Class Of Small Molecules Research Articles

Left ventricular outflow tract obstruction in hypertrophic cardiomyopathy and the impact of mavacamten.

Hypertrophic cardiomyopathy (HCM) is a common genetic disorder characterised by unexplained left ventricular hypertrophy. Left ventricular outflow tract obstruction is an integral component of the disease, often resulting in significant symptoms, but also carrying a risk of progression to heart failure and death. Advancements in our understanding of the pathophysiology of HCM have led to the development of new therapies targeting the molecular basis of the disease at the level of the cardiac sarcomere, the basic contractile apparatus of the myocardium. Myosin modulators are a novel class of small molecules which target cardiac myosins directly to modulate cardiac contractility. The myosin inhibitors present the first advancement in pharmacological management of obstructive HCM in almost 35 years, with a growing body of evidence for the safety, tolerability and efficacy of mavacamten, and to a lesser extent aficamten. The aim of this review is to summarise the current management of patients with obstructive HCM and review the most recent available data from clinical trials pertaining to myosin inhibition.

The small molecule class IIa HDAC inhibitor TMP269 protects against degeneration in in vitro models of Parkinson’s disease

The small molecule class IIa HDAC inhibitor TMP269 protects against degeneration in in vitro models of Parkinson’s disease

MALDI-2 and t-MALDI-2 Mass Spectrometry Imaging.

Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) combined with laser-induced postionization for MALDI-2 enables the simultaneous registration of numerous classes of small molecules (e.g., secondary metabolites including sterols) as well as phospholipids, glycolipids, and glycans from tissue sections and from cell cultures with strongly boosted ion yields. Here, we describe methodological aspects that are key for optimizing the analytical sensitivity and spatial resolution of a MALDI-2 imaging experiment. We will include both top-illumination MALDI-2 as well as the recently introduced transmission (t-) mode MALDI-2 approach.

An unanticipated discovery towards novel naphthalimide corbelled aminothiazoximes as potential anti-MRSA agents and allosteric modulators for PBP2a

Available therapeutic strategies are urgently needed to conquer multidrug resistance of MRSA. A visible effort was guided towards the advancement of novel antibacterial framework of naphthalimide corbelled aminothiazoximes, and desired to assert some insight on the conjunction of individual pharmacophore with distinct biological activities and unique action mechanism. Preliminary assessment displayed that dimethylenediamine derivative 13d presented a wonderful inhibition on MRSA (MIC = 0.5 μg/mL), and showed excellent membrane selectivity (HC50 > 200 μg/mL) from an electrostatic distinction of the electronegative bacterial membranes and the electroneutral mammalian membranes. Moreover, 13d could effectually relieve the development of MRSA resistance. Investigations into explaining the mechanism of anti-MRSA disclosed that 13d displayed strong lipase affinity, which facilitated its permeation into cell membrane, causing membrane depolarization, leakage of cytoplasmic contents and lactate dehydrogenase (LDH) inhibition. Meanwhile, 13d could exert interaction with DNA to hinder biological function of DNA, and disrupt the antioxidant defense system of MRSA through up-regulation of ROS subjected the strain to oxidative stress. In particular, the unanticipated mechanism for naphthalimide corbelled aminothiazoximes that 13d could suppress the expression of PBP2a by inducing allosteric modulation of PBP2a and triggering the open of the active site, was discovered for the first time. These findings of naphthalimide corbelled aminothiazoximes as a small-molecule class of anti-MRSA agents held promise in strategies for treatment of MRSA infections.

Positioning Ozanimod in Ulcerative Colitis: Restoring Leukocyte Traffic Under Control

Positioning Ozanimod in Ulcerative Colitis: Restoring Leukocyte Traffic Under Control

Mcc1229, an Stx2a-Amplifying Microcin, Is Produced In Vivo and Requires CirA for Activity.

