Low Molecular Weight Inhibitors Research Articles

Molecular Regulation of Bone Turnover in Juvenile Idiopathic Arthritis: Animal Models, Cellular Features and TNFα.

We review the abnormal bone turnover that is the basis of idiopathic inflammatory or rheumatoid arthritis and bone loss, with emphasis on Tumor Necrosis Factor-alpha (TNFα)-related mechanisms. We review selected data on idiopathic arthritis in juvenile human disease, and discuss mouse models focusing on induction of bone resorbing cells by TNFα and Receptor Activator of Nuclear Factor kappa B Ligand (RANKL). In both humans and animal models, macrophage-derived cells in the joint, particularly in the synovium and periosteum, degrade bone and cartilage. Mouse models of rheumatoid arthritis share with human disease bone resorbing cells and strong relation to TNFα expression. In humans, differences in therapy and prognosis of arthritis vary with age, and results from early intervention for inflammatory cytokines in juvenile patients are particularly interesting. Mechanisms that contribute to inflammatory arthritis reflect, in large part, inflammatory cytokines that play minor roles in normal bone turnover. Changes in inflammatory cytokines, particularly TNFα, are many times larger, and presented in different locations, than cytokines that regulate normal bone turnover. Recent data from in vitro and mouse models include novel mechanisms described in differentiation of bone resorbing cells in inflammatory arthritis dependent on the Transient Receptor Potential Channel (TRPC) family of calcium channels. Low-molecular weight (MW) inhibitors of TRPC channels add to their potential importance. Associations with inflammatory arthritis unrelated to TNFα are briefly summarized as pointing to alternative mechanisms. We suggest that early detection and monoclonal antibodies targeting cytokines mediating disease progression deserves emphasis.

Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase

Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.

Recent Progress in Alzheimer’s Disease: Pathophysiology, Newer Natural & Synthetic Inhibitors, and Therapeutic Targets

The inability to remember recent events, process new information, or complete even the most basic of tasks is a hallmark of Alzheimer’s disease, an irreversible neurodegenerative brain illness. Among those 65 and older, it is the leading cause of dementia. When a person’s cognitive and behavioural skills deteriorate to the point that they become a burden in everyday life, we say that they have dementia.There is currently no known way to halt the progression of AD or stop its symptoms from occurring. Huge literature survey was conducted from various popular medical databases such as Google Scholar, PubMed, ScienceDirect, etc. through the internet and the available data were classified according to their targets.The article focuses on basics of AD, History, Symptoms, Stages, Beta-amyloid peptide, Modulators of amyloid aggregation, Amyloid beta-oligomer, Targets for inhibiting the β-amyloid production (Monoclonal antibodies, Hormones, Inhibition of Aβ-peptide formation, Inhibition of Aβ-peptide formation [molecules like Posiphen, JNJ-54861911, LY3202626, E2609, AZD-3293, CNP520, MK-8931, LY2886721, and LY2811376],and Clearance of Aβ), and List of beta-amyloid inhibitors in clinical trials. This literature evidences may be a convenient reference (particularly, the low molecular-weight inhibitors) to the modernday researchers (pharmacognosists, pharmacologists, clinicians, medicinal chemists, medical practitioners, scientists, etc.) working dedicatedly in AD research.This study will certainly open novel avenues for ligand development and revolutionary applications in pharmacotherapeutics.

Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR.

The RNA-binding protein human antigen R (HuR) regulates stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. This protein has been progressively recognized as a relevant therapeutic target for several pathologies, like cancer, neurodegeneration, as well as inflammation. Inhibitors of mRNA binding to HuR might thus be beneficial against a variety of diseases. Here, we present the rational identification of structurally novel HuR inhibitors. In particular, by combining chemoinformatic approaches, high-throughput virtual screening, and RNA-protein pulldown assays, we demonstrate that the 4-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)benzoate ligand exhibits a dose-dependent HuR inhibition effect in binding experiments. Importantly, the chemical scaffold is new with respect to the currently known HuR inhibitors, opening up a new avenue for the design of pharmaceutical agents targeting this important protein.

