Design Of Novel Ligands Research Articles

Computer-aided pattern scoring – A multitarget dataset-driven workflow to predict ligands of orphan targets

The identification of lead molecules and the exploration of novel pharmacological drug targets are major challenges of medical life sciences today. Genome‐wide association studies, multi-omics, and systems pharmacology steadily reveal new protein networks, extending the known and relevant disease-modifying proteome. Unfortunately, the vast majority of the disease-modifying proteome consists of ‘orphan targets’ of which intrinsic ligands/substrates, (patho)physiological roles, and/or modulators are unknown. Undruggability is a major challenge in drug development today, and medicinal chemistry efforts cannot keep up with hit identification and hit-to-lead optimization studies. New ‘thinking-outside-the-box’ approaches are necessary to identify structurally novel and functionally distinctive ligands for orphan targets. Here we present a unique dataset that includes critical information on the orphan target ABCA1, from which a novel cheminformatic workflow – computer-aided pattern scoring (C@PS) – for the identification of novel ligands was developed. Providing a hit rate of 95.5% and molecules with high potency and molecular-structural diversity, this dataset represents a suitable template for general deorphanization studies.

Development of an analytical platform for the affinity screening of natural extracts by SEC-MS towards PPARα and PPARγ receptors

BackgroundPeroxisome proliferator-activated receptors (PPARs) belong to the superfamily of nuclear receptors and represent the targets for the therapeutical treatment of type 2 diabetes, dyslipidemia and hyperglycemia associated with metabolic syndrome. Some medicinal plants have been traditionally used to treat this kind of metabolic diseases. Today only few drugs targeting PPARs have been approved and for this reason, the rapid identification of novel ligands and/or chemical scaffolds starting from natural extracts would benefit of a selective affinity ligand fishing assay. ResultsIn this paper we describe the development of a new ligand fishing assay based on size exclusion chromatography (SEC) coupled to LC-MS for the analysis of complex samples such as botanical extracts. The known PPARα and PPARγ ligands, WY-14643 and rosiglitazone respectively, were used for system development and evaluation. The system has found application on an Allium lusitanicum methanolic extract, containing saponins, a class of chemical compounds which have attracted interest as PPARs ligands because of their hypolipidemic and insulin-like properties. SignificanceA new SEC-AS-MS method has been developed for the affinity screening of PPARα and PPARγ ligands. The system proved to be highly specific and will be used to improve the throughput for the identification of new selective metabolites from natural souces targeting PPARα and PPARγ.

Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview.

Drug discovery is a lengthy and intricate process, and in its early stage, crucial steps are the selection of the therapeutic target and the identification of novel ligands. Most targets are dysregulated in pathogenic cells; typically, their activation or deactivation leads to the desired effect, while in other cases, interfering with the target-natural binder complex achieves the therapeutic results. Biophysical assays are a suitable strategy for finding new ligands or interferent agents, being able to evaluate ligand-protein interactions and assessing the effect of small molecules (SMols) on macromolecular complexes. This mini-review provides a detailed analysis of widely used biophysical methods, including fluorescence-based approaches, circular dichroism, isothermal titration calorimetry, microscale thermophoresis, and NMR spectroscopy. After a brief description of the methodologies, examples of interaction and competition experiments are described, together with an analysis of the advantages and disadvantages of each technique. This mini-review provides an overview of the most relevant biophysical technologies that can help in identifying SMols able not only to bind proteins but also to interfere with macromolecular complexes.

In silico structure prediction and molecular docking analyses to reveal potential binding domain of Hepatitis B virus genotype A2