ABSTRACTEnterohemorrhagic Escherichia coli (EHEC) strains, including the foodborne pathogen E. coli O157:H7, are responsible for thousands of hospitalizations each year. Various environmental triggers can modulate pathogenicity in EHEC by inducing the expression of Shiga toxin (Stx), which is encoded on a lambdoid prophage and transcribed together with phage late genes. Cell-free supernatants of the sequence type 73 (ST73) E. coli strain 0.1229 are potent inducers of Stx2a production in EHEC, suggesting that 0.1229 secretes a factor that activates the SOS response and leads to phage lysis. We previously demonstrated that this factor, designated microcin 1229 (Mcc1229), was proteinaceous and plasmid-encoded. To further characterize Mcc1229 and support its classification as a microcin, we investigated its regulation, determined its receptor, and identified loci providing immunity. The production of Mcc1229 was increased upon iron limitation, as determined by an enzyme-linked immunosorbent assay (ELISA), lacZ fusions, and quantitative real-time PCR (qRT-PCR). Spontaneous Mcc1229-resistant mutants and targeted gene deletion revealed that CirA was the Mcc1229 receptor. TonB, which interacts with CirA in the periplasm, was also essential for Mcc1229 import. Subcloning of the Mcc1229 plasmid indicated that Mcc activity was neutralized by two open reading frames (ORFs), each predicted to encode a domain of unknown function (DUF)-containing protein. In a germfree mouse model of infection, colonization with 0.1229 suppressed subsequent colonization by EHEC. Although Mcc1229 was produced in vivo, it was dispensable for colonization suppression. The regulation, import, and immunity determinants identified here are consistent with features of other Mccs, suggesting that Mcc1229 should be included in this class of small molecules.

Abstract P081: In vitro activity and efficacy of novel dual PARP-HDAC inhibitors

Abstract Introduction: Inhibition of poly adenosine diphosphate-ribose polymerase (PARP) is an effective treatment strategy against tumors with homologous recombination (HR) DNA repair deficiencies. Combination treatments utilizing PARP inhibitors (PARPi) in concert with inhibitors of key DNA repair or PARPi-resistance pathways, may expand the utility of PARPi beyond cancers harboring germ-line HR deficiencies. Acetylation and deacetylation of histones is an important regulatory event in the DNA damage response. Combining histone deacetylation inhibitors (HDACi) and PARPi have sensitized PARPi-resistant cells to treatment; however, combination regimens often require sequential administration to manage overlapping toxicities and accommodate diverse pharmacokinetics, constituting a significant limitation of these strategies in a clinical setting. Here, we test the activity of kt-3000 series, a novel bi-functional class of small molecules with dual PARP and HDAC inhibitor activity in HR-proficient cancer cells where PARPi have historically lacked single-agent activity. Methods: PARP enzyme activity was measured using the Trevigen Universal Colorimetric PARP Assay Kit. HDAC activity was measured using nuclear extracts of treated cells and the HDAC Fluorometric Activity Assay Kit from Cayman Chemical, as per the manufacturer’s protocol. PARP activity was measured by fluorescence in C41 cells following compound treatment for 2 hours and PARP-activation with 1M H2O2 by staining cells with an anti-PARP Ab followed by a FITC-coupled secondary antibodies. Cell survival EC50 values were obtained by treating cells with a range of inhibitor concentrations, then quantifying cell confluency after 72-hours of treatment based on images taken with an Incucyte S3 system. Results: kt-3000 series compounds are potent inhibitors of PARP and HDAC with IC50 values for PARP enzyme activity in the low nM range, comparable to those of FDA-approved PARP inhibitors (olaparib, rucaparib, niraparib, and talazoparib) and IC50 values for the inhibition of HDAC activity comparable to FDA-approved HDAC inhibitors (panabinostat, belinostat, and vorinostat). Fluorescent assays of PARP activity in C41 cells also resulted in IC50 values in the nM range and cell survival EC50 values of the dual inhibitors are comparable to FDA-approved PARP inhibitors alone and in similar range with FDA-approved HDAC inhibitors alone. Conclusion: Our novel dual PARP-HDAC inhibitors show potent inhibition of PARP activity in vitro comparable to FDA-approved PARP inhibitors and also show potent inhibition of HDAC activity. The potency and activity of kt-3000 series compounds exhibit potential superiority to FDA-approved PARP inhibitors and HDAC inhibitors, in formulation as a single molecule. Development of these multi-target inhibitors will target unmet medical needs in the treatment of HR-proficient cancer types with dysregulation of histone deacetylation. Citation Format: Sarah Truong, Fariba Ghaidi, Louise Ramos, Jay Joshi, Dennis Brown, Neil Sankar, John Langlands, Jeffrey Bacha, Wang Shen, Mads Daugaard. In vitro activity and efficacy of novel dual PARP-HDAC inhibitors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P081.

New Physical Hydrogels Based on Co-Assembling of FMOC-Amino Acids.