Abstract B064: ONECUT2 inhibition, a potential treatment for lethal prostate cancer

Abstract Prostate cancer (PCa) is the most common cancer and the second most lethal cancer in men, claiming over 30,000 lives each year in the US alone. These PCa patient deaths are typically due to castration-resistant PCa (CRPC) which is resistant to androgen deprivation therapy, androgen receptor signaling inhibitors, and chemotherapies. Our group and others have shown that the transcription factor ONECUT2 (OC2) is a critical driver of CRPC. We have discovered a low molecular weight inhibitor of OC2 (OC2i), known as CSRM617, which inhibits metastatic PCa in cell culture (IC50 of 5-15 uM depending on cell line used) and effectively treats xenograft CRPC tumors in mouse models. We have developed a large series of these OC2i based on the CSRM617 scaffold. A thorough understanding of how these OC2i bind to and inhibit OC2 function are imperative to developing them into a clinically viable treatment option. Our recent work shows CSRM617 binds Fe and that this Fe:CSRM617 complex is necessary in order to inhibit OC2 binding of DNA. We have solved the crystal structure of OC2 bound to its conjugate DNA response element, demonstrating their atomic-level interactions. We are working towards solving a crystal structure of these OC2i bound to OC2 in order understand their specific interactions and make rational modifications to the chemical scaffold for improvements in binding affinity and pharmacokinetic properties. Citation Format: Brad Gallent, Chen Qian, Avradip Chatterjee, Madhusudhanarao Katiki, Ramachandran Murali, Michael R Freeman. ONECUT2 inhibition, a potential treatment for lethal prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B064.

Computational Screening of Inhibitory Compounds for SARS-Cov-2 3CL Protease with a Database Consisting of Approved and Investigational Chemicals.

Computational screening is one of the fundamental techniques in drug discovery. Each compound in a chemical database is bound to the target protein in virtual, and candidate compounds are selected from the binding scores. In this work, we carried out combinational computation of docking simulation to generate binding poses and molecular mechanics calculation to estimate binding scores. The coronavirus infectious disease has spread worldwide, and effective chemotherapy is strongly required. The viral 3-chymotrypsin-like (3CL) protease is a good target of low molecular-weight inhibitors. Hence, computational screening was performed to search for inhibitory compounds acting on the 3CL protease. As a preliminary assessment of the performance of this approach, we used 51 compounds for which inhibitory activity had already been confirmed. Docking simulations and molecular mechanics calculations were performed to evaluate binding scores. The preliminary evaluation suggested that our approach successfully selected the inhibitory compounds identified by the experiments. The same approach was applied to 8820 compounds in a database consisting of approved and investigational chemicals. Hence, docking simulations, molecular mechanics calculations, and re-evaluation of binding scores including solvation effects were performed, and the top 200 poses were selected as candidates for experimental assays. Consequently, 25 compounds were chosen for in vitro measurement of the enzymatic inhibitory activity. From the enzymatic assay, 5 compounds were identified to have inhibitory activities against the 3CL protease. The present work demonstrated the feasibility of a combination of docking simulation and molecular mechanics calculation for practical use in computational virtual screening.

A Promising Way to Overcome Temozolomide Resistance through Inhibition of Protein Neddylation in Glioblastoma Cell Lines.

There is no effective therapy for the lately increased incidence of glioblastoma multiforme (GBM)-the most common primary brain tumor characterized by a high degree of invasiveness and genetic heterogeneity. Currently, DNA alkylating agent temozolomide (TMZ) is the standard chemotherapy. Nevertheless, TMZ resistance is a major problem in the treatment of GBM due to numerous molecular mechanisms related to DNA damage repair, epigenetic alterations, cellular drug efflux, apoptosis-autophagy, and overactive protein neddylation. Low molecular weight inhibitors of NEDD8-activating enzyme (NAE), such as MLN4924, attenuate protein neddylation and present a promising low-toxicity anticancer agent. The aim of our study was to find an effective combination treatment with TMZ and MLN4924 in our TMZ-resistant GBM cell lines and study the effect of these combination treatments on different protein expressions such as O6-methylguanine methyltransferase (MGMT) and p53. The combination treatment successfully decreased cell viability and sensitized TMZ-resistant cells to TMZ, foreshadowing a new treatment strategy for GBM.

Modulation of Aβ42 Aggregation Kinetics and Pathway by Low-Molecular-Weight Inhibitors.