Hepatitis B Virus (HBV) infects the hepatocytes to cause serious liver diseases. HBeAg regulates the response of immune system to the intracellular capsid act as T-cell tolerogen. The immune response regulation may predispose to chronicity during perinatal infections to prevent the severe liver injuries. Various in silico approaches including comparative modeling, threading approach and ab initio approach were employed for the prediction of 3D structures of the selected protein followed by the validation of the predicted structures through Errat, Procheck and Anolea. The predicted 3D structure of HBeAg revealed overall quality factor of 95.9184%. Interestingly, it was observed that only 1.97% residues were present in outlier region while 98.03% in favored and allowed region. Molecular docking analyses were performed and the attempt was for the identification of novel ligands for HBeAg. The reported compound may regulate the activity and act as regulator of HBeAg. Interestingly, least binding energy of -7.1 Kcal/mol was observed in the reported compound and high binding affinity to predict the binding residues (Asp-51, Phe-53, Val-56, Arg-57, Met-95, Ala-98, Asn-103, Arg-111, Asp-112, Val-115, Val-118 and Asn-119). The function determination of the selected target protein is due to the identification of effective binding sites in protein structures. The reported compound may act as potent molecule and the predicted structure is reliable for the functional studies and structural insights.

Pharmacophore Mapping Combined with dbCICA Reveal New Structural Features for the Development of Novel Ligands Targeting α4β2 and α7 Nicotinic Acetylcholine Receptors

The neuronal nicotinic acetylcholine receptors (nAChRs) belong to the ligand-gated ion channel (GLIC) group, presenting a crucial role in several biological processes and neuronal disorders. The α4β2 and α7 nAChRs are the most abundant in the central nervous system (CNS), being involved in challenging diseases such as epilepsy, Alzheimer's disease, schizophrenia, and anxiety disorder, as well as alcohol and nicotine dependencies. In addition, in silico-based strategies may contribute to revealing new insights into drug design and virtual screening to find new drug candidates to treat CNS disorders. In this context, the pharmacophore maps were constructed and validated for the orthosteric sites of α4β2 and α7 nAChRs, through a docking-based Comparative Intermolecular Contacts Analysis (dbCICA). In this sense, bioactive ligands were retrieved from the literature for each receptor. A molecular docking protocol was developed for all ligands in both receptors by using GOLD software, considering GoldScore, ChemScore, ASP, and ChemPLP scoring functions. Output GOLD results were post-processed through dbCICA to identify critical contacts involved in protein-ligand interactions. Moreover, Crossminer software was used to construct a pharmacophoric map based on the most well-behaved ligands and negative contacts from the dbCICA model for each receptor. Both pharmacophore maps were validated by using a ROC curve. The results revealed important features for the ligands, such as the presence of hydrophobic regions, a planar ring, and hydrogen bond donor and acceptor atoms for α4β2. Parallelly, a non-planar ring region was identified for α7. These results can enable fragment-based drug design (FBDD) strategies, such as fragment growing, linking, and merging, allowing an increase in the activity of known fragments. Thus, our results can contribute to a further understanding of structural subunits presenting the potential for key ligand-receptor interactions, favoring the search in molecular databases and the design of novel ligands.

Insights into the Small Molecule Targeting of Biologically Relevant G-Quadruplexes: An Overview of NMR and Crystal Structures.

G-quadruplexes turned out to be important targets for the development of novel targeted anticancer/antiviral therapies. More than 3000 G-quadruplex small-molecule ligands have been described, with most of them exerting anticancer/antiviral activity by inducing telomeric damage and/or altering oncogene or viral gene expression in cancer cells and viruses, respectively. For some ligands, in-depth NMR and/or crystallographic studies were performed, providing detailed knowledge on their interactions with diverse G-quadruplex targets. Here, the PDB-deposited NMR and crystal structures of the complexes between telomeric, oncogenic or viral G-quadruplexes and small-molecule ligands, of both organic and metal-organic nature, have been summarized and described based on the G-quadruplex target, from telomeric DNA and RNA G-quadruplexes to DNA oncogenic G-quadruplexes, and finally to RNA viral G-quadruplexes. An overview of the structural details of these complexes is here provided to guide the design of novel ligands targeting more efficiently and selectively cancer- and virus-related G-quadruplex structures.

Identification of Novel Ligands for Targeted Antifibrotic Therapy of Chronic Pancreatitis.

