer reduced Schiff base coumarin derivatives with human serum albumin investigated by fluorescence quenching and molecular modeling

The specific binding of five reduced Schiff base derived 7-amino-coumarin compounds with antitumor activity to human serum albumin, the principal binding protein of blood, was studied by fluorescence spectroscopy. Their conditional binding constants were computed and the reversible binding at the Sudlow’s site I was found to be strong (KD ~ 0.03-2.09 M). Based on the data albumin can provide a depot for the compounds and is responsible for their biodistribution and transport processes. The experimental data is complemented by protein– ligand docking calculations for two representatives which support the observations. The proton dissociation constants of the compounds were also determined by UV-Vis spectrophotometric and fluorometric titrations to obtain the actual charges and distribution of the species in the various protonation states at physiological pH

Salicylaldoxime derivatives as new leads for the development of carbonic anhydrase inhibitors

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