The aggregation of amyloid-β 42 (Aβ42) is directly related to the pathogenesis of Alzheimer's disease. Here, we have investigated the early stages of the aggregation process, during which most of the cytotoxic species are formed. Aβ42 aggregation kinetics, characterized by the quantification of Aβ42 monomer consumption, were tracked by real-time solution NMR spectroscopy (RT-NMR) allowing the impact that low-molecular-weight (LMW) inhibitors and modulators exert on the aggregation process to be analysed. Distinct differences in the Aβ42 kinetic profiles were apparent and were further investigated kinetically and structurally by using thioflavin T (ThT) and transmission electron microscopy (TEM), respectively. LMW inhibitors were shown to have a differential impact on early-state aggregation. Insight provided here could direct future therapeutic design based on kinetic profiling of the process of fibril formation.

Low-molecular weight inhibitors of the alternative complement pathway.

Dysregulation of the alternative complement pathway predisposes individuals to a number of diseases. It can either be evoked by genetic alterations in or by stabilizing antibodies to important pathway components and typically leads to severe diseases such as paroxysmal nocturnal hemoglobinuria, atypical hemolytic uremic syndrome, C3 glomerulopathy, and age-related macular degeneration. In addition, the alternative pathway may also be involved in many other diseases where its amplifying function for all complement pathways might play a role. To identify specific alternative pathway inhibitors that qualify as therapeutics for these diseases, drug discovery efforts have focused on the two central proteases of the pathway, factor B and factor D. Although drug discovery has been challenging for a number of reasons, potent and selective low-molecular weight (LMW) oral inhibitors have now been discovered for both proteases and several molecules are in clinical development for multiple complement-mediated diseases. While the clinical development of these inhibitors initially focuses on diseases with systemic and/or peripheral tissue complement activation, the availability of LMW inhibitors may also open up the prospect of inhibiting complement in the central nervous system where its activation may also play an important role in several neurodegenerative diseases.

THE INFLUENCE OF NON-PROTEIN AMINO ACIDS AND PEPTIDES ON BACTERIAL COLLAGENASE

Bacterial collagenolytic proteases have drawn increasing attention due to their essential role in the global nitrogen cycling and their virulent role in some diseases. The inhibition of these enzymes is attractive, as it does not attack the pathogen directly but rather blocks the colonization and infiltration of the host by the clostridia. Optically active non-protein α-amino acids have been screened for their ability to inhibit collagenase of Clostridium histolyticum. Both structure-based drug design approach (modeling) and that of determining enzyme activity in the presence of amino acids have been used to identify low molecular weight inhibitors of collagenase. The compounds able to inhibit collagenase activity have been revealed and IC50 values have been estimated.

De novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico

Epstein-Barr virus is a DNA-containing virus that, according to current data, is associated with approximately 1% of all cancers in the world. This viral effect on the human body is associated with its pronounced antiapoptotic activity. An important role in this process is played by the protein BHRF1, which is a structural and functional homologue of antiapoptotic proteins of the BCL-2 family. In this study, we investigate the selective low molecular weight inhibitor of the above viral protein – EBAI (Epstein-Barr virus Antiapoptotic Inhibitor), which we designed using in silico methods. We conducted two parallel simulation experiments where EBAI was intentionally destabilized to demonstrate its high-affinity recognition potential of the BHRF1 pocket, which binds BH3.Thus, although the potential inhibitor was in close proximity to the site of interaction, it contacted it only through orientation interactions (hydrogen and Coulomb interactions). Despite this complication of the standard ligand-receptor complex simulation procedure, we demonstrated in two parallel computational experiments the high affinity of EBAI for the BH3-binding pocket of BHRF1. In both cases, in the first nanoseconds of modeling, our inhibitor underwent the necessary conformational rearrangements and formed all the required interactions for effective complexation. Thus, further in vitro studies are logical and necessary step to fully evaluate the potential of EBAI as an inhibitor of the antiapoptotic protein BHRF1 of Epstein-Barr virus. Communicated by Ramaswamy H. Sarma

Inhibition of Sema-3A Promotes Cell Migration, Axonal Growth, and Retinal Ganglion Cell Survival.

PurposeSemaphorin 3A (Sema-3A) is a secreted protein that deflects axons from inappropriate regions and induces neuronal cell death. Intravitreal application of polyclonal antibodies against Sema-3A prevents loss of retinal ganglion cells ensuing from axotomy of optic nerves. This suggested a therapeutic approach for neuroprotection via inhibition of the Sema-3A pathway.MethodsTo develop potent and specific Sema-3A antagonists, we isolated monoclonal anti-Sema-3A antibodies from a human antibody phage display library and optimized low-molecular weight Sema-3A signaling inhibitors. The best inhibitors were identified using in vitro scratch assays and semiquantitative repulsion assays.ResultsA therapeutic approach for neuroprotection must have a long duration of action. Therefore, antibodies and low-molecular weight inhibitors were formulated in extruded implants to allow controlled and prolonged release. Following release from the implants, Sema-3A inhibitors antagonized Sema-3A effects in scratch and repulsion assays and protected retinal ganglion cells in animal models of optic nerve injury, retinal ischemia, and glaucoma.Conclusions and Translational RelevanceCollectively, our findings indicate that the identified Sema-3A inhibitors should be further evaluated as therapeutic candidates for the treatment of Sema-3A-driven central nervous system degenerative processes.

