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The pharmacological space comprises all the dynamic events that determine the bioactivity (and/or the metabolism and toxicity) of a given ligand. The pharmacological space accounts for the structural flexibility and property variability of the two interacting molecules as well as for the mutual adaptability characterizing their molecular recognition process. The dynamic behavior of all these events can be described by a set of possible states (e.g., conformations, binding modes, isomeric forms) that the simulated systems can assume. For each monitored state, a set of state-dependent ligand- and structure-based descriptors can be calculated. Instead of considering only the most probable state (as routinely done), the pharmacological space proposes to consider all the monitored states. For each state-dependent descriptor, the corresponding space can be evaluated by calculating various dynamic parameters such as mean and range values.The reviewed examples emphasize that the pharmacological space can find fruitful applications in structure-based virtual screening as well as in toxicity prediction. In detail, in all reported examples, the inclusion of the pharmacological space parameters enhances the resulting performances. Beneficial effects are obtained by combining both different binding modes to account for ligand mobility and different target structures to account for protein flexibility/adaptability.The proposed computational workflow that combines docking simulations and rescoring analyses to enrich the arsenal of docking-based descriptors revealed a general applicability regardless of the considered target and utilized docking engine. Finally, the EFO approach that generates consensus models by linearly combining various descriptors yielded highly performing models in all discussed virtual screening campaigns.
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Simulação de Acoplamento Molecular , Ligantes , Humanos , Ligação Proteica , Proteínas/química , Proteínas/metabolismo , Descoberta de Drogas/métodos , Sítios de LigaçãoRESUMO
The search for new drugs fulfilling One Health and Green Chemistry requirements is an urgent call. Here, for the first time, we envisaged developing SAHA analogues by starting from the cashew nutshell liquid (CNSL) agro-industrial waste and employing a metathesis approach. This sustainable combination (comprising principles #7 and #9) allowed a straightforward synthesis of compounds 13-20. All of them were found to not be toxic on HepG2, IMR-32, and L929 cell lines. Then, their potential against major human and animal vector-borne parasitic diseases (VBPDs) was assessed. Compound 13 emerged as a green hit against the trypomastigote forms of T. b. brucei. In silico studies showed that the T. b. brucei HDAC (TbDAC) catalytic pocket could be occupied with a similar binding mode by both SAHA and 13, providing a putative explanation for its antiparasitic mechanism of action (13, EC50 = 0.7 ± 0.2 µM).
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In silico prediction of xenobiotic metabolism is an important strategy to accelerate the drug discovery process, as candidate compounds often fail in clinical phases due to their poor pharmacokinetic profiles. Here we present MetaQM, a dataset of quantum-mechanical (QM) optimized metabolic substrates, including force field parameters, electronic and physicochemical properties. MetaQM comprises 2054 metabolic substrates extracted from the MetaQSAR database. We provide QM-optimized geometries, General Amber Force Field (FF) parameters for all studied molecules, and an extended set of structural and physicochemical descriptors as calculated by DFT and PM7 methods. The generated data can be used in different types of analysis. FF parameters can be applied to perform classical molecular mechanics calculations as exemplified by the validating molecular dynamics simulations reported here. The calculated descriptors can represent input features for developing improved predictive models for metabolism and drug design, as exemplified in this work. Finally, the QM-optimized molecular structures are valuable starting points for both ligand- and structure-based analyses such as pharmacophore mapping and docking simulations.
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Teoria Quântica , Simulação de Dinâmica Molecular , Xenobióticos/química , Xenobióticos/metabolismo , Descoberta de DrogasRESUMO
[This corrects the article DOI: 10.1016/j.csbj.2024.05.024.].