In the last years, physical hydrogels have been widely studied due to the characteristics of these structures, respectively the non-covalent interactions and the absence of other necessary components for the cross-linking processes. Low molecular weight gelators are a class of small molecules which form higher ordered structures through hydrogen bonding and π–π interactions. In this context it is known that the formation of hydrogels based on FMOC–amino acids is determined by the primary structures of amino acids and the secondary structure arrangement (alpha–helix or beta–sheet motifs). The present study aimed to obtain supramolecular gels through co-assembly phenomenon using FMOC–amino acids as low molecular weight gelators. The stability of the new structures was evaluated by the vial inversion test, while FTIR spectra put into evidence the interaction between the compounds. The gel-like structure is evidenced by viscoelastic parameters in oscillatory shear conditions. SEM microscopy was used to obtain the visual insight into the morphology of the physical hydrogel network while DLS measurements highlighted the sol-gel transition. The molecular arrangement of gels was determined by circular dichroism, fluorescence and UV-Vis spectroscopy.

Kinetin stimulates differentiation of C2C12 myoblasts.

Kinetin or N6-furfuryladenine (K) belongs to a class of plant hormones called cytokinins, which are biologically active molecules modulating many aspects of plant growth and development. However, biological activities of cytokinins are not only limited to plants; their effects on animals have been widely reported in the literature. Here, we found that Kinetin is a potent small molecule that efficiently stimulates differentiation of C2C12 myoblasts into myotubes in vitro. The highest efficacy was achieved at 1μM and 10μM Kinetin concentrations, in both mitogen-poor and rich media. More importantly, Kinetin was able to strongly stimulate the MyoD-dependent conversion of fibroblasts into myotubes. Kinetin alone did not give rise to fibroblast conversion and required MyoD; this demonstrates that Kinetin augments the molecular repertoire of necessary key regulatory factors to facilitate MyoD-mediated myogenic differentiation. This novel Kinetin pro-myogenic function may be explained by its ability to alter intracellular calcium levels and by its potential to impact on Reactive Oxygen Species (ROS) signalling. Taken together, our findings unravel the effects of a new class of small molecules with potent pro-myogenic activities. This opens up new therapeutic avenues with potential for treating skeletal muscle diseases related to muscle aging and wasting.

Nucleic Acid Drugs-Current Status, Issues, and Expectations for Exosomes.

Simple SummaryNucleic acid drugs provide novel therapeutic modalities with characteristics that differ from those of small molecules and antibodies. In this review, I focus on the various mechanisms through which nucleic acid drugs act on, the status of their clinical development, and discuss several hurdles that need to be surmounted. In addition, by listing examples of how the progress in exosome biology can lead to the solution of problems in nucleic acid drug therapy, I hope that many more nucleic acid drugs including anticancer drugs will be developed in the future.Nucleic acid drugs are being developed as novel therapeutic modalities. They have great potential to treat human diseases such as cancers, viral infections, and genetic disorders due to unique characteristics that make it possible to approach undruggable targets using classical small molecule or protein/antibody-based biologics. In this review, I describe the advantages, classification, and clinical status of nucleic acid therapeutics. To date, more than 10 products have been launched, and many products have been tested in clinics. To promote the use of nucleic acid therapeutics such as antibodies, several hurdles need to be surmounted. The most important issue is the delivery of nucleic acids and several other challenges have been reported. Recent advanced delivery platforms are lipid nanoparticles and ligand conjugation approaches. With the progress of exosome biology, exosomes are expected to contribute to the solution of various problems associated with nucleic acid drugs.

NBD2 Is Required for the Rescue of Mutant F508del CFTR by a Thiazole-Based Molecule: A Class II Corrector for the Multi-Drug Therapy of Cystic Fibrosis.

Cystic fibrosis (CF) is caused by loss-of-function mutations in the CF transmembrane conductance regulator (CFTR) protein, an anion channel that regulates epithelial surface fluid secretion. The deletion of phenylalanine at position 508 (F508del) is the most common CFTR mutation. F508del CFTR is characterized by folding and trafficking defects, resulting in decreased functional expression of the protein on the plasma membrane. Several classes of small molecules, named correctors, have been developed to rescue defective F508del CFTR. Although individual correctors failed to improve the clinical status of CF patients carrying the F508del mutation, better results were obtained using correctors combinations. These results were obtained according to the premise that the administration of correctors having different sites of action should enhance F508del CFTR rescue. We investigated the putative site of action of an aminoarylthiazole 4-(3-chlorophenyl)-N-(3-(methylthio)phenyl)thiazol-2-amine, named FCG, with proven CFTR corrector activity, and its synergistic effect with the corrector VX809. We found that neither the total expression nor the maturation of WT CFTR transiently expressed in human embryonic kidney 293 cells was influenced by FCG, administrated alone or in combination with VX809. On the contrary, FCG was able to enhance F508del CFTR total expression, and its combination with VX809 provided a further effect, being able to increase not only the total expression but also the maturation of the mutant protein. Analyses on different CFTR domains and groups of domains, heterologously expressed in HEK293 cells, show that NBD2 is necessary for FCG corrector activity. Molecular modelling analyses suggest that FCG interacts with a putative region located into the NBD2, ascribing this molecule to class II correctors. Our study indicates that the continuous development and testing of combinations of correctors targeting different structural and functional defects of mutant CFTR is the best strategy to ensure a valuable therapeutic perspective to a larger cohort of CF patients.