FC 036IPTACOPAN (LNP023): A NOVEL ORAL COMPLEMENT ALTERNATIVE PATHWAY FACTOR B INHIBITOR SAFELY AND EFFECTIVELY STABILISES EGFR IN C3 GLOMERULOPATHY

Abstract Background and Aims Iptacopan (LNP023) is a highly selective oral low molecular weight inhibitor of Factor B, a key complement alternative pathway protease. We have previously reported data from an interim analysis (IA) of a Phase 2 study in patients with native C3G (NCT03832114) showing that a 12-week course of iptacopan results in a 49% reduction in proteinuria with no adverse safety findings (ASN 2020 SU-OR39). The aim of this analysis was to determine whether iptacopan treatment altered eGFR slope in this same population. Method Adults with biopsy-proven native C3G received open-label iptacopan for 12w (10-100mg bid during w1-3 then 200mg bid w4-12). All had proteinuria >1g/24h, low plasma C3, were receiving maximally tolerated stable ACEi/ARB and were vaccinated against N. meningitidis, H. influenzae and S. pneumoniae. On study completion, all patients received ongoing iptacopan in a long-term extension study (NCT03955445). Historical data were collected on eGFR (CKD-EPI) for the two-year period prior to patients entering the study or since diagnosis where this was less than two years, and were compared with those obtained in the IA following the commencement of iptacopan. A generalized linear mixed model, with a common intercept, a pre-treatment slope and a change in the slope following iptacopan treatment was used to predict the pre-post iptacopan change in eGFR over time. Results 12 patients (10 male, 2 female; 11 C3GN, 1 DDD) participated in the IA. Study baseline mean (SD) age was 26.1 (12.1) yrs, geometric mean (CV%) urine PCR 397 (56) g/mol and eGFR 57.9 (65.5) ml/min/1.73m2. Complete data sets were collected for all 12 patients; one patient entered the study immediately following biopsy diagnosis. During the two years prior to the iptacopan treatment, the mean eGFR slope was -14.8 ml/min/1.73m2/year (p=0.0016), consistent with the known natural history of native C3G (Nephron 2020; 144: 272–280). Treatment with iptacopan was associated with a mean increase in eGFR of 3.1 ml/min/1.73m2 from baseline to 12w, corresponding to a mean predicted eGFR preservation of 6.4 ml/min/1.73m2 over 12w as a result of iptacopan administration (Figure 1, p=0.0459). Data collected in seven patients who entered the extension study confirmed ongoing eGFR stability until 25 weeks. There were no deaths or SAEs related to iptacopan and no AEs leading to iptacopan discontinuation in this patient cohort. Conclusion 12 weeks treatment with iptacopan 200mg bid in patients with C3G resulted in statistically significant and clinically important improvement in eGFR slope with favourable safety and tolerability in addition to significantly reducing proteinuria. Extended iptacopan treatment up to 25 weeks resulted in ongoing stability of eGFR, suggesting that this may result in clinically relevant prolongation of the time to or even potentially prevention of the development of kidney failure.

An orally available PD-1/PD-L1 blocking peptide OPBP-1-loaded trimethyl chitosan hydrogel for cancer immunotherapy