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A new series of muscarinic acetylcholine receptor (mAChR) ligands obtained by inserting different substituents in position 2 of the potent 6,6-diphenyl-1,4-dioxane antagonists 4 and 5 was designed and synthesized to investigate the influence of steric bulk on the mAChR affinity. Specifically, the insertion of a 2-methyl group, affording compounds 6 and 9, resulted as the most favorable modification in terms of affinity for all muscarinic subtypes. As supported by computational studies performed on the hM1 receptor, this substituent may contribute to stabilize the ligand within the binding site by favoring the formation of stable interactions between the cationic head of the ligand and the residue D105. The increase of steric bulk, obtained by replacing the methyl group with an ethyl (7 and 10) and especially a phenyl substituent (8 and 11), caused a marked decrease of mAChR affinity, demonstrating the crucial role played by the steric bulk of the 2-substituent in the mAChR interaction. The most intriguing result was obtained with the tertiary amine 9, which, surprisingly, showed two different pKi values for all mAChRs, with preferential subpicomolar affinities for the M1, M3, and M4 subtypes. Interestingly, biphasic curves were also observed with both the eutomer (S)-(-)-9 and the distomer (R)-( + )-9.
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We describe a facile method to prepare water-compatible molecularly imprinted polymer nanogels (MIP NGs) as synthetic antibodies against target glycans. Three different phenylboronic acid (PBA) derivatives were explored as monomers for the synthesis of MIP NGs targeting either α2,6- or α2,3-sialyllactose, taken as oversimplified models of cancer-related sT and sTn antigens. Starting from commercially available 3-acrylamidophenylboronic acid, also its 2-substituted isomer and the 5-acrylamido-2-hydroxymethyl cyclic PBA monoester derivative were initially evaluated by NMR studies. Then, a small library of MIP NGs imprinted with the α2,6-linked template was synthesized and tested by mobility shift Affinity Capillary Electrophoresis (msACE), to rapidly assess an affinity ranking. Finally, the best monomer 2-acrylamido PBA was selected for the synthesis of polymers targeting both sialyllactoses. The resulting MIP NGs display an affinity constant≈106â M-1 and selectivity towards imprinted glycans. This general procedure could be applied to any non-modified carbohydrate template possessing a reducing end.
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Ácidos Borônicos , Lactose , Nanogéis , Ácidos Borônicos/química , Lactose/química , Lactose/análogos & derivados , Nanogéis/química , Polímeros Molecularmente Impressos/química , Impressão Molecular , Polímeros/química , Eletroforese Capilar , Polietilenoglicóis/química , Polissacarídeos/química , Ácidos SiálicosRESUMO
Molecular docking is a widely used technique in drug discovery to predict the binding mode of a given ligand to its target. However, the identification of the near-native binding pose in docking experiments still represents a challenging task as the scoring functions currently employed by docking programs are parametrized to predict the binding affinity, and, therefore, they often fail to correctly identify the ligand native binding conformation. Selecting the correct binding mode is crucial to obtaining meaningful results and to conveniently optimizing new hit compounds. Deep learning (DL) algorithms have been an area of a growing interest in this sense for their capability to extract the relevant information directly from the protein-ligand structure. Our review aims to present the recent advances regarding the development of DL-based pose selection approaches, discussing limitations and possible future directions. Moreover, a comparison between the performances of some classical scoring functions and DL-based methods concerning their ability to select the correct binding mode is reported. In this regard, two novel DL-based pose selectors developed by us are presented.
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BACKGROUND: The viral main protease (Mpro) of SARS-CoV-2 has been recently proposed as a key target to inhibit virus replication in the host. Therefore, molecules that can bind the catalytic site of Mpro could be considered as potential drug candidates in the treatment of SARS-CoV-2 infections. Here we proposed the application of a state-of-the-art analytical platform which combines metabolomics and protein structure analysis to fish-out potential active compounds deriving from a natural matrix, i.e., a blueberry extract. METHODS: The experiments focus on finding MS covalent inhibitors of Mpro that contain in their structure a catechol/pyrogallol moiety capable of binding to the nucleophilic amino acids of the enzyme's catalytic site. RESULTS: Among the potential candidates identified, the delphinidin-3-glucoside showed the most promising results. Its antiviral activity has been confirmed in vitro on Vero E6 cells infected with SARS-CoV-2, showing a dose-dependent inhibitory effect almost comparable to the known Mpro inhibitor baicalin. The interaction of delphinidin-3-glucoside with the Mpro pocket observed was also evaluated by computational studies. CONCLUSIONS: The HRMS analytical platform described proved to be effective in identifying compounds that covalently bind Mpro and are active in the inhibition of SARS-CoV-2 replication, such as delphinidin-3-glucoside.
