Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?

Molecular docking- and reporter-based screening identify dicoumarol against ER stress-induced liver injury in mice through inhibiting IRE1α activity

AIMS

Drug-induced liver injury is among the most challenging liver disorders. Endoplasmic reticulum (ER) is responsible for the correct protein folding and secretion, which are highly active in hepatocytes. Failure in maintaining the proper protein folding under pathological condition or external stimuli leads to the unfolded protein response (UPR) to restore ER homeostasis or induce cell death. IRE1α pathway is the most conserved UPR branch with diverse physiological and pathological functions. This study aimed to screen for natural compounds to alleviate hepatic ER stress and liver injury by modulating IRE1α activity.

MATERIALS AND METHODS

ATP-competitive molecules from chemical libraries were recognized by virtual screening for targeting the IRE1α kinase domain. IRE1α activity-based XBP1s-reporter cell lines with flow cytometric analysis were employed to validate candidates from chemical libraries. Then the functions of the top candidate compound on IRE1α signaling were analyzed followed by the treatment with ER stress agonists in vitro. Finally, the candidate compound was used to treat ER stress-induced acute liver injury to evaluate its protective effect in vivo.

KEY FINDINGS

Dicoumarol (DIC) was discovered as a potential inhibitor of IRE1α activation in HEK293T cells, HepG2 cells and primary hepatocytes. Particularly, DIC ameliorates tunicamycin (Tm)- and carbon tetrachloride (CCl4)-induced acute hepatic ER stress to protect against liver injury.

SIGNIFICANCE

This study established a drug screening strategy against IRE1α activation and identified potential new therapeutic effects of DIC in treating liver injury-related diseases.

Molecular simulations guided drugs repurposing to inhibit human GPx1 enzyme for cancer therapy

Overexpression of the antioxidant enzyme glutathione peroxidase-1 (GPx1) is associated with different cancer types. Inhibitors of GPx1, including mercaptosuccinic acid and pentathiepins derivatives, have been proposed previously and investigated as potent drugs to combat cancer. However, these compounds often lack specificity and demonstrate off-target effects, which necessitates the need for more targeted, non-toxic, and effective GPx1 inhibitors. This study utilized molecular docking and dynamic simulations based computational pipeline to repurpose drugs, approved by The Food and Drug Administration [1], as potent GPx1 inhibitors from a library containing 1615 synthetic compounds. The drug suitability and stability of the selected compounds were further investigated using ADMET, bioactivity probability, Molecular Mechanics-Generalized Born Surface Area (MM-GBSA), and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) analyses. Initially, 13 compounds were virtually screened based on the Triangle Matcher algorithm, docking modules, and GBVI/WSA dG scoring function. Of these 13 screened compounds, three compounds, including dronedarone, nilotinib, and thonzonium, were rigorously selected based on their ADMET profiles, physicochemical properties, drug suitability, and stability and were subjected to Molecular Dynamic (MD) simulations. MD simulations further validated the stability of the dronedarone, nilotinib, and thonzonium complexes with GPx1 and provided further insights into the mechanism of their interaction. The in-silico approaches used herein revealed thonzonium, dronedarone, and nilotinib as potent GPx1 inhibitors.

Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery

Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. While these methods are effective and are considered the gold standard, they are very resource-intensive and time-consuming, ultimately limiting their scalability. However, with recent developments in computational biology and artificial intelligence (AI), the field of protein prediction has been revolutionized. Innovations like AlphaFold and RoseTTAFold enable protein structure predictions to be made directly from amino acid sequences with remarkable speed and accuracy. Despite the enormous enthusiasm associated with these newly developed AI-approaches, their true potential in structure-based drug discovery remains uncertain. In fact, although these algorithms generally predict overall protein structures well, essential details for computational ligand docking, such as the exact location of amino acid side chains within the binding pocket, are not predicted with the necessary accuracy. Additionally, docking methodologies are considered more as a hypothesis generator rather than a precise predictor of ligand-target interactions, and thus, usually identify many false-positive hits among only a few correctly predicted interactions. In this paper, we are reviewing the latest development in this cutting-edge field with emphasis on the GPCR target class to assess the potential role of AI approaches in structure-based drug discovery.

Rapid traversal of vast chemical space using machine learning-guided docking screens

The accelerating growth of make-on-demand chemical libraries provides unprecedented opportunities to identify starting points for drug discovery with virtual screening. However, these multi-billion-scale libraries are challenging to screen, even for the fastest structure-based docking methods. Here we explore a strategy that combines machine learning and molecular docking to enable rapid virtual screening of databases containing billions of compounds. In our workflow, a classification algorithm is trained to identify top-scoring compounds based on molecular docking of 1 million compounds to the target protein. The conformal prediction framework is then used to make selections from the multi-billion-scale library, reducing the number of compounds to be scored by docking. The CatBoost classifier showed an optimal balance between speed and accuracy and was used to adapt the workflow for screens of ultralarge libraries. Application to a library of 3.5 billion compounds demonstrated that our protocol can reduce the computational cost of structure-based virtual screening by more than 1,000-fold. Experimental testing of predictions identified ligands of G protein-coupled receptors and demonstrated that our approach enables discovery of compounds with multi-target activity tailored for therapeutic effect.

Discovery of highly potent and novel LSD1 inhibitors for the treatment of acute myeloid leukemia: structure-based virtual screening, molecular dynamics simulation, and biological evaluation

Acute myeloid leukemia (AML) is a highly aggressive hematological malignancy with a significant unmet clinical need for new therapeutic agents. Lysine-specific demethylase 1 (LSD1), a key regulator of leukemia stem cell self-renewal, has emerged as a promising epigenetic target for AML treatment. Herein, we employed an innovative multi-step integrated screening protocol, encompassing pharmacophore modeling, docking screening, molecular dynamics simulation, and biological evaluation, to identify novel LSD1 inhibitors. This comprehensive approach led to the discovery of six potent LSD1 inhibitors (we named these inhibitors LTMs 1-6), with LTM-1 exhibiting the most pronounced inhibitory effects on LSD1 (IC50 = 2.11 ± 0.14 nM) and the highest selectivity for LSD1 over LSD2 (>2370-fold). Notably, LTM-1 demonstrated outstanding antitumor activity both in vitro and in vivo. In vitro, LTM-1 showed potent anti-proliferative effects against LSD1-addicted MV-4-11 leukemia cells (IC50 = 0.16 ± 0.01 μM). In vivo, LTM-1 treatment significantly reduced tumor growth in MV-4-11 xenografted mice. Moreover, LTM-1 did not induce significant changes in liver and kidney function indices, suggesting a favorable safety profile. These results indicate that LTM-1 is a highly promising preclinical candidate for AML treatment, offering a new strategy for the development of more effective and selective LSD1 inhibitors.

Improving the Reliability of Language Model-Predicted Structures as Docking Targets through Geometric Graph Learning

Applying artificial intelligence techniques to flexibly model the binding between the ligand and protein has attracted extensive interest in recent years, but their applicability remains improved. In this study, we have developed CarsiDock-Flex, a novel two-step flexible docking paradigm that generates binding poses directly from predicted structures. CarsiDock-Flex consists of an equivariant deep learning-based model termed CarsiInduce to refine ESMFold-predicted protein pockets with the induction of specific ligands and our existing CarsiDock algorithm to redock the ligand into the induced binding pockets. Extensive evaluations demonstrate the effectiveness of CarsiInduce, which can successfully guide the transition of ESMFold-predicted pockets into their holo-like conformations for numerous cases, thus leading to the superior docking accuracy of CarsiDock-Flex even on unseen sequences. Overall, our approach offers a novel design for flexible modeling of protein-ligand binding poses, paving the way for a deeper understanding of protein-ligand interactions that account for protein flexibility.