PurposeChronic pancreatitis (CP) is an inflammatory disorder of the pancreas that leads to impaired pancreatic function. The limited therapeutic options and the lack of molecular targeting ligands or non-serum-based biomarkers hinder the development of target-specific drugs. Thus, there is a need for an unbiased, comprehensive discovery and evaluation of pancreatitis-specific ligands.MethodsThis study utilized a computational-guided in vivo phage display approach to select peptide ligands selective for cellular components in the caerulein-induced mouse model of CP. The identified peptides were conjugated to pegylated DOPC liposomes via the reverse-phase evaporation method, and the in vivo specificity and pharmacokinetics were determined. As proof of concept, CP-targeted liposomes were used to deliver an antifibrotic small molecular drug, apigenin. Antifibrotic effects determined by pancreatic histology, fibronectin expression, and collagen deposition were evaluated.ResultsWe have identified five peptides specific for chronic pancreatitis and demonstrated selectivity to activated pancreatic stellate cells, acinar cells, macrophages, and extracellular matrix, respectively. MDLSLKP-conjugated liposomes demonstrated an increased particle accumulation by 1.3-fold in the inflamed pancreas compared to the control liposomes. We also observed that targeted delivery of apigenin resulted in improved acini preservation, a 37.2% and 33.1% respective reduction in collagen and fibronectin expression compared to mice receiving the free drug, and reduced oxidative stress in the liver.ConclusionIn summary, we have developed a systematic approach to profile peptide ligands selective for cellular components of complex disease models and demonstrated the biomedical applications of the identified peptides to improve tissue remodeling in the inflamed pancreas.

Beam‐Search zum automatisierten Entwurf und Scoring neuer ROR‐Liganden mithilfe maschineller Intelligenz**

AbstractChemische Sprachmodelle ermöglichen ein De‐novo‐Wirkstoff‐Design ohne explizite chemische Konstruktionsregeln. Während solche Modelle angewendet wurden, um neuartige Verbindungen mit angestrebter biologischer Aktivität zu generieren, bleibt die tatsächliche Priorisierung und Auswahl der vielversprechendsten Molekülentwürfe (“Designs”) eine Herausforderung. Wir haben hier die von chemischen Sprachmodellen gelernten Wahrscheinlichkeiten mithilfe des Beam‐Search‐Algorithmus als Modell‐intrinsische Technik für das Moleküldesign und die Bewertung der Designs (“Scoring”) genutzt. Die prospektive Anwendung dieser Methode führte zu neuartigen inversen Agonisten der Retinoid‐related‐Orphan‐Rezeptoren (RORs). Jedes Design war in drei Reaktionsschritten synthetisierbar und zeigte eine niedrig‐mikromolare bis nanomolare Potenz gegenüber RORγ. Als Modell‐intrinsische Technik eliminiert das Beam‐Search‐Sampling die strikte Notwendigkeit externer Molekül‐Scoring‐Funktionen und erweitert damit die Anwendbarkeit generativer künstlicher Intelligenz in der datengetriebenen Wirkstoffforschung.

Unusual orthologs shed new light on the binding mechanism of ghrelin to its receptor GHSR1a

The gastric peptide ghrelin has important functions in energy metabolism and cellular homeostasis by activating growth hormone secretagogue receptor type 1a (GHSR1a). The N-terminal residues of ghrelin orthologs from all vertebrates are quite conserved; however, in orthologs from Cavia porcellus and Phyllostomus discolor, Ser2 and Leu5 are replaced by a smaller Ala and a positively charged Arg, respectively. In the present study, we first demonstrated that the hydrophobic Leu5 is essential for the function of human ghrelin, because Ala replacement caused an approximately 100-fold decrease in activity. However, replacement of Leu5 by an Arg residue caused much less disruption; further replacement of Ser2 by Ala almost restored full activity, although the [S2A] mutation itself showed slight detriments, implying that the positively charged Arg5 in the [S2A,L5R] mutant might form alternative interactions with certain receptor residues to compensate for the loss of the essential Leu5. To identify the responsible receptor residues, we screened GHSR1a mutants in which all conserved negatively charged residues in the extracellular regions and all aromatic residues in the ligand-binding pocket were mutated separately. According to the decrease in selectivity of the mutant receptors towards [S2A,L5R]ghrelin, we deduced that the positively charged Arg5 of the ghrelin mutant primarily interacts with the essential aromatic Phe286 at the extracellular end of the sixth transmembrane domain of GHSR1a by forming cation−π and π−π interactions. The present study provided new insights into the binding mechanism of ghrelin with its receptor, and thus would facilitate the design of novel ligands for GHSR1a.