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Antocianinas , Antivirais , Mirtilos Azuis (Planta) , Proteases 3C de Coronavírus , Extratos Vegetais , Inibidores de Proteases , SARS-CoV-2 , Mirtilos Azuis (Planta)/química , Antocianinas/farmacologia , Antocianinas/química , Antivirais/farmacologia , Antivirais/química , Chlorocebus aethiops , Células Vero , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/enzimologia , Animais , Extratos Vegetais/farmacologia , Extratos Vegetais/química , Inibidores de Proteases/farmacologia , Inibidores de Proteases/química , Proteases 3C de Coronavírus/antagonistas & inibidores , Proteases 3C de Coronavírus/metabolismo , Tratamento Farmacológico da COVID-19 , Humanos , Simulação de Acoplamento Molecular , COVID-19/virologia , GlucosídeosRESUMO
Extracellular vesicles (EVs) appear to play an important role in intercellular communication in various physiological processes and pathological conditions such as cancer. Like enveloped viruses, EVs can transport their contents into the nucleus of recipient cells, and a new intracellular pathway has been described to explain the nuclear shuttling of EV cargoes. It involves a tripartite protein complex consisting of vesicle-associated membrane protein-associated protein A (VAP-A), oxysterol-binding protein (OSBP)-related protein-3 (ORP3) and late endosome-associated Rab7 allowing late endosome entry into the nucleoplasmic reticulum. Rab7 binding to ORP3-VAP-A complex can be blocked by the FDA-approved antifungal drug itraconazole. Here, we design a new series of smaller triazole derivatives, which lack the dioxolane moiety responsible for the antifungal function, acting on the hydrophobic sterol-binding pocket of ORP3 and evaluate their structure-activity relationship through inhibition of VOR interactions and nuclear transfer of EV and HIV-1 cargoes. Our investigation reveals that the most effective compounds that prevent nuclear transfer of EV cargo and productive infection by VSV-G-pseudotyped HIV-1 are those with a side chain between 1 and 4 carbons, linear or branched (methyl) on the triazolone region. These potent chemical drugs could find clinical applications either for nuclear transfer of cancer-derived EVs that impact metastasis or viral infection.
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Infecções por HIV , Triazóis , Triazóis/química , Triazóis/farmacologia , Triazóis/síntese química , Humanos , Relação Estrutura-Atividade , Estrutura Molecular , Infecções por HIV/tratamento farmacológico , Infecções por HIV/metabolismo , HIV-1/efeitos dos fármacos , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/síntese química , Relação Dose-Resposta a Droga , Transporte Ativo do Núcleo Celular/efeitos dos fármacos , Vesículas Extracelulares/metabolismo , Vesículas Extracelulares/efeitos dos fármacos , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Neoplasias/patologiaRESUMO
(1) Background: Within the framework of the European Interreg Italy-Switzerland B-ICE & Heritage project (2018-2022), this study originated from a three-year ethnobotanical survey in Valmalenco (Sondrio, Italy). Following a preliminary work published by our group, this research further explored the folk therapeutic use of Achillea erba-rotta subsp. moschata (Wulfen) I.Richardson (Asteraceae) for dyspepsia disorders, specifically its anti-inflammatory potential at a gastrointestinal level. (2) Methods: Semi-structured interviews were performed. The bitter taste was investigated through molecular docking software (PLANTS, GOLD), while the anti-inflammatory activity of the hydroethanolic extract, infusion, and decoction was evaluated based on the release of IL-8 and IL-6 after treatment with TNFα or Helicobacter pylori. The minimum inhibitory concentration and bacterial adhesion on the gastric epithelium were evaluated. (3) Results: In total, 401 respondents were interviewed. Molecular docking highlighted di-caffeoylquinic acids as the main compounds responsible for the interaction with bitter taste receptors. The moderate inhibition of IL-6 and IL-8 release was recorded, while, in the co-culture with H. pylori, stronger anti-inflammatory potential was expressed (29-45 µg/mL). The concentration-dependent inhibition of H. pylori growth was recorded (MIC = 100 µg/mL), with a significant anti-adhesive effect. (4) Conclusions: Confirming the folk tradition, the study emphasizes the species' potentiality for dyspepsia disorders. Future studies are needed to identify the components mostly responsible for the biological effects.