Blockade of the immune checkpoint PD-1/PD-L1 with monoclonal antibodies demonstrated unprecedented clinical efficacies in many cancers. But the orally available low molecular weight inhibitors remain infancy. Compared to small molecules, peptide exhibits better selectivity and fewer side effects, but poor half-life and a big challenge to be orally administrated. Here, we developed a proteolysis-resistant D peptide OPBP-1 (Oral PD-L1 Binding Peptide 1) which could selectively bind PD-L1, significantly block PD-1/PD-L1 interaction and enhance IFN-γ (interferon γ) secretion from CD8+ T cells in human PBMCs (Peripheral blood mononuclear cells). OPBP-1 could significantly inhibit tumor growth in murine colorectal CT26 and melanoma B16-OVA models at a relatively low dose of 0.5 mg/kg, with enhancing the infiltration and function of CD8+ T cells. More interestingly, oral delivery of OPBP-1 loaded TMC (N, N, N-trimethyl chitosan) hydrogel (OPBP-1@TMC) showed promising OPBP-1 oral bioavailability (52.8%) and prolonged half-life (14.55 h) in rats, and also significantly inhibited tumor growth in CT26 model. In conclusion, we discovered and optimized a PD-1/PD-L1 blocking peptide OPBP-1, and subsequently loaded into a TMC based hydrogel oral delivery system, in order to maximally elevate the oral bioavailability of the peptide drug and effectively inhibit tumor growth. These results opened up a new prospect for oral drug development in cancer immunotherapy.

In silico Identification of a Viral Surface Glycoprotein Site Suitable for the Development of Low Molecular Weight Inhibitors for Various Variants of the SARS-CoV-2

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) is a new coronavirus that today has an extremely significant impact on both global economy and society as a whole, due to its pandemic status and risk of complications. Therefore, understanding the molecular features of the interaction of receptor binding domain (RBD), which determines most of the dangerous properties of this pathogen, with human angiotensin-converting enzyme 2 (hACE2) is an important step in the process of developing a successful strategy to combat SARS-CoV-2. In addition, given the significant rate of accumulation of mutations in RBD, it makes sense to consider its different variants. Goal. Identification of a pocket potentially suitable for the search for low molecular weight inhibitors of interaction of different variants of SARS-CoV-2 RBD and hACE2. Methods. The initial structure of different variants of the RBD/hACE2 complex was obtained from Protein Data Bank (PDB). Separate RBD variants were isolated from the same data. To obtain the Y453F mutant, variant P.1 was mutagenized in PyMol 1.8. The construction of the system, which included the resulting associate or individual protein, solvent and physiological concentration of sodium chloride, was performed using CHARMM-GUI (graphical user interface for CHARMM) tools according to the standard protocol for glycoproteins. The actual simulation and balancing of the system was performed in GROMACS (GROningen MAchine for Chemical Simulation) version 2019.6 for 50 ns. Results. The interface of RBD/hACE2 interaction is formed by amino acids Q24, D30, H34, E35, E37, Y41, Y83, K353, D355 and R393 – for hACE2 and K417, Y453, F486, N487, Y489, Q493, Q498, T500, N501, Y505 – for RBD. However, it is heterogeneous and can be divided into two subinterfaces, and each includes its own pool of interactions: hACE2 Q24/Y83 + RBD N487, hACE2 H34 + RBD Y453, hACE2 E35 + RBD Q493 and hACE2 D30 + RBD K417 – for N- terminal relative to H1 hACE2 subinterface and hACE2 E37/R393 + RBD Y505, hACE2 K353 + RBD Q498/G502 and hACE2 D355 + RBD T500 – for C-terminal. According to the considered N501Y mutation, changes are observed in the mentioned interaction patterns – hydrogen bonds of hACE2 Q42 + RBD Q498, hACE2 K31 + RBD Q493 and hACE2 K31 + RBD F490 are formed, and hACE2 H34 + RBD Y453 is lost. Similar aberrations, except for the hydrogen bond with F490, are observed in the case of the N501Y + Y453F variant. Despite significant changes in the pool of interactions, the gross number of hydrogen bonds for the complexes of all three variants is relatively stable and ranges from 9 to 10. Between the defined interaction subinterfaces for all considered variants of RBD are characterized by the presence of a pocket, which is formed by residues R403, Y453, Q493, S494, Y495, G496, F497, Q498, N501 and Y505 conditionally original variant. According to the results of the molecular dynamics simulation, the Y453F replacement has little effect on the overall topology of the cavity, but sufficiently reduces the polarity of the pocket part of its localization, which leads to the impossibility of forming any polar interactions. In contrast, N501Y, due to the larger size of the tyrosine radical and the presence of parahydroxyl, forms two equivalent mutually exclusive hydrogen bonds with the carbonyls of the peptide groups G496 and Y495. Additional stabilization of the Y501 is provided by interplanar stacking with the Y505. In addition to the anchored position in ~ 25% of the trajectory there is another “open” conformation Y501. At which the radical of this tyrosine does not interact with the rest of the protein. Conclusions. 1) The interface of interaction of SARS-CoV-2 RBD with hACE2 is not continuous and it can be conditionally divided into two subiterfaces: N-terminal and C-terminal. Each is characterized by its own pattern of connections and changes according to the RBD N501Y and Y453F replacements we have considered. However, despite the presence of significant molecular rearrangements caused by N501Y and Y453F, the total number of hydrogen bonds is relatively the same for all mutants. 2) Between the identified interaction subinterfaces, SARS-CoV-2 RBD contains caveola, which due to its location may be potentially suitable for finding promising candidates for drugs aimed at inhibiting the interaction of this protein with hACE2. In this case, the substitutions of N501Y and Y453F have a significant impact on the topology of a particular pocket and can potentially modify the activity of inhibitors directed to this area.