Structure and Function of Somatostatin and Its Receptors in Endocrinology

Somatostatin analogs, such as octreotide, lanreotide, and pasireotide, which function as somatostatin receptor ligands (SRLs), are the main drugs used for the treatment of acromegaly. These ligands are also used as important molecules for radiation therapy and imaging of neuroendocrine tumors. Somatostatin receptors (SSTRs) are canonical G protein-coupled proteins that play a role in metabolism, growth, and pathological conditions such as hormone disorders, neurological diseases, and cancers. Cryogenic electron microscopy combined with the protein structure prediction platform AlphaFold has been used to determine the 3-dimensional structures of many proteins. Recently, several groups published a series of papers illustrating the 3-dimensional structure of SSTR2, including that of the inactive/activated SSTR2-G protein complex bound to different ligands. The results revealed the residues that contribute to the ligand binding pocket and demonstrated that Trp8-Lys9 (the W-K motif) in somatostatin analogs is the key motif in stabilizing the bottom part of the binding pocket. In this review, we discuss the recent findings related to the structural analysis of SSTRs and SRLs, the relationships between the structural data and clinical findings, and the future development of novel structure-based therapies.

CPNE7 promotes colorectal tumorigenesis by interacting with NONO to initiate ZFP42 transcription

Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related death globally. Also, there is still a lack of effective therapeutic strategies for CRC patients owing to a poor understanding of its pathogenesis. Here, we analysed differentially expressed genes in CRC and identified CPNE7 as a novel driver of colorectal tumorigenesis. CPNE7 is highly expressed in CRC and negatively correlated with patients' prognosis. Upregulation of CPNE7 promotes proliferation and metastasis of cancer cells in vitro and in vivo, and vice versa. Mechanistically, CPNE7 interacts with NONO to initiate ZFP42 transcription, thus promoting CRC progression. Moreover, ZFP42 knockdown inhibits tumor cell proliferation and migration while promoting apoptosis. Notably, delivery of CPNE7 shRNA or the small molecule gramicidin, which blocks the interaction between CPNE7 and NONO, hinders tumor growth in vivo. In conclusion, our findings demonstrate that the CPNE7-NONO-ZFP42 axis promotes colorectal tumorigenesis and may be a new potential therapeutic target.

Targeting adhesion G protein-coupled receptors. Current status and future perspectives

G protein-coupled receptors (GPCRs) orchestrate many physiological functions and are a crucial target in drug discovery. Adhesion GPCRs (aGPCRs), the second largest family within this superfamily, are promising yet underexplored targets for treating various diseases, including obesity, psychiatric disorders, and cancer. However, the receptors' unique and complex structure and miscellaneous interactions complicate comprehensive pharmacological studies. Despite recent progress in determining structures and elucidation of the activation mechanism, the function of many receptors remains to be determined. This review consolidates current knowledge on aGPCR ligands, focusing on small molecule orthosteric ligands and allosteric modulators identified for the ADGRGs subfamily (subfamily VIII), (GPR56/ADGRG1, GPR64/ADGRG2, GPR97/ADGRG3, GPR114/ADGRG5, GPR126/ADGRG6, and GPR128/ADGRG7). We discuss challenges in hit identification, target validation, and drug discovery, highlighting molecular compositions and recent structural breakthroughs. ADGRG ligands can offer new insights into aGPCR modulation and have significant potential for novel therapeutic interventions targeting various diseases.

Machine learning-aided search for ligands of P2Y6 and other P2Y receptors

The P2Y6 receptor, activated by uridine diphosphate (UDP), is a target for antagonists in inflammatory, neurodegenerative, and metabolic disorders, yet few potent and selective antagonists are known to date. This prompted us to use machine learning as a novel approach to aid ligand discovery, with pharmacological evaluation at three P2YR subtypes: initially P2Y6 and subsequently P2Y1 and P2Y14. Relying on extensive published data for P2Y6R agonists, we generated and validated an array of classification machine learning model using the algorithms deep learning (DL), adaboost classifier (ada), Bernoulli NB (bnb), k-nearest neighbors (kNN) classifier, logistic regression (lreg), random forest classifier (rf), support vector classification (SVC), and XGBoost (XGB) classifier models, and the common consensus was applied to molecular selection of 21 diverse structures. Compounds were screened using human P2Y6R-induced functional calcium transients in transfected 1321N1 astrocytoma cells and fluorescent binding inhibition at closely related hP2Y14R expressed in CHO cells. The hit compound ABBV-744, an experimental anticancer drug with a 6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine scaffold, had multifaceted interactions with the P2YR family: hP2Y6R inhibition in a non-surmountable fashion, suggesting that noncompetitive antagonism, and hP2Y1R enhancement, but not hP2Y14R binding inhibition. Other machine learning-selected compounds were either weak (experimental anti-asthmatic drug AZD5423 with a phenyl-1H-indazole scaffold) or inactive in inhibiting the hP2Y6R. Experimental drugs TAK-593 and GSK1070916 (100 µM) inhibited P2Y14R fluorescent binding by 50% and 38%, respectively, and all other compounds by < 20%. Thus, machine learning has led the way toward revealing previously unknown modulators of several P2YR subtypes that have varied effects.

DSDPFlex: Flexible-Receptor Docking with GPU Acceleration

Molecular docking is an essential tool in structure-based drug discovery, widely utilized to model ligand-protein interactions and enrich potential hits. Among the different docking strategies, semiflexible docking (rigid-receptor and flexible-ligand model) is the most popular, benefiting from its balance of docking accuracy and speed. However, this approach ignores the conformational changes of proteins and hence demands suitable protein conformations as input. When the binding interaction adheres to an induced-fit model, flexible methods such as molecular dynamics simulation can be utilized, but they are computationally demanding. To balance between speed and accuracy, the flexible docking approach is an effective choice, as exemplified by AutoDock Vina and AutoDockFR, which treat selected protein side chains as flexible parts. However, the efficiency of flexible docking methods is yet to be improved for virtual screening usage. In this article, we introduce DSDPFlex, an improved flexible-receptor docking method accelerated by GPU parallelization. Beyond acceleration, optimizations with respect to sampling, scoring, and search space are implemented in DSDPFlex to further improve its capability in flexible tasks. In cross-docking evaluation, DSDPFlex demonstrates superior accuracy compared to AutoDock Vina and is 100 times faster than Vina in flexible-receptor tasks. We also show the advantage of flexible-receptor methods on suboptimal pockets and validate the advantage of DSDPFlex in screening on apo and AlphaFold2-predicted structures. With improvements in both efficiency and accuracy, DSDPFlex is expected to hold potential in future docking-based studies.

Exploring the potential anti-diabetic peripheral neuropathy mechanisms of Huangqi Guizhi Wuwu Decoction by network pharmacology and molecular docking

Diabetic peripheral neuropathy (DPN) is the most prevalent microvascular complication of diabetes and Huangqi Guizhi Wuwu Decoction (HGWD) is frequently employed in classical Chinese medicine for treating DPN. This study aims to investigate the potential therapeutic targets and mechanisms of HGWD for treating DPN using network pharmacology and molecular docking methodologies. The intersection targets of DPN and HGWD were retrieved from the databases, with the resulting intersection targets being imported into the STRING database to construct the protein-protein interaction (PPI) network. Cytoscape 3.9.1 was used to screen the core targets and plot the herb-active ingredient-target (H-A-T) network. To identify the pivotal signaling pathways, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on intersection targets. Molecular docking was subsequently conducted with AutoDock Vina to validate the binding energy between the core active ingredients and the core targets. 91 potential targets of HGWD were identified for the treatment of DPN. Topological analysis revealed core targets, including AKT1, TNF, PPARG, NFKB1, TP53, STAT3, PTGS2, HIF1A, ESR1, and GSK3B, alongside core active ingredients such as protoporphyrin, jaranol, kaempferol, quercetin, and isorhamnetin. GO and KEGG analyses indicated that PI3K/AKT, HIF-1, and AGE/RAGE signaling pathways could be crucial in treating DPN using HGWD. Furthermore, molecular docking results demonstrated robust binding activities between the active ingredients in HGWD and the identified core targets. The above results indicated that HGWD may exerting an anti-DPN effect by modulating the PI3K/AKT, HIF-1, and AGE/RAGE signaling pathways.

Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies

In recent years, the advent of computational techniques to predict the potential activity of a drug interacting with a receptor or to predict the structure of unidentified proteins with aberrant characteristics has significantly impacted the field of drug design. We provide a comprehensive review of the current state of in silico approaches and software for investigating the effects of receptor mutations associated with human diseases, focusing on both frequent and rare mutations. The reported techniques include virtual screening, homology modeling, threading, docking, and molecular dynamics. This review clearly shows that it is common for successful studies to integrate different techniques in drug design, with docking and molecular dynamics being the most frequently used techniques. This trend reflects the current emphasis on developing novel therapies for diseases resulting from receptor mutations with the recently discovered AlphaFold algorithm as the driving force.

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential

The steadily growing number of experimental G-protein-coupled receptor (GPCR) structures has revealed diverse locations of allosteric modulation, and yet few drugs target them. This gap highlights the need for a deeper understanding of allosteric modulation in GPCR drug discovery. The current work introduces a systematic annotation scheme to structurally classify GPCR binding sites based on receptor class, transmembrane helix contacts, and, for membrane-facing sites, membrane sublocation. This GPCR specific annotation scheme was applied to 107 GPCR structures bound by small molecules contributing to 24 distinct allosteric binding sites for comparative evaluation of three binding site detection methods (BioGPS, SiteMap, and FTMap). BioGPS identified the most in 22 of 24 sites. In addition, our property analysis showed that extrahelical allosteric ligands and binding sites represent a distinct chemical space characterized by shallow pockets with low volume, and the corresponding allosteric ligands showed an enrichment of halogens. Furthermore, we demonstrated that combining receptor and ligand similarity can be a viable method for ligandability assessment. One challenge regarding site prediction is the ligand shaping effect on the observed binding site, especially for extrahelical sites where the ligand-induced effect was most pronounced. To our knowledge, this is the first study presenting a binding site annotation scheme standardized for GPCRs, and it allows a comparison of allosteric binding sites across different receptors in an objective way. The insight from this study provides a framework for future GPCR binding site studies and highlights the potential of targeting allosteric sites for drug development.

Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer

Focused screening on target-prioritized compound sets can be an efficient alternative to high throughput screening (HTS). For most biomolecular targets, compound prioritization models depend on prior screening data or a target structure. For phenotypic or multi-protein pathway targets, it may not be clear which public assay records provide relevant data. The question also arises as to whether data collected from disparate assays might be usefully consolidated. Here, we report on the development and application of a data mining pipeline to examine these issues. To illustrate, we focus on identifying inhibitors of oxidative phosphorylation, a druggable metabolic process in epithelial ovarian tumors. The pipeline compiled 8415 available OXPHOS-related bioassays in the PubChem data repository involving 312,093 unique compound records. Application of PubChem assay activity annotations, PAINS (Pan Assay Interference Compounds), and Lipinski-like bioavailability filters yields 1852 putative OXPHOS-active compounds that fall into 464 clusters. These chemotypes are diverse but have relatively high hydrophobicity and molecular weight but lower complexity and drug-likeness. These chemotypes show a high abundance of bicyclic ring systems and oxygen containing functional groups including ketones, allylic oxides (alpha/beta unsaturated carbonyls), hydroxyl groups, and ethers. In contrast, amide and primary amine functional groups have a notably lower than random prevalence. UMAP representation of the chemical space shows strong divergence in the regions occupied by OXPHOS-inactive and -active compounds. Of the six compounds selected for biological testing, 4 showed statistically significant inhibition of electron transport in bioenergetics assays. Two of these four compounds, lacidipine and esbiothrin, increased in intracellular oxygen radicals (a major hallmark of most OXPHOS inhibitors) and decreased the viability of two ovarian cancer cell lines, ID8 and OVCAR5. Finally, data from the pipeline were used to train random forest and support vector classifiers that effectively prioritized OXPHOS inhibitory compounds within a held-out test set (ROCAUC 0.962 and 0.927, respectively) and on another set containing 44 documented OXPHOS inhibitors outside of the training set (ROCAUC 0.900 and 0.823). This prototype pipeline is extensible and could be adapted for focus screening on other phenotypic targets for which sufficient public data are available.Scientific contributionHere, we describe and apply an assay data mining pipeline to compile, process, filter, and mine public bioassay data. We believe the procedure may be more broadly applied to guide compound selection in early-stage hit finding on novel multi-protein mechanistic or phenotypic targets. To demonstrate the utility of our approach, we apply a data mining strategy on a large set of public assay data to find drug-like molecules that inhibit oxidative phosphorylation (OXPHOS) as candidates for ovarian cancer therapies.

Investigation on the mechanism of androsta-4,6,8,14-tetraene-3,11,16-trione against acute lymphoblastic leukemia

Steroids are potential anti-leukemia agents, and Epigynum auritum is a Yunnan folk medicine with high levels of androsterone, pregnane, and steroid derivatives. However, the underlying therapeutic mechanism of androsta-4,6,8,14-tetraene-3,11,16-trione (ATT), an androsterone isolated from Epigynum auritum, is not yet clear. This study aimed to explore the anti-leukemia mechanism of ATT using molecular biology, network pharmacology, and molecular docking technology. The cell viability results showed that ATT had an anti-proliferation effect in acute lymphoblastic leukemia cells (CEM/C1, MOLT-4, Jurkat, BALL-1, Nalm-6, and RS4;11). Further studies showed that ATT reduced the mitochondrial membrane potential in B-cell acute lymphoblastic leukemia cell lines (BALL-1, Nalm-6, and RS4;11) and induced cell cycle arrest in MOLT-4 and BALL-1. ATT induced BALL-1 cell apoptosis by activating Caspase 3/7 activity and causing DNA fragmentation. Network pharmacology results suggested that ATT exerts its anti-leukemia activity via the PI3K/Akt signaling pathway. In addition, molecular docking analysis showed that ATT had high scores in docking with PTGS2, NR3C1, and AR. Western blotting results showed that ATT reduced the relative protein level of P-PI3K and P-Akt, thereby increasing the relative level of pro-apoptosis protein Bax and reducing the relative level of anti-apoptosis protein Bcl-2, the apoptosis downstream protein pro-caspase3, and cell proliferation-related proteins (P-GSK3B and CyclinD1). In conclusion, these results demonstrated that ATT could be a potential candidate drug with apoptosis-induction and cell cycle arrest effects for further investigation in acute lymphoblastic leukemia therapy.