Structural Investigations of Aroylindole Derivatives through 3D-QSAR and Multiple Pharmacophore Modeling for the Search of Novel Colchicines Inhibitor

Background : The ligand and structure based integrated strategies are being repeatedly and effectively employed for the precise search and design of novel ligands against various disease targets. Aroylindole derivative has a similar structural analogy as Combretastatin A-4, and exhibited potent anticancer activity on several cancer cell lines. Objective: To identify structural features of aroylindole derivatives through 3D-QSAR and multiple pharmacophore modelling for the search of novel colchicines inhibitor via virtual screening. Method: The present study utilizes ligand and structure based methodology for the establishment of structure activity correlation among trimethoxyaroylindole derivatives and the search of novel colchicines inhibitor via virtual screening. The 3D-QSAR studies were performed using Phase module and provided details of relationship between structure and biological activity. A single ligand based pharmacophore model was generated from Phase on compound 3 and compound 29 and three energetically optimized structure based pharmacophore models were generated from epharmacophore for co-crystallized ligand, compound 3 and compound 29 with protein PBD ID 1SA0, 5EYP and 5LYJ. These pharmacophoric features containing hit-like compounds were collected from commercially available ZINC database and screened using virtual screening workflow. Results and Discussion: The 3D-QSAR model studies with good PLSs statistics for factor four was characterized by the best prediction coefficient Q2 (0.8122), regression R2 (0.9405), SD (0.2581), F (102.7), P (1.56e-015), RMSE (0.402), Stability (0.5411) and Pearson-r (0.9397). The generated epharmacophores have GH scores over 0.5 and AUAC ≥ 0.7 indicated that all the pharmacophores were suitable for pharmacophore-based virtual screening. The virtual screened compounds ZINC12323179, ZINC01642724, and ZINC14238006 have showed similar structural alignment as co-crystallized ligand and showed the hydrogen bonding of ligand with ASN101, SER178, THR179, VAL238, CYS241 amino acid of protein. Conclusion: The study illustrates that the ligand and structure based pharmacophoric approach is beneficial for identification of structurally diverse hits, having better binding affinity on colchicines binding site as novel anticancer agents.

Main Avenues in Gold Coordination Chemistry.

In this contribution, we provide an overview of the main avenues that have emerged in gold coordination chemistry during the last years. The unique properties of gold have motivated research in gold chemistry, and especially regarding the properties and applications of gold compounds in catalysis, medicine, and materials chemistry. The advances in the synthesis and knowledge of gold coordination compounds have been possible with the design of novel ligands becoming relevant motifs that have allowed the preparation of elusive complexes in this area of research. Strong donor ligands with easily modulable electronic and steric properties, such as stable singlet carbenes or cyclometalated ligands, have been decisive in the stabilization of gold(0) species, gold fluoride complexes, gold hydrides, unprecedented π complexes, or cluster derivatives. These new ligands have been important not only from the fundamental structure and bonding studies but also for the synthesis of sophisticated catalysts to improve activity and selectivity of organic transformations. Moreover, they have enabled the facile oxidative addition from gold(I) to gold(III) and the design of a plethora of complexes with specific properties.