Antitumour Activity of Dehydroxymethylepoxyquinomycin (DHMEQ): a Literature Review

Carcinogenesis research uncovers new pathogenesis links as vulnerable targets of effective antitumour therapies. Among the key mediators of immune response, cell proliferation, cell apoptosis and inflammation is transcription factor NF-κB. Misregulation of an NF-κB-dependent pathway is found in solid and haematopoietic tumour cells. One of the best known NF-κB functions is expression regulation of genes involved in the apoptosis inhibition or activation and survival in both intact and malignant cells. The NF-κB-mediated pathways’ involvement in carcinogenesis, angiogenesis and tumour resistance to chemo- and radiotherapies makes this factor a promising target for drug anti-cancer interventions. This review summarises evidence on the antitumour and anti-inflammatory activity of a high-potent and specific low molecular-weight NF-κB inhibitor, dehydroxymethylhepoxyquinomycin (DHMEQ), as a candidate therapeutic agent in treatment for variant malignancies.

Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells

Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein-protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor ([Formula: see text] Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein-protein interaction involved in actin filament processing and cell migration.

The Role of ERBB2/HER2 Tyrosine Kinase Receptor in the Regulation of Cell Death.

HER2 (Human Epidermal Growth Factor Receptor 2), also known as ERBB2, CD340, and Neu protooncogene, is a member of the epidermal growth factor receptor (EGRF) family. Members of the ERBB family, including HER2, activate molecular cascades that stimulate proliferation and migration of cancer cells, as well as their resistance to the anticancer therapy. These proteins are often overexpressed and/or mutated in various cancer types and represent promising targets for the anti-cancer therapy. Currently, anti-HER2 drugs have been approved for the treatment of several types of solid tumors. HER2-specific therapy includes monoclonal antibodies and low-molecular weight inhibitors of tyrosine kinase receptors, such as lapatinib, neratinib, and pyrotinib. In addition to the activation of molecular pathways responsible for cell proliferation and survival under stress conditions, HER2 directly regulates programmed cell death. Here, we review the studies focused on the involvement of HER2 in various signaling pathways and its role in the regulation of apoptosis.

Discovery of small molecule inhibitors against the NS3/4A serine protease of Hepatitis C virus genotype 3 via highthroughput virtual screening and in vitro evaluations

The hepatitis C virus (HCV) consists of eight genotypes and 90 subtypes, with genotype (GT) 3 being the second most common globally and is linked to higher incidences of steatosis and rapid development of fibrosis and cirrhosis. The NS3/4A serine protease, a heterodimer complex of two HCV non-structural proteins, is an effective target for pharmaceutical intervention due to its essential roles in processing HCV polyproteins and inhibiting innate immunity. This study combines structure-based virtual screening (SBVS) of predefined compound libraries, pharmacokinetic prediction (ADME/T) and in vitro evaluation to identify potential low molecular weight (<500 Dalton) inhibitors of the NS3/4A serine protease (GT3). In silico screening of ZINC and PubChem libraries yielded five selected compounds as potential candidates. Dose-dependent inhibition of the NS3/4A serine protease and HCV replication in HuH-7.5 cells revealed that compound A (PubChem ID No. 16672637) exhibited inhibition towards HCV GT3 with an IC50 of 106.7µM and EC50 of 25.8µM, respectively. Thus, compound A may be developed as a potent, low molecular weight drug against the HCV NS3/4A serine protease of GT3.

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

Inhibition of the reverse transcriptase (RT) enzyme of the human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. The parent molecule and derivatives were then docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in drug-likeness screening by Swiss-ADME or at the docking stage. The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to - 58.3 and -54.5 KJ/mol, respectively. In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using a fragment-based approach.