GPCR-mediated natural products and compounds: Potential therapeutic targets for the treatment of neurological diseases

G protein-coupled receptors (GPCRs), widely expressed in the human central nervous system (CNS), perform numerous physiological functions and play a significant role in the pathogenesis of diseases. Consequently, identifying key therapeutic GPCRs targets for CNS-related diseases is garnering immense interest in research labs and pharmaceutical companies. However, using GPCRs drugs for treating neurodegenerative diseases has limitations, including side effects and uncertain effective time frame. Recognizing the rich history of herbal treatments for neurological disorders like stroke, Alzheimer's disease (AD), and Parkinson's disease (PD), modern pharmacological research is now focusing on the understanding of the efficacy of traditional Chinese medicinal herbs and compounds in modulating GPCRs and treatment of neurodegenerative conditions. This paper will offer a comprehensive, critical review of how certain natural products and compounds target GPCRs to treat neurological diseases. Conducting an in-depth study of herbal remedies and their efficacies against CNS-related disorders through GPCRs targeting will augment our strategies for treating neurological disorders. This will not only broaden our understanding of effective therapeutic methodologies but also identify the root causes of altered GPCRs signaling in the context of pathophysiological mechanisms in neurological diseases. Moreover, it would be informative for the creation of safer and more effective GPCR-mediated drugs, thereby establishing a foundation for future treatment of various neurological diseases.

The path to the G protein-coupled receptor structural landscape: Major milestones and future directions

G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand-binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial-temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting-edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR-based applications.

Machine Learning Guided AQFEP: A Fast and Efficient Absolute Free Energy Perturbation Solution for Virtual Screening

Structure-based methods in drug discovery have become an integral part of the modern drug discovery process. The power of virtual screening lies in its ability to rapidly and cost-effectively explore enormous chemical spaces to select promising ligands for further experimental investigation. Relative free energy perturbation (RFEP) and similar methods are the gold standard for binding affinity prediction in drug discovery hit-to-lead and lead optimization phases, but have high computational cost and the requirement of a structural analog with a known activity. Without a reference molecule requirement, absolute FEP (AFEP) has, in theory, better accuracy for hit ID, but in practice, the slow throughput is not compatible with VS, where fast docking and unreliable scoring functions are still the standard. Here, we present an integrated workflow to virtually screen large and diverse chemical libraries efficiently, combining active learning with a physics-based scoring function based on a fast absolute free energy perturbation method. We validated the performance of the approach in the ranking of structurally related ligands, virtual screening hit rate enrichment, and active learning chemical space exploration; disclosing the largest reported collection of free energy simulations to date.

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1

Artificial intelligence is revolutionizing protein structure prediction, providing unprecedented opportunities for drug design. To assess the potential impact on ligand discovery, we compared virtual screens using protein structures generated by the AlphaFold machine learning method and traditional homology modeling. More than 16 million compounds were docked to models of the trace amine-associated receptor 1 (TAAR1), a G protein-coupled receptor of unknown structure and target for treating neuropsychiatric disorders. Sets of 30 and 32 highly ranked compounds from the AlphaFold and homology model screens, respectively, were experimentally evaluated. Of these, 25 were TAAR1 agonists with potencies ranging from 12 to 0.03 μM. The AlphaFold screen yielded a more than twofold higher hit rate (60%) than the homology model and discovered the most potent agonists. A TAAR1 agonist with a promising selectivity profile and drug-like properties showed physiological and antipsychotic-like effects in wild-type but not in TAAR1 knockout mice. These results demonstrate that AlphaFold structures can accelerate drug discovery.

Unveiling potential drug targets for lung squamous cell carcinoma through the integration of druggable genome and genome-wide association data

Background: Lung squamous cell carcinoma (LSCC) is a major subtype of lung cancer with poor prognosis and low survival rate. Compared with lung adenocarcinoma, yet no FDA-approved targeted-therapy has been found for lung squamous cell carcinoma. Methods: To identify potential drug targets for LSCC, Summary-data-based Mendelian randomization (SMR) analysis was used to examine the potential association between 4,543 druggable genes and LSCC, followed by colocalization analysis and HEIDI tests to confirm the robustness of the result. Phenome-wide association study (PheWAS) explored potential side effects of candidate drug targets. Enrichment analysis and protein-protein interaction networks revealed the function and significance of therapeutic targets. Single-cell expression analysis was used to examine cell types with enrichment expression of druggable genes in LSCC tissue. Drug prediction included screening potential drug candidates and evaluating their interactions with targets through molecular docking. Results: This research has identified ten significant drug targets for LSCC through a comprehensive SMR analysis. These targets included (COPA, PKD2L1, CCR1, C2, CYP21A2, and NCSTN as risk factors, and CCNA2, C4A, APOM, and LPAR2 as protective factors). PheWAS demonstrated that C2, CCNA2, LPAR2, and NCSTN exhibited associations with other phenotypes at the genetic level. Then, we found four potentially effective drugs with the Dsigdb database. Subsequently, molecular docking indicated that favorable binding interactions between drug candidates and potential target molecules. In the druggability evaluation, five out of ten drug target genes have been used in drug development (APOM, C4A, CCNA2, COPA, and PKD2L1). Six out of ten druggable genes showed significant expression in LSCC tissues (COPA, PKD2L1, CCR1, C2, NCSTN, LPAR2). Besides, Single-cell expression analysis revealed that C2 and CCNA2 were primarily enriched in macrophages, while COPA and NCSTN were enriched in both macrophages and epithelial cells. Conclusion: Our research revealed ten potential druggable genes for LSCC treatment, which might help to advance the precise and efficient therapeutic approaches of LSCC.

Structure-based virtual screening of vast chemical space as a starting point for drug discovery

Structure-based virtual screening aims to find molecules forming favorable interactions with a biological macromolecule using computational models of complexes. The recent surge of commercially available chemical space provides the opportunity to search for ligands of therapeutic targets among billions of compounds. This review offers a compact overview of structure-based virtual screens of vast chemical spaces, highlighting successful applications in early drug discovery for therapeutically important targets such as G protein-coupled receptors and viral enzymes. Emphasis is placed on strategies to explore ultra-large chemical libraries and synergies with emerging machine learning techniques. The current opportunities and future challenges of virtual screening are discussed, indicating that this approach will play an important role in the next-generation drug discovery pipeline.

Advances in GPCR-targeted drug development in dermatology

Achieving the efficacy and specificity of G-protein-coupled receptor (GPCR) targeting-drugs in the skin remains challenging. Understanding the molecular mechanism underlying GPCR dysfunction is crucial for developing targeted therapies. Recent advances in genetic, signal transduction, and structural studies have significantly improved our understanding of cutaneous GPCR functions in both normal and pathological states. In this review, we summarize recent discoveries of pathogenic GPCRs in dermal injuries, chronic inflammatory dermatoses, cutaneous malignancies, as well as the development of potent potential drugs. We also discuss targeting of cutaneous GPCR complexes via the transient receptor potential (TRP) channel and structure elucidation, which provide new opportunities for therapeutic targeting of GPCRs involved in skin disorders. These insights are expected to lead to more effective and specific treatments for various skin conditions.

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods

Alchemical relative binding free energy (ΔΔG) calculations have shown high accuracy in predicting ligand binding affinity and have been used as important tools in computer-aided drug discovery and design. However, there has been limited research on the application of ΔΔG methods to membrane proteins despite the fact that these proteins represent a significant proportion of drug targets, play crucial roles in biological processes, and are implicated in numerous diseases. In this study, to predict the binding affinity of ligands to G protein-coupled receptors (GPCRs), we employed two ΔΔG calculation methods: thermodynamic integration (TI) with AMBER and the alchemical transfer method (AToM) with OpenMM. We calculated ΔΔG values for 53 transformations involving four class A GPCRs and evaluated the performance of AMBER-TI and AToM-OpenMM. In addition, we conducted tests using different numbers of windows and varying simulation times to achieve reliable ΔΔG results and to optimize resource utilization. Overall, both AMBER-TI and AToM-OpenMM show good agreement with the experimental data. Our results validate the applicability of AMBER-TI and AToM-OpenMM for optimization of lead compounds targeting membrane proteins.