A novel ligand of the translationally controlled tumor protein (TCTP) identified by virtual drug screening for cancer differentiation therapy

SummaryIntroduction Differentiation therapy is a promising strategy for cancer treatment. The translationally controlled tumor protein (TCTP) is an encouraging target in this context. By now, this field of research is still at its infancy, which motivated us to perform a large-scale screening for the identification of novel ligands of TCTP. We studied the binding mode and the effect of TCTP blockade on the cell cycle in different cancer cell lines. Methods Based on the ZINC-database, we performed virtual screening of 2,556,750 compounds to analyze the binding of small molecules to TCTP. The in silico results were confirmed by microscale thermophoresis. The effect of the new ligand molecules was investigated on cancer cell survival, flow cytometric cell cycle analysis and protein expression by Western blotting and co-immunoprecipitation in MOLT-4, MDA-MB-231, SK-OV-3 and MCF-7 cells. Results Large-scale virtual screening by PyRx combined with molecular docking by AutoDock4 revealed five candidate compounds. By microscale thermophoresis, ZINC10157406 (6-(4-fluorophenyl)-2-[(8-methoxy-4-methyl-2-quinazolinyl)amino]-4(3H)-pyrimidinone) was identified as TCTP ligand with a KD of 0.87 ± 0.38. ZINC10157406 revealed growth inhibitory effects and caused G0/G1 cell cycle arrest in MOLT-4, SK-OV-3 and MCF-7 cells. ZINC10157406 (2 × IC50) downregulated TCTP expression by 86.70 ± 0.44% and upregulated p53 expression by 177.60 ± 12.46%. We validated ZINC10157406 binding to the p53 interaction site of TCTP and replacing p53 by co-immunoprecipitation. Discussion ZINC10157406 was identified as potent ligand of TCTP by in silico and in vitro methods. The compound bound to TCTP with a considerably higher affinity compared to artesunate as known TCTP inhibitor. We were able to demonstrate the effect of TCTP blockade at the p53 binding site, i.e. expression of TCTP decreased, whereas p53 expression increased. This effect was accompanied by a dose-dependent decrease of CDK2, CDK4, CDK, cyclin D1 and cyclin D3 causing a G0/G1 cell cycle arrest in MOLT-4, SK-OV-3 and MCF-7 cells. Our findings are supposed to stimulate further research on TCTP-specific small molecules for differentiation therapy in oncology.

Identifying key residues and key interactions for the binding of LEAP2 to receptor GHSR1a.

Liver-expressed antimicrobial peptide 2 (LEAP2) was recently identified as a competitive antagonist for the G protein-coupled receptor GHSR1a, the cognate receptor for the gastric peptide ghrelin. LEAP2 plays important functions in energy metabolism by tuning the ghrelin-GHSR1a system. However, the molecular mechanism by which LEAP2 binds to GHSR1a is largely unknown. In the present study, we first conducted alanine-scanning mutagenesis on the N-terminal fragment of human LEAP2 and demonstrated that the positively charged Arg6 and the aromatic Phe4 are essential for LEAP2 binding to GHSR1a. To identify the receptor residues interacting with the essential Arg6 and Phe4 of LEAP2, we conducted extensive site-directed mutagenesis on GHSR1a. After all conserved negatively charged residues in the extracellular regions of human GHSR1a were mutated, only mutation of Asp99 caused much more detriments to GHSR1a binding to LEAP2 than binding to ghrelin, suggesting that the absolutely conserved Asp99 of GHSR1a probably interacts with the essential Arg6 of LEAP2. After five conserved Phe residues in the predicted ligand-binding pocket of human GHSR1a were mutated, three of them were identified as important for GHSR1a binding to LEAP2. According to a structural model of GHSR1a, we deduced that the adjacent Phe279 and Phe312 might interact with the essential Phe4 of LEAP2, while Phe119 might interact with the aromatic Trp5 of LEAP2. The present study provided new insights into the interaction of LEAP2 with its receptor, and would facilitate the design of novel ligands for GHSR1a in future studies.

Quantitative structure-activity relationship (QSAR) and design of novel ligands that demonstrate high potency and target selectivity as protein tyrosine phosphatase 1B (PTP 1B) inhibitors as an effective strategy used to model anti-diabetic agents

Diabetes and obesity have increased dramatically in recent decades worldwide. Diabetes mainly emerged as a major health care burden disease in both the US and other industrialized countries, among which type II diabetes is the most common. Discovering new and effective treatments for diabetes is currently a high international health priority. In the present study a computational technique was used to model 97 compounds with PTP-1B inhibitory activity, in order to demonstrate the Quantitative structure-activity relationship (QSAR) of these compounds a genetic function approximation (GFA) algorithm was applied to pick the best descriptors and multiple linear regression (MLR) was used to establish a relationship between the PTP-1B inhibitory activity of these compounds and the best molecular descriptors. This QSAR study allowed investigating the influence of very simple and easy-to-compute descriptors in determining biological activities, which shed light on the key factors that aid in the design of novel potent molecules using computer-aided drug design tools.

