Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development

Deciphering the molecular interactions between monocyte chemoattractant protein and its potential inhibitor suramin

Chemokines, in coordination with glycosaminoglycans (GAGs) and G protein-coupled receptors (GPCRs), play a critical role in regulating inflammatory responses. Among these, monocyte chemoattractant protein-1, also known as CCL2 stands out for its role in coordinating with other immune molecules to direct macrophage migration, infiltration, and recruitment to inflamed tissues, highlighting this pathway as a promising target for therapeutic intervention. In the present study, suramin, a polysulfonated napthylurea compound, having structure similarity with heparin, initially developed therapeutic for treating