Ligand-Receptor Interactions and Structure-Function Relationships in Off-Target Binding of the β3-Adrenergic Agonist Mirabegron to α1A-Adrenergic Receptors

The β3-adrenoceptor agonist mirabegron is available for the treatment of storage symptoms of overactive bladder, including frequency, urgency, and incontinence. The off-target effects of mirabegron include binding to α1-adrenoceptors, which are central in the treatment of voiding symptoms. Here, we examined the structure-function relationships in the binding of mirabegron to a cryo-electron microscopy structure of α1A. The binding was simulated by docking mirabegron to a 3D structure of a human α1A-adrenoceptor (7YMH) using Autodock Vina. The simulations identified two binding states: slope orientation involving 10 positions and horizontal binding to the receptor surface involving 4 positions. No interactions occurred with positions constituting the α1A binding pocket, including Asp-106, Ser-188, or Phe-312, despite the positioning of the phenylethanolamine moiety in transmembrane regions close to the binding pocket by contact with Phe-288, -289, and Val-107. Contact with the unique positions of α1A included the transmembrane Met-292 during slope binding and exosite Phe-86 during horizontal binding. Exosite binding in slope orientation involved contact of the anilino part, rather than the aminothiazol end, to Ile-178, Ala-103, and Asn-179. In conclusion, contact with Met-292 and Phe-86, which are unique positions of α1A, accounts for mirabegron binding to α1A. Because of its lack of interactions with the binding pocket, mirabegron has lower affinity compared to α1A-blockers and no effects on voiding symptoms.

G protein-coupled receptors and traditional Chinese medicine: new thinks for the development of traditional Chinese medicine

G protein-coupled receptors (GPCRs) widely exist in vivo and participate in many physiological processes, thus emerging as important targets for drug development. Approximately 30% of the Food and Drug Administration (FDA)-approved drugs target GPCRs. To date, the 'one disease, one target, one molecule' strategy no longer meets the demands of drug development. Meanwhile, small-molecule drugs account for 60% of FDA-approved drugs. Traditional Chinese medicine (TCM) has garnered widespread attention for its unique theoretical system and treatment methods. TCM involves multiple components, targets and pathways. Centered on GPCRs and TCM, this paper discusses the similarities and differences between TCM and GPCRs from the perspectives of syndrome of TCM, the consistency of TCM's multi-component and multi-target approaches and the potential of GPCRs and TCM in the development of novel drugs. A novel strategy, 'simultaneous screening of drugs and targets', was proposed and applied to the study of GPCRs. We combine GPCRs with TCM to facilitate the modernisation of TCM, provide valuable insights into the rational application of TCM and facilitate the research and development of novel drugs. This study offers theoretical support for the modernisation of TCM and introduces novel ideas for development of safe and effective drugs.

Discovery and development of macrocyclic peptide modulators of the cannabinoid 2 receptor

The cannabinoid type 2 receptor (CB2R), a G protein-coupled receptor, is an important regulator of immune cell function and a promising target to treat chronic inflammation and fibrosis. While CB2R is typically targeted by small molecules, including endo-, phyto-, and synthetic cannabinoids, peptides-owing to their size-may offer a different interaction space to facilitate differential interactions with the receptor. Here, we explore plant-derived cyclic cystine-knot peptides as ligands of the CB2R. Cyclotides are known for their exceptional biochemical stability. Recently, they gained attention as G protein-coupled receptor modulators and as templates for designing peptide ligands with improved pharmacokinetic properties over linear peptides. Cyclotide-based ligands for CB2R were profiled based on a peptide-enriched extract library comprising nine plants. Employing pharmacology-guided fractionation and peptidomics, we identified the cyclotide vodo-C1 from sweet violet (Viola odorata) as a full agonist of CB2R with an affinity (Ki) of 1 μM and a potency (EC50) of 8 μM. Leveraging deep learning networks, we verified the structural topology of vodo-C1 and modeled its molecular volume in comparison to the CB2R ligand binding pocket. In a fragment-based approach, we designed and characterized vodo-C1-based bicyclic peptides (vBCL1-4), aiming to reduce size and improve potency. Opposite to vodo-C1, the vBCL peptides lacked the ability to activate the receptor but acted as negative allosteric modulators or neutral antagonists of CB2R. This study introduces a macrocyclic peptide phytocannabinoid, which served as a template for the development of synthetic CB2R peptide modulators. These findings offer opportunities for future peptide-based probe and drug development at cannabinoid receptors.

Utilizing a structure-based virtual screening approach to discover potential LSD1 inhibitors

BACKGROUND

Lysine-specific demethylase 1 (LSD1) is highly expressed in a variety of malignant tumors, rendering it a crucial epigenetic target for anti-tumor therapy. Therefore, the inhibition of LSD1 activity has emerged as a promising innovative therapeutic approach for targeted cancer treatment.

METHODS

In our study, we employed innovative structure-based drug design methods to meticulously select compounds from the ZINC15 database. Utilizing virtual docking, we evaluated docking scores and binding modes to identify potential inhibitors. To further validate our findings, we harnessed molecular dynamic simulations and conducted meticulous biochemical experiments to deeply analyze the binding interactions between the protein and compounds.

RESULTS

Our results showcased that ZINC10039815 exhibits an exquisite binding mode with LSD1, fitting perfectly into the active pocket and forming robust interactions with multiple critical residues of the protein.

CONCLUSIONS

With its significant inhibitory effect on LSD1 activity, ZINC10039815 emerges as a highly promising candidate for the development of novel LSD1 inhibitors.

Discovery of a SUCNR1 antagonist for potential treatment of diabetic nephropathy: In silico and in vitro studies

Diabetic nephropathy (DN) is one of the most severe complications of diabetes mellitus. Succinate Receptor 1 (SUCNR1), a member of the G-protein-coupled receptor (GPCR) family, represents a potential target for treatment of DN. Here, utilizing multi-strategy in silico virtual screening methods containing AlphaFold2 modelling, molecular dynamics (MD) simulation, ligand-based pharmacophore screening, molecular docking and machine learning-based similarity clustering, we successfully identified a novel antagonist of SUCNR1, AK-968/12117473 (Cpd3). Through extensive in vitro experiments, including dual-luciferase reporter assay, cellular thermal shift assay, immunofluorescence, and western blotting, we substantiated that Cpd3 could specifically target SUCNR1, inhibit the activation of NF-κB pathway, and ameliorate epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) deposition in renal tubular epithelial cells (NRK-52E) under high glucose conditions. Further in silico simulations revealed the molecular basis of the SUCNR1-Cpd3 interaction, and the in vitro metabolic stability assay indicated favorable drug-like pharmacokinetic properties of Cpd3. This work not only successfully pinpointed Cpd3 as a specific antagonist of SUCNR1 to serve as a promising candidate in the realm of therapeutic interventions for DN, but also provides a paradigm of dry-wet combined discovery strategies for GPCR-based therapeutics.

Exploring NAD+ metabolism and NNAT: Insights from structure, function, and computational modeling

Nicotinamide Adenine Dinucleotide (NAD+), a coenzyme, is ubiquitously distributed and serves crucial functions in diverse biological processes, encompassing redox reactions, energy metabolism, and cellular signalling. This review article explores the intricate realm of NAD + metabolism, with a particular emphasis on the complex relationship between its structure, function, and the pivotal enzyme, Nicotinate Nucleotide Adenylyltransferase (NNAT), also known as nicotinate mononucleotide adenylyltransferase (NaMNAT), in the process of its biosynthesis. Our findings indicate that NAD + biosynthesis in humans and bacteria occurs via the same de novo synthesis route and the pyridine ring salvage pathway. Maintaining NAD homeostasis in bacteria is imperative, as most bacterial species cannot get NAD+ from their surroundings. However, due to lower sequence identity and structurally distant relationship of bacteria, including E. faecium and K. pneumonia, to its human counterpart, inhibiting NNAT, an indispensable enzyme implicated in NAD + biosynthesis, is a viable alternative in curtailing infections orchestrated by E. faecium and K. pneumonia. By merging empirical and computational discoveries and connecting the intricate NAD + metabolism network with NNAT's crucial role, it becomes clear that the synergistic effect of these insights may lead to a more profound understanding of the coenzyme's function and its potential applications in the fields of therapeutics and biotechnology.