Identification of novel ligands that alter the function of type II NKT cells

Abstract Natural killer T (NKT) cells are distinct innate lymphocytes which recognize lipid antigens in the context of the major histocompatibility complex-like molecule CD1d. When activated, these cells can rapidly produce a variety of cytokines and modulate innate and adaptive immune responses. There are two main subsets of NKT cells, termed type I and type II NKT cells. Type I NKT cells are characterized primarily on the basis of their invariant TCRα expression and reactivity to the glycolipid α-galactosyl ceramide (αGalCer), whereas type II NKT cells express a different and more diverse TCR repertoire than type I NKT cells. Currently, the most widely studied antigen for type II NKT cells is sulfatide. Sulfatide-reactive type II NKT cells are reported to have the immunosuppressive function in autoimmune diseases and cancer. We previously showed a role for sulfatide-reactive type II NKT cells in suppressing tumor immunosurveillance in a murine model of lung metastasis. The activation of type II NKT cells in this model by the injection of sulfatide increased the development of lung metastasis. We synthesized diverse sulfatide-analogues varying in the number of double bonds and hydroxyl groups in the ceramide. In vitro, analogues having a phytosphingosine sphingoid base activated both type II and type I NKT cell hybridomas. On the other hand, the analogue C24:2 with a sphingosine base activated only the type II NKT cell hybridoma. In vivo, the C24:2 analogue significantly reduced the development of lung metastasis, showing distinct and opposite effects from sulfatide. The identification of new ligands inducing altered functional activity of type II NKT cells could be of great interest for developing new anti-tumor immunotherapies.

High-Content Imaging for Large-Scale Detection of Low-Affinity Extracellular Protein Interactions

Extracellular protein interactions coordinate cellular responses with their local environment and have important roles in pathogen invasion and disease. Due to technical challenges associated with studying binding events at the cell surface, the systematic and reliable identification of novel ligand–receptor pairs remains difficult. Here, we describe the development of a cell-based assay using large-scale transient transfections and high-content imaging (HCI) to detect extracellular binding events. We optimized the parameters for efficient transfection of human cells with cDNA plasmids encoding full-length cell surface receptors in 384-well plates. Using a range of well-characterized structurally diverse low-affinity cell surface interactions, we show that transfected cells probed with highly avid ligands can be used to successfully identify ligand–receptor pairs using an HCI platform and automated image analysis software. To establish the high-throughput potential of this approach, we also screened a pool of ligands against a collection of 2455 cell surface expression clones and found that known ligand–receptor interactions could be robustly and consistently detected across the library using this technology.

Functional Cross-Talk between Adenosine and Metabotropic Glutamate Receptors.

: G-protein coupled receptors are transmembrane proteins widely expressed in cells and their transduction pathways are mediated by controlling second messenger levels through different G-protein interactions. Many of these receptors have been described as involved in the physiopathology of neurodegenerative diseases and even considered as potential targets for the design of novel therapeutic strategies. Endogenous and synthetic allosteric and orthosteric selective ligands are able to modulate GPCRs at both gene and protein expression levels and can also modify their physiological function. GPCRs that coexist in the same cells can homo- and heteromerize, therefore, modulating their function. Adenosine receptors are GPCRs which stimulate or inhibit adenylyl cyclase activity through Gi/Gs protein and are involved in the control of neurotransmitter release as glutamate. In turn, metabotropic glutamate receptors are also GPCRs which inhibit adenylyl cyclase or stimulate phospholipase C activities through Gi or Gq proteins, respectively. In recent years, evidence of crosstalk mechanisms be-tween different GPCRs have been described. The aim of the present review was to summarize the described mechanisms of interaction and crosstalking between adenosine and metabotropic glutamate receptors, mainly of group I, in both in vitro and in vivo systems, and their possible use for the design of novel ligands for the treatment of neurodegenerative diseases.