AZD5438-PROTAC: A selective CDK2 degrader that protects against cisplatin- and noise-induced hearing loss

Cyclin-dependent kinase 2 (CDK2) is a potential therapeutic target for the treatment of hearing loss and cancer. Previously, we identified AZD5438 and AT7519-7 as potent inhibitors of CDK2, however, they also targeted additional kinases, leading to unwanted toxicities. Proteolysis Targeting Chimeras (PROTACs) are a new promising class of small molecules that can effectively direct specific proteins to proteasomal degradation. Herein we report the design, synthesis, and characterization of PROTACs of AT7519-7 and AZD5438 and the identification of PROTAC-8, an AZD5438-PROTAC, that exhibits selective, partial CDK2 degradation. Furthermore, PROTAC-8 protects against cisplatin ototoxicity and kainic acid excitotoxicity in zebrafish. Molecular dynamics simulations reveal the structural requirements for CDK2 degradation. Together, PROTAC-8 is among the first-in-class PROTACs with in vivo therapeutic activities and represents a new lead compound that can be further developed for better efficacy and selectivity for CDK2 degradation against hearing loss and cancer.

State of the Art on Approved Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Modulators and Triple-Combination Therapy.

Cystic fibrosis (CF) is the most common life-limiting inherited disease in Caucasian populations, affecting approximately 80,000 people worldwide. CF is a complex multi-organ monogenic autosomal recessive disorder caused by a mutation in cystic fibrosis transmembrane conductance regulator (CFTR) gene. Since the discovery of the CFTR gene in 1989, more than 2000 mutations have been identified so far and about 240 can cause CF. Until recently, the treatment for CF was aimed to prevent and manage the manifestations of CFTR dysfunction, primarily recurrent pulmonary infections and pancreatic exocrine failure. Over the past few decades, the therapeutic approach to CF has been revolutionized by the development of a new class of small molecules called CFTR modulators that target specific defects caused by mutations in the CFTR gene. CFTR modulators have been shown to change profoundly the clinical course of the CF, leading to meaningful improvements in the lives of a large proportion of people of CF heterozygous for F508del, especially if started in young children. Further studies are needed to extend the use of triple CFTR modulation therapy also for young children in order to prevent the irreversible effects of the disease and for patients with very rare mutations with a personalized approach to treatment.

Halting Coronavirus Replication

Sirtuin 1 (SIRT1) inhibitors can reduce replication of many viruses with certain characteristics similar to those of coronaviruses, while the p53 protein is another important factor in the down-regulation of viral growth. Tenovin is a class of small molecules that inhibit Sirtuin 1 and 2, in addition to activating the p53 protein, by means of regulating the interactions used by coronaviruses as a self-defense mechanism. By blocking virus growth and continuous replication, with already tested antiviral medicines, the promise of coronavirus disease 2019 (COVID-19) eradication exists.

Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) inhibitors: identification of a new class of small molecules

Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) inhibitors: identification of a new class of small molecules

The Molecular Tweezer CLR01 Inhibits Antibody-Resistant Cell-to-Cell Spread of Human Cytomegalovirus.