Flexible scaffold-based cheminformatics approach for polypharmacological drug design

Effective treatments for complex central nervous system (CNS) disorders require drugs with polypharmacology and multifunctionality, yet designing such drugs remains a challenge. Here, we present a flexible scaffold-based cheminformatics approach (FSCA) for the rational design of polypharmacological drugs. FSCA involves fitting a flexible scaffold to different receptors using different binding poses, as exemplified by IHCH-7179, which adopted a "bending-down" binding pose at 5-HT2AR to act as an antagonist and a "stretching-up" binding pose at 5-HT1AR to function as an agonist. IHCH-7179 demonstrated promising results in alleviating cognitive deficits and psychoactive symptoms in mice by blocking 5-HT2AR for psychoactive symptoms and activating 5-HT1AR to alleviate cognitive deficits. By analyzing aminergic receptor structures, we identified two featured motifs, the "agonist filter" and "conformation shaper," which determine ligand binding pose and predict activity at aminergic receptors. With these motifs, FSCA can be applied to the design of polypharmacological ligands at other receptors.

Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking

Structure-based drug discovery is a process for both hit finding and optimization that relies on a validated three-dimensional model of a target biomolecule, used to rationalize the structure-function relationship for this particular target. An ultralarge virtual screening approach has emerged recently for rapid discovery of high-affinity hit compounds, but it requires substantial computational resources. This study shows that active learning with simple linear regression models can accelerate virtual screening, retrieving up to 90% of the top-1% of the docking hit list after docking just 10% of the ligands. The results demonstrate that it is unnecessary to use complex models, such as deep learning approaches, to predict the imprecise results of ligand docking with a low sampling depth. Furthermore, we explore active learning meta-parameters and find that constant batch size models with a simple ensembling method provide the best ligand retrieval rate. Finally, our approach is validated on the ultralarge size virtual screening data set, retrieving 70% of the top-0.05% of ligands after screening only 2% of the library. Altogether, this work provides a computationally accessible approach for accelerated virtual screening that can serve as a blueprint for the future design of low-compute agents for exploration of the chemical space via large-scale accelerated docking. With recent breakthroughs in protein structure prediction, this method can significantly increase accessibility for the academic community and aid in the rapid discovery of high-affinity hit compounds for various targets.

Orphan G protein-coupled receptors: the ongoing search for a home

G protein-coupled receptors (GPCRs) make up the largest receptor superfamily, accounting for 4% of protein-coding genes. Despite the prevalence of such transmembrane receptors, a significant number remain orphans, lacking identified endogenous ligands. Since their conception, the reverse pharmacology approach has been used to characterize such receptors. However, the multifaceted and nuanced nature of GPCR signaling poses a great challenge to their pharmacological elucidation. Considering their therapeutic relevance, the search for native orphan GPCR ligands continues. Despite limited structural input in terms of 3D crystallized structures, with advances in machine-learning approaches, there has been great progress with respect to accurate ligand prediction. Though such an approach proves valuable given that ligand scarcity is the greatest hurdle to orphan GPCR deorphanization, the future pairings of the remaining orphan GPCRs may not necessarily take a one-size-fits-all approach but should be more comprehensive in accounting for numerous nuanced possibilities to cover the full spectrum of GPCR signaling.

Exploring Novel Antidepressants Targeting G Protein-Coupled Receptors and Key Membrane Receptors Based on Molecular Structures

Major Depressive Disorder (MDD) is a complex mental disorder that involves alterations in signal transmission across multiple scales and structural abnormalities. The development of effective antidepressants (ADs) has been hindered by the dominance of monoamine hypothesis, resulting in slow progress. Traditional ADs have undesirable traits like delayed onset of action, limited efficacy, and severe side effects. Recently, two categories of fast-acting antidepressant compounds have surfaced, dissociative anesthetics S-ketamine and its metabolites, as well as psychedelics such as lysergic acid diethylamide (LSD). This has led to structural research and drug development of the receptors that they target. This review provides breakthroughs and achievements in the structure of depression-related receptors and novel ADs based on these. Cryo-electron microscopy (cryo-EM) has enabled researchers to identify the structures of membrane receptors, including the N-methyl-D-aspartate receptor (NMDAR) and the 5-hydroxytryptamine 2A (5-HT2A) receptor. These high-resolution structures can be used for the development of novel ADs using virtual drug screening (VDS). Moreover, the unique antidepressant effects of 5-HT1A receptors in various brain regions, and the pivotal roles of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) and tyrosine kinase receptor 2 (TrkB) in regulating synaptic plasticity, emphasize their potential as therapeutic targets. Using structural information, a series of highly selective ADs were designed based on the different role of receptors in MDD. These molecules have the favorable characteristics of rapid onset and low adverse drug reactions. This review offers researchers guidance and a methodological framework for the structure-based design of ADs.

Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5

By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.

Computational drug development for membrane protein targets

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.

CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training

The expertise accumulated in deep neural network-based structure prediction has been widely transferred to the field of protein-ligand binding pose prediction, thus leading to the emergence of a variety of deep learning-guided docking models for predicting protein-ligand binding poses without relying on heavy sampling. However, their prediction accuracy and applicability are still far from satisfactory, partially due to the lack of protein-ligand binding complex data. To this end, we create a large-scale complex dataset containing ∼9 M protein-ligand docking complexes for pre-training, and propose CarsiDock, the first deep learning-guided docking approach that leverages pre-training of millions of predicted protein-ligand complexes. CarsiDock contains two main stages, i.e., a deep learning model for the prediction of protein-ligand atomic distance matrices, and a translation, rotation and torsion-guided geometry optimization procedure to reconstruct the matrices into a credible binding pose. The pre-training and multiple innovative architectural designs facilitate the dramatically improved docking accuracy of our approach over the baselines in terms of multiple docking scenarios, thereby contributing to its outstanding early recognition performance in several retrospective virtual screening campaigns. Further explorations demonstrate that CarsiDock can not only guarantee the topological reliability of the binding poses but also successfully reproduce the crucial interactions in crystalized structures, highlighting its superior applicability.

Discovery of 4-aminophenylacetamide derivatives as intestine-specific farnesoid X receptor antagonists for the potential treatment of nonalcoholic steatohepatitis

Farnesoid X receptor (FXR) plays a key role in bile acid homeostasis, inflammation, fibrosis, lipid and glucose metabolism and is emerging as a promising therapeutic target for nonalcoholic steatohepatitis (NASH). Emerging evidence suggested that intestine-specific FXR antagonists exhibited remarkable metabolic improvements and slowed NASH progression. In this study, we discovered several potent FXR antagonists using a multistage ligand- and structure-based virtual screening approach. Notably, compound V023-9340, which possesses a 4-aminophenylacetamide scaffold, emerged as the most potent FXR antagonist with an IC50 value of 4.27 μM. In vivo, V023-9340 demonstrated selective accumulation in the intestine, substantially ameliorating high-fat diet (HFD)-induced NASH in mice by mitigating hepatic steatosis and inflammation. Mechanistic studies revealed that V023-9340 strongly inhibited intestinal FXR while concurrently feedback-activated hepatic FXR. Further structure-activity relationship optimization employing V023-9340 has resulted in the synthesis of a more efficacious compound V02-8 with an IC50 value of 0.89 μM, which exhibited a 4.8-fold increase in FXR antagonistic activity compared to V023-9340. In summary, 4-aminophenylacetamide derivative V023-9340 represented a novel intestine-specific FXR antagonist and showed improved effects against HFD-induced NASH in mice, which may serve as a promising lead in discovering potential therapeutic drugs for NASH treatment.