Discovery of a small molecule modulator of the Kv1.1/Kvβ1 channel complex that reduces neuronal excitability and in vitro epileptiform activity.

Kv1.1 (KCNA1) channels contribute to the control of neuronal excitability and have been associated with epilepsy. Kv1.1 channels can associate with the cytoplasmic Kvβ1 subunit resulting in rapid inactivating A-type currents. We hypothesized that removal of channel inactivation, by modulating Kv1.1/Kvβ1 interaction with a small molecule, would lead to decreased neuronal excitability and anticonvulsant activity. We applied high-throughput screening to identify ligands able to modulate the Kv1.1-T1 domain/Kvβ1 protein complex. We then selected a compound that was characterized on recombinant Kv1.1/Kvβ1 channels by electrophysiology and further evaluated on sustained neuronal firing and on in vitro epileptiform activity using a high K+ -low Ca2+ model in hippocampal slices. We identified a novel compound able to modulate the interaction of the Kv1.1/Kvβ1 complex and that produced a functional inhibition of Kv1.1/Kvβ1 channel inactivation. We demonstrated that this compound reduced the sustained repetitive firing in hippocampal neurons and was able to abolish the development of in vitro epileptiform activity. This study describes a rational drug discovery approach for the identification of novel ligands that inhibit Kv1.1 channel inactivation and provides pharmacological evidence that such a mechanism translates into physiological effects by reducing in vitro epileptiform activity.

Identification of Novel Ligands for Therapeutic Lipopeptides: Daptomycin, Surfactin and Polymyxin.

Due to increase in antibiotic-resistance among pathogens, there is a need for potent and safe drugs. An alternative to antibiotics is lipopeptides which are produced as a secondary metabolite by many microorganisms. They exhibit broad-spectrum activities against pathogens along with anticancer properties. Among various lipopeptides produced by microorganisms, daptomycin, surfactin, and polymyxin have gained popularity as medicines but their mechanism of action is not described properly. In silico drug design of these lipopeptides becomes a challenge due to their complex structures. In order to initiate a physiological response, specific agonists (ligands) of their receptor (lipopeptide) must be identified. The objective of this study was molecular docking of three lipopeptides, daptomycin, surfactin and polymyxin, with their ligands as a means of drug design. Schrödinger software was used for molecular docking of lipopeptides with their corresponding ligands whereas the ligand search was done using RCSB. Once the ligands were identified, they were docked with their corresponding lipopeptide. Docking score and glide energy were used as the parameters to test docking. All four of the identified ligands were found to dock with daptomycin, whereas for both surfactin and polymyxin one out of two ligands docked with the lipopeptides. The knowledge of the docking sites and docking characteristics of the lipopeptide mentioned in the paper with the ligands can provide advantages of high speed and reliability, reduced costs on chemicals and experiments and the ethical issues concerned with the use of animal models for screening of drug toxicity.

High-throughput identification of G protein-coupled receptor modulators through affinity mass spectrometry screening.

G protein-coupled receptors (GPCRs) represent the largest class of cell surface proteins and thus constitute an important family of therapeutic targets. Therefore, significant effort has been put towards the identification of novel ligands that can modulate the activity of a GPCR target with high efficacy and selectivity. However, due to limitations inherent to the most common techniques for GPCR ligand discovery, there is a pressing need for more efficient and effective ligand screening methods especially for the identification of potential allosteric modulators. Here we present a high-throughput, label-free and unbiased screening approach for the identification of small molecule ligands towards GPCR targets based on affinity mass spectrometry. This new approach features the usage of target-expressing cell membranes rather than purified proteins for ligand screening and allows the detection of both orthosteric and allosteric ligands targeting specific GPCRs. Screening a small compound library with this approach led to the rapid discovery of an antagonist for the 5-HT receptor and four positive allosteric modulators for GLP-1 receptor that were not previously reported.