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The conversion of chemical structures into computer-readable descriptors, able to capture key structural aspects, is of pivotal importance in the field of cheminformatics and computer-aided drug design. Molecular fingerprints represent a widely employed class of descriptors; however, their generation process is time-consuming for large databases and is susceptible to bias. Therefore, descriptors able to accurately detect predefined structural fragments and devoid of lengthy generation procedures would be highly desirable. To meet additional needs, such descriptors should also be interpretable by medicinal chemists, and suitable for indexing databases with trillions of compounds. To this end, we developed-as integral part of EXSCALATE, Dompé's end-to-end drug discovery platform-the DompeKeys (DK), a new substructure-based descriptor set, which encodes the chemical features that characterize compounds of pharmaceutical interest. DK represent an exhaustive collection of curated SMARTS strings, defining chemical features at different levels of complexity, from specific functional groups and structural patterns to simpler pharmacophoric points, corresponding to a network of hierarchically interconnected substructures. Because of their extended and hierarchical structure, DK can be used, with good performance, in different kinds of applications. In particular, we demonstrate how they are very well suited for effective mapping of chemical space, as well as substructure search and virtual screening. Notably, the incorporation of DK yields highly performing machine learning models for the prediction of both compounds' activity and metabolic reaction occurrence. The protocol to generate the DK is freely available at https://dompekeys.exscalate.eu and is fully integrated with the Molecular Anatomy protocol for the generation and analysis of hierarchically interconnected molecular scaffolds and frameworks, thus providing a comprehensive and flexible tool for drug design applications.
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Cancer spreading through metastatic processes is one of the major causes of tumour-related mortality. Metastasis is a complex phenomenon which involves multiple pathways ranging from cell metabolic alterations to changes in the biophysical phenotype of cells and tissues. In the search for new effective anti-metastatic agents, we modulated the chemical structure of the lead compound AA6, in order to find the structural determinants of activity, and to identify the cellular target responsible of the downstream anti-metastatic effects observed. New compounds synthesized were able to inhibit in vitro B16-F10 melanoma cell invasiveness, and one selected compound, CM365, showed in vivo anti-metastatic effects in a lung metastasis mouse model of melanoma. Septin-4 was identified as the most likely molecular target responsible for these effects. This study showed that CM365 is a promising molecule for metastasis prevention, remarkably effective alone or co-administered with drugs normally used in cancer therapy, such as paclitaxel.