Human cytomegalovirus (HCMV) uses two major ways for virus dissemination: infection by cell-free virus and direct cell-to-cell spread. Neutralizing antibodies can efficiently inhibit infection by cell-free virus but mostly fail to prevent cell-to-cell transmission. Here, we show that the ‘molecular tweezer’ CLR01, a broad-spectrum antiviral agent, is not only highly active against infection with cell-free virus but most remarkably inhibits antibody-resistant direct cell-to-cell spread of HCMV. The inhibition of cell-to-cell spread by CLR01 was not limited to HCMV but was also shown for the alphaherpesviruses herpes simplex viruses 1 and 2 (HSV-1, -2). CLR01 is a rapid acting small molecule that inhibits HCMV entry at the attachment and penetration steps. Electron microscopy of extracellular virus particles indicated damage of the viral envelope by CLR01, which likely impairs the infectivity of virus particles. The rapid inactivation of viral particles by CLR01, the viral envelope as the main target, and the inhibition of virus entry at different stages are presumably the key to inhibition of cell-free virus infection and cell-to-cell spread by CLR01. Importance: While cell-free spread enables the human cytomegalovirus (HCMV) and other herpesviruses to transmit between hosts, direct cell-to-cell spread is thought to be more relevant for in vivo dissemination within infected tissues. Cell-to-cell spread is resistant to neutralizing antibodies, thus contributing to the maintenance of virus infection and virus dissemination in the presence of an intact immune system. Therefore, it would be therapeutically interesting to target this mode of spread in order to treat severe HCMV infections and to prevent dissemination of virus within the infected host. The molecular tweezer CLR01 exhibits broad-spectrum antiviral activity against a number of enveloped viruses and efficiently blocks antibody-resistant cell-to-cell spread of HCMV, thus representing a novel class of small molecules with promising antiviral activity.

Benzotrithiophene and triphenylamine based covalent organic frameworks as heterogeneous photocatalysts for benzimidazole synthesis

Metal-free covalent organic frameworks (COFs) as visible-light active and recyclable photocatalysts afford an eco-friendly and sustainable option to classical photosensitizers, which usually require noble metals (iridium, ruthenium, rhodium, etc.) to produce photocatalytic activity. Most classical small molecule photosensitizers have poor recyclability with certain limitations. As a result, it is of great significance to develop a metal-free and easily recyclable COF photocatalyst. In this study, we designed and synthesized a new type of COF photocatalyst (BTT-TPA-COF) in which benzotrithiophene and triphenylamine units are alternately connected. It has high specific surface area, permanent porosity and good stability. In addition, this design strategy can effectively adjust the band gap, energy level and photoelectric performance of BTT-TPA-COF. As a metal-free photocatalyst, BTT-TPA-COF exhibits high-efficiency photocatalytic activity, excellent substrate tolerance and excellent recyclability for the synthesis of 2-arylbenzimidazole compounds. This research not only puts forward a design strategy for high-efficiency photocatalysts, but also broadens the application range of COF materials in photocatalytic organic reactions.

Structure and function of retroviral integrase.

A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.

Emerging small-molecule therapeutic approaches for Alzheimer's disease and Parkinson's disease based on targeting microRNAs.

Emerging small-molecule therapeutic approaches for Alzheimer's disease and Parkinson's disease based on targeting microRNAs.

Model-Based Meta-Analysis in Psoriasis: A Quantitative Comparison of Biologics and Small Targeted Molecules.

Background: The response time-course information of biologics and small targeted molecules for the treatment of moderate to severe plaque psoriasis which helps clinicians to understand the onset of action and maintenance of effect are unclear. Quantitative information about the efficacy comparation of different systemic agents are needed. Methods: Model-based meta-analysis was conducted and longitudinal models were developed by applying two clinical end points commonly reported in the clinical trials of psoriasis: the proportion of patients achieving ≥75% reduction from baseline Psoriasis Area and Severity Index score (PASI75) and the proportion of patients achieving ≥90% reduction from baseline Psoriasis Area and Severity Index score (PASI90). Results: A total of 80 trials of thirteen biological agents and four small targeted molecules covering 235 treatment arms and 40323 patients with moderate to severe plaque psoriasis were included in this analysis. The drugs were divided into five classes of biologics and three classes of small molecules. Two longitudinal models of PASI75 and PASI90 were used to describe the time-varying drug effect and dose-effect relationship. The typical response-time courses for PASI75 and PASI90 increased over time and finally reached to the platform. For PASI75 end point at week 12, of all the therapeutic drugs, risankizumab administered as 150 mg at week 0, week 4, and q12w showed the most efficacious with PASI75 was 85.95% (95%CI, 75.71–92.60%), followed by ixekizumab administered as 160 mg at week 0, and q4w with PASI75 was 85.9% (95%CI, 76.12–92.79%). As for PASI90 end point at week 12, ixekizumab 160 mg at week 0, and q4w showed the greatest percentage of person achieved PASI90 (67.2%; 95%CI, 49.91–77.2%), followed by risankizumab 150 mg at week 0, week 4, and q12w (65.5%; 95%CI, 47.8–75.7%). What’s more, the risankizumab provided the highest response of PASI90 at week 16 and week 24. Conclusions: This study provided a quantitative efficacy comparation of 17 systemic agents for psoriasis in term of efficacy only and that safety was not considered. Risankizumab and ixekizumab showed superiority for both the two end points.