Advances in Drug Discovery and Design using Computer-aided Molecular Modeling

Computer-aided molecular modeling is a rapidly emerging technology that is being used to accelerate the discovery and design of new drug therapies. It involves the use of computer algorithms and 3D structures of molecules to predict interactions between molecules and their behavior in the body. This has drastically improved the speed and accuracy of drug discovery and design. Additionally, computer-aided molecular modeling has the potential to reduce costs, increase the quality of data, and identify promising targets for drug development. Through the use of sophisticated methods, such as virtual screening, molecular docking, pharmacophore modeling, and quantitative structure-activity relationships, scientists can achieve higher levels of efficacy and safety for new drugs. Moreover, it can be used to understand the activity of known drugs and simplify the process of formulating, optimizing, and predicting the pharmacokinetics of new and existing drugs. In conclusion, computer-aided molecular modeling is an effective tool to rapidly progress drug discovery and design by predicting the interactions between molecules and anticipating the behavior of new drugs in the body.

GPR146 regulates pulmonary vascular remodeling by promoting pulmonary artery smooth muscle cell proliferation through 5-lipoxygenase

The pathological feature of hypoxic pulmonary hypertension (PH) is pulmonary vascular remodeling (PVR), primarily attributed to the hyperproliferation and apoptosis resistance of pulmonary artery smooth muscle cells (PASMCs). Existing PH-targeted drugs have difficulties in reversing PVR. Therefore, it is vital to discover a new regulatory mechanism for PVR and develop new targeted drugs. G protein-coupled receptor 146 (GPR146) is believed to participate in this process. This study aimed to investigate the role of GPR146 in PASMCs during PH. We investigated the role of GPR146 in PVR and its underlying mechanism using hypoxic PASMCs and mouse model (Sugen 5416 (20 mg/kg)/hypoxia). In our recent study, we have observed a significant increase in the expression of GPR146 protein in animal models of PH as well as in patients diagnosed with pulmonary arterial hypertension (PAH). Through immunohistochemistry, we found that GPR146 was mainly localized in the smooth muscle and endothelial layers of the pulmonary vasculature. GPR146 deficiency induction exhibited protective effects against hypoxia-induced elevation of right ventricular systolic blood pressure (RVSP), right ventricular hypertrophy, and pulmonary vascular remodeling in mice. In particular, the deletion of GPR146 attenuated the hypoxia-triggered proliferation of PASMCs. Furthermore, 5-lipoxygenase (5-LO) was related to PH development. Hypoxia and overexpression of GPR146 increased 5-LO expression, which was reversed through GPR146 knockdown or siRNA intervention. Our study discovered that GPR146 exhibited high expression in the pulmonary vessels of pulmonary hypertension. Subsequent research revealed that GPR146 played a crucial role in the development of hypoxic PH by promoting lipid peroxidation and 5-LO expression. In conclusion, GPR146 may regulate pulmonary vascular remodeling by promoting PASMCs proliferation through 5-LO, which presents a feasible target for PH prevention and treatment.

Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family

Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52cs), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52cs reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52cs demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.

Glimepiride, a novel soluble epoxide hydrolase inhibitor, protects against heart failure via increasing epoxyeicosatrienoic acids

BACKGROUND

Epoxyeicosatrienoic acids (EETs), which exert multiple endogenous protective effects, are hydrolyzed into less active dihydroxyeicosatrienoic acids (DHETs) by soluble epoxide hydrolase (sEH). However, commercial drugs related to EETs or sEH are not yet in clinical use.

METHODS

Firstly, the plasma concentration of EETs and DHETs of 316 patients with heart failure (HF) were detected and quantitated by liquid chromatography-tandem mass spectrometry. Then, transverse aortic constriction (TAC)-induced HF was introduced in cardiomyocyte-specific Ephx2-/- mice. Moreover, Western blot, real-time PCR, luciferase reporter, ChIP assays were employed to explore the underlying mechanism. Finally, multiple sEH inhibitors were designed, synthesized, and validated in vitro and in vivo.

RESULTS

The ratios of DHETs/EETs were increased in the plasma from patients with HF. Meanwhile, the expression of sEH was upregulated in the heart of patients and mice with HF, especially in cardiomyocytes. Cardiomyocyte-specific Ephx2-/- mice ameliorated cardiac dysfunction induced by TAC. Consistently, Ephx2 knockdown protected Angiotensin II (AngII)-treated cardiomyocytes via increasing EETs in vitro. Mechanistically, AngII could enhance the expression of transcript factor Krüppel-like factor 15 (KLF15), which in turn upregulated sEH. Importantly, glimepiride was identified as a novel sEH inhibitor, which benefited from the elevated EETs during HF.

CONCLUSIONS

Glimepiride attenuates HF in mice in part by increasing EETs.

CLINICAL TRIAL IDENTIFIER

NCT03461107 (https://clinicaltrials.gov).

A Natural Compound Containing a Disaccharide Structure of Glucose and Rhamnose Identified as Potential N-Glycanase 1 (NGLY1) Inhibitors

N-glycanase 1 (NGLY1) is an essential enzyme involved in the deglycosylation of misfolded glycoproteins through the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which could hydrolyze N-glycan from N-glycoprotein or N-glycopeptide in the cytosol. Recent studies indicated that NGLY1 inhibition is a potential novel drug target for antiviral therapy. In this study, structure-based virtual analysis was applied to screen candidate NGLY1 inhibitors from 2960 natural compounds. Three natural compounds, Poliumoside, Soyasaponin Bb, and Saikosaponin B2 showed significantly inhibitory activity of NGLY1, isolated from traditional heat-clearing and detoxifying Chinese herbs. Furthermore, the core structural motif of the three NGLY1 inhibitors was a disaccharide structure with glucose and rhamnose, which might exert its action by binding to important active sites of NGLY1, such as Lys238 and Trp244. In traditional Chinese medicine, many compounds containing this disaccharide structure probably targeted NGLY1. This study unveiled the leading compound of NGLY1 inhibitors with its core structure, which could guide future drug development.

Identifying a New Target for BtOBP8: Discovery of a Small Amino Ketone Molecule Containing Benzothiazole Fragments

Insects rely on odorant-binding proteins (OBPs) for chemical perception, making OBPs a promising target for studying attractants and repellents of pests, such as Bemisia tabaci. However, no reports have reported using B. tabaci OBPs (BtOBPs) as pesticide screening targets. To fill this gap, we obtained BtOBP8 through prokaryotic expression and purification. Then, we confirmed its identity using western blotting and mass spectrometry. Next, we used the sitting drop and hanging drop methods to screen its crystal conditions. Using microscale thermophoresis and isothermal titration calorimetry, we identified the highest affinity ligand, 3l, from 30 compounds. Furthermore, point mutation techniques identified Val119 as a key amino acid residue in binding 31 to BtOBP8. Finally, we tested the bioactivity of B. tabaci Mediterranean and found that 3l more effectively inhibits the bioactivity of B. tabaci MED than imidacloprid. This study presents a new approach for developing green insecticides specific to B. tabaci MED by targeting OBPs. Conclusively, identifying and targeting specific OBPs can create more targeted and effective pest control strategies without relying on toxic chemicals.

Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists

Trace amine-associated receptors (TAARs) were discovered in 2001 as new members of class A G protein-coupled receptors (GPCRs). With the only exception of TAAR1, TAAR members (TAAR2-9, also known as noncanonical olfactory receptors) were originally described exclusively in the olfactory epithelium and believed to mediate the innate perception of volatile amines. However, most noncanonical olfactory receptors are still orphan receptors. Given its recently discovered nonolfactory expression and therapeutic potential, TAAR5 has been the focus of deorphanization campaigns that led to the discovery of a few druglike antagonists. Here, we report four novel TAAR5 antagonists identified through high-throughput screening, which, along with the four ligands published in the literature, constituted our starting point to design a computational strategy for the identification of TAAR5 ligands. We developed a structure-based virtual screening protocol that allowed us to identify three new TAAR5 antagonists with a hit rate of 10%. Despite lacking an experimental structure, we accurately modeled the TAAR5 binding site by integrating comparative sequence- and structure-based analyses of serotonin receptors with homology modeling and side-chain optimization. In summary, we have identified seven new TAAR5 antagonists that could serve as lead candidates for the development of new treatments for depression, anxiety, and neurodegenerative diseases.

The Trends and Future Prospective of In Silico Models from the Viewpoint of ADME Evaluation in Drug Discovery

Drug discovery and development are aimed at identifying new chemical molecular entities (NCEs) with desirable pharmacokinetic profiles for high therapeutic efficacy. The plasma concentrations of NCEs are a biomarker of their efficacy and are governed by pharmacokinetic processes such as absorption, distribution, metabolism, and excretion (ADME). Poor ADME properties of NCEs are a major cause of attrition in drug development. ADME screening is used to identify and optimize lead compounds in the drug discovery process. Computational models predicting ADME properties have been developed with evolving model-building technologies from a simplified relationship between ADME endpoints and physicochemical properties to machine learning, including support vector machines, random forests, and convolution neural networks. Recently, in the field of in silico ADME research, there has been a shift toward evaluating the in vivo parameters or plasma concentrations of NCEs instead of using predictive results to guide chemical structure design. Another research hotspot is the establishment of a computational prediction platform to strengthen academic drug discovery. Bioinformatics projects have produced a series of in silico ADME models using free software and open-access databases. In this review, we introduce prediction models for various ADME parameters and discuss the currently available academic drug discovery platforms.

Scutellarin suppresses the metastasis of triple-negative breast cancer via targeting TNFα/TNFR2-RUNX1-triggered G-CSF expression in endothelial cells

Triple-negative breast cancer (TNBC) is heterogeneous and aggressive, with high vascularity and frequent metastasis. We have already found natural flavonoid scutellarin (SC) suppressed spontaneous TNBC metastasis via normalizing tumor vasculature in vivo. In this study, supernatant from tumor necrosis factorα (TNFα)-treated human mammary microvascular endothelial cell (HMMEC) promoted cell migration and pseudopod formation in TNBC cells, but these phenomena were disappeared in SC-co-treated HMMEC. TNFα enhanced the expression of granulocyte colony-stimulating factor (G-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) in both HMMEC and human umbilical vein endothelial cell (HUVEC). G-CSF promoted TNBC migration and invasion in vitro, while G-CSF neutralization antibody and SC both inhibited TNBC metastasis in Balb/c mice. SC had no inhibition on the G-CSF-induced TNBC cell migration, but reduced G-CSF content in TNBC tumor tissues and TNFα-stimulated endothelial cells (ECs). SC restricted the nuclear translocation of runt-related transcription factor 1 (RUNX1) in TNBC tumor vessels and TNFα-treated ECs. RUNX1 was found to directly bind to the promoter of G-CSF in TNBC tumor vessels and regulated G-CSF expression. TNF receptor 2 (TNFR2) was crucial for regulating the TNFα-induced RUNX1 activation and G-CSF expression. Notably, SC hindered the interaction between TNFα and TNFR2 via binding to TNFR2. This work demonstrated that SC reduced TNBC metastasis by targeting TNFα/TNFR2-initiated RUNX1 activation and subsequent G-CSF production in TNBC-associated ECs.

Virtual Insights into Natural Compounds as Potential 5α-Reductase Type II Inhibitors: A Structure-Based Screening and Molecular Dynamics Simulation Study

Androgenic alopecia (AGA) is a dermatological disease with psychosocial consequences for those who experience hair loss. AGA is linked to an increase in androgen levels caused by an excess of dihydrotestosterone in blood capillaries produced from testosterone by 5α-reductase type II (5αR2), which is expressed in scalp hair follicles; 5αR2 activity and dihydrotestosterone levels are elevated in balding scalps. The diverse health benefits of flavonoids have been widely reported in epidemiological studies, and research interest continues to increase. In this study, a virtual screening approach was used to identify compounds that interact with active site residues of 5αR2 by screening a library containing 241 flavonoid compounds. Here, we report two potent flavonoid compounds, eriocitrin and silymarin, that interacted strongly with 5αR2, with binding energies of -12.1 and -11.7 kcal/mol, respectively, which were more significant than those of the control, finasteride (-11.2 kcal/mol). Molecular dynamic simulations (200 ns) were used to optimize the interactions between compounds and 5αR2 and revealed that the interaction of eriocitrin and silymarin with 5αR2 was stable. The study shows that eriocitrin and silymarin provide developmental bases for novel 5αR2 inhibitors for the management of AGA.

Molecular Docking and Molecular Dynamics Simulations in Related to Leishmania donovani: An Update and Literature Review

Leishmaniasis, a disease caused by Leishmania parasites and transmitted via sandflies, presents in two main forms: cutaneous and visceral, the latter being more severe. With 0.7 to 1 million new cases each year, primarily in Brazil, diagnosing remains challenging due to diverse disease manifestations. Traditionally, the identification of Leishmania species is inferred from clinical and epidemiological data. Advances in disease management depend on technological progress and the improvement of parasite identification programs. Current treatments, despite the high incidence, show limited efficacy due to factors like cost, toxicity, and lengthy regimens causing poor adherence and resistance development. Diagnostic techniques have improved but a significant gap remains between scientific progress and application in endemic areas. Complete genomic sequence knowledge of Leishmania allows for the identification of therapeutic targets. With the aid of computational tools, testing, searching, and detecting affinity in molecular docking are optimized, and strategies that assess advantages among different options are developed. The review focuses on the use of molecular docking and molecular dynamics (MD) simulation for drug development. It also discusses the limitations and advancements of current treatments, emphasizing the importance of new techniques in improving disease management.

Structure-Based Ligand Discovery Targeting the Transmembrane Domain of Frizzled Receptor FZD7

Despite the essential roles of Frizzled receptors (FZDs) in mediating Wnt signaling in embryonic development and tissue homeostasis, ligands targeting FZDs are rare. A few antibodies and peptide modulators have been developed that mainly bind to the family-conserved extracellular cysteine-rich domain of FZDs, while the canonical binding sites in the transmembrane domain (TMD) are far from sufficiently addressed. Based on the recent structures of FZDs, we explored small-molecule ligand discovery by targeting TMD. From the ChemDiv library with ∼1.6 million compounds, we identified compound F7H as an antagonist of FZD7 with an IC50 at 1.25 ± 0.38 μM. Focusing on this hit, the structural dissection study, together with computing studies such as molecular docking, molecular dynamics simulation, and free energy perturbation calculations, defined the binding pocket with key residue recognition. Our results revealed the structural basis of ligand recognition and demonstrated the feasibility of structure-guided ligand discovery for FZD7-TMD.