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Neoplasias Pulmonares , Melanoma Experimental , Animais , Camundongos , Septinas , Melanoma Experimental/tratamento farmacológico , Melanoma Experimental/patologia , Neoplasias Pulmonares/tratamento farmacológico , Paclitaxel , Modelos Animais de Doenças , Camundongos Endogâmicos C57BLRESUMO
The ability to determine and predict metabolically labile atom positions in a molecule (also called "sites of metabolism" or "SoMs") is of high interest to the design and optimization of bioactive compounds, such as drugs, agrochemicals, and cosmetics. In recent years, several in silico models for SoM prediction have become available, many of which include a machine-learning component. The bottleneck in advancing these approaches is the coverage of distinct atom environments and rare and complex biotransformation events with high-quality experimental data. Pharmaceutical companies typically have measured metabolism data available for several hundred to several thousand compounds. However, even for metabolism experts, interpreting these data and assigning SoMs are challenging and time-consuming. Therefore, a significant proportion of the potential of the existing metabolism data, particularly in machine learning, remains dormant. Here, we report on the development and validation of an active learning approach that identifies the most informative atoms across molecular data sets for SoM annotation. The active learning approach, built on a highly efficient reimplementation of SoM predictor FAME 3, enables experts to prioritize their SoM experimental measurements and annotation efforts on the most rewarding atom environments. We show that this active learning approach yields competitive SoM predictors while requiring the annotation of only 20% of the atom positions required by FAME 3. The source code of the approach presented in this work is publicly available.
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Aprendizado de Máquina , SoftwareRESUMO
Carnosine, an endogenous dipeptide, has been found to have a plethora of medicinal properties, such as antioxidant, antiageing, and chelating effects, but with one downside: a short half-life. Carnosinases and two hydrolytic enzymes, which remain enigmatic, are responsible for these features. Hence, here we emphasize why research is valuable for better understanding crucial concepts like ageing, neurodegradation, and cancerogenesis, given that inhibition of carnosinases might significantly prolong carnosine bioavailability and allow its further use in medicine. Herein, we explore the literature regarding carnosinases and present a short in silico analysis aimed at elucidating the possible recognition pattern between CN1 and its ligands.
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Carnosina , Dipeptidases , Humanos , Carnosina/química , Carnosina/metabolismo , Antioxidantes , Dipeptidases/química , Dipeptidases/metabolismo , EnvelhecimentoRESUMO
TRPM8 is a non-selective cation channel permeable to both monovalent and divalent cations that is activated by multiple factors, such as temperature, voltage, pressure, and changes in osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathological conditions. Here, we present a cryo-electron microscopy structure of a human TRPM8 channel in the closed state that was solved at 2.7 Å resolution. Our structure comprises the most complete model of the N-terminal pre-melastatin homology region. We also visualized several lipids that are bound by the protein and modeled how the human channel interacts with icilin. Analyses of pore helices in available TRPM structures showed that all these structures can be grouped into different closed, desensitized and open state conformations based on the register of the pore helix S6 which positions particular amino acid residues at the channel constriction.
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Canais de Cátion TRPM , Humanos , Microscopia Crioeletrônica , Proteínas de Membrana/metabolismo , Temperatura , Canais de Cátion TRPM/metabolismoRESUMO
The prediction of drug metabolism is attracting great interest for the possibility of discarding molecules with unfavorable ADME/Tox profile at the early stage of the drug discovery process. In this context, artificial intelligence methods can generate highly performing predictive models if they are trained by accurate metabolic data. MetaQSAR-based datasets were collected to predict the sites of metabolism for most metabolic reactions. The models were based on a set of structural, physicochemical, and stereo-electronic descriptors and were generated by the random forest algorithm. For each considered biotransformation, two types of models were developed: the first type involved all non-reactive atoms and included atom types among the descriptors, while the second type involved only non-reactive centers having the same atom type(s) of the reactive atoms. All the models of the first type revealed very high performances; the models of the second type show on average worst performances while being almost always able to recognize the reactive centers; only conjugations with glucuronic acid are unsatisfactorily predicted by the models of the second type. Feature evaluation confirms the major role of lipophilicity, self-polarizability, and H-bonding for almost all considered reactions. The obtained results emphasize the possibility of recognizing the sites of metabolism by classification models trained on MetaQSAR database. The two types of models can be synergistically combined since the first models identify which atoms can undergo a given metabolic reactions, while the second models detect the truly reactive centers. The generated models are available as scripts for the VEGA program.
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Inteligência Artificial , Bases de Dados Factuais , Fenômenos Químicos , BiotransformaçãoRESUMO
INTRODUCTION: Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific collaborations while avoiding physical interactions. Thus, the E4C consortium presents the MEDIATE initiative which invited researchers to contribute via their virtual screening simulations that will be combined with AI-based consensus approaches to provide robust and method-independent predictions. The best compounds will be tested, and the biological results will be shared with the scientific community. AREAS COVERED: In this paper, the MEDIATE initiative is described. This shares compounds' libraries and protein structures prepared to perform standardized virtual screenings. Preliminary analyses are also reported which provide encouraging results emphasizing the MEDIATE initiative's capacity to identify active compounds. EXPERT OPINION: Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organized as challenges. The MEDIATE platform is focused on SARS-CoV-2 targets but can be seen as a prototype which can be utilized to perform collaborative virtual screening campaigns in any therapeutic field by sharing the appropriate input files.
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COVID-19 , SARS-CoV-2 , Humanos , Simulação de Acoplamento Molecular , Proteínas , AntiviraisRESUMO
As a rich source of biological active compounds, marine natural products have been increasingly screened as candidates for developing new drugs. Among the several marine products and metabolites, (+)-Harzialactone A has drawn considerable attention for its antitumor and antileishmanial activity. In this work a chemoenzymatic approach has been implemented for the preparation of the marine metabolite (+)-Harzialactone A. The synthesis involved a stereoselective, biocatalyzed reduction of the prochiral ketone 4-oxo-5-phenylpentanoic acid or the corresponding esters, all generated by chemical reactions. A collection of different promiscuous oxidoreductases (both wild-type and engineered) and diverse microorganism strains were investigated to mediate the bioconversions. After co-solvent and co-substrate investigation in order to enhance the bioreduction performance, T. molischiana in presence of NADES (choline hydrochloride-glucose) and ADH442 were identified as the most promising biocatalysts, allowing the obtainment of the (S)-enantiomer with excellent ee (97% to > 99% respectively) and good to excellent conversion (88% to 80% respectively). The successful attempt in this study provides a new chemoenzymatic approach for the synthesis of (+)-Harzialactone A.
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Cetonas , Oxirredutases , Biocatálise , Cetonas/química , Oxirredutases/metabolismo , EstereoisomerismoRESUMO
The paper presents the VEGA Online web service, which includes a set of freely available tools deriving from the development of the VEGA suite of programs. In detail, the paper is focused on two tools: the VEGA Web Edition (WE) and the Score tool. The former is a versatile file format converter including relevant features for 2D/3D conversion, for surface mapping and for editing/preparing input files. The Score application allows rescoring docking poses and in particular includes the MLP Interactions Scores (MLPInS) for describing hydrophobic interactions. To the best of our knowledge, this web service is the only available resource by which one can calculate both the virtual log P of a given input molecule according to the MLP approach plus the corresponding MLP surface.
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Modelos Moleculares , Software , InternetRESUMO
Obesity and type 2 diabetes (T2DM) are major public health concerns associated with serious morbidity and increased mortality. Both obesity and T2DM are strongly associated with adiposopathy, a term that describes the pathophysiological changes of the adipose tissue. In this review, we have highlighted adipose tissue dysfunction as a major factor in the etiology of these conditions since it promotes chronic inflammation, dysregulated glucose homeostasis, and impaired adipogenesis, leading to the accumulation of ectopic fat and insulin resistance. This dysfunctional state can be effectively ameliorated by the loss of at least 15% of body weight, that is correlated with better glycemic control, decreased likelihood of cardiometabolic disease, and an improvement in overall quality of life. Weight loss can be achieved through lifestyle modifications (healthy diet, regular physical activity) and pharmacotherapy. In this review, we summarized different effective management strategies to address weight loss, such as bariatric surgery and several classes of drugs, namely metformin, GLP-1 receptor agonists, amylin analogs, and SGLT2 inhibitors. These drugs act by targeting various mechanisms involved in the pathophysiology of obesity and T2DM, and they have been shown to induce significant weight loss and improve glycemic control in obese individuals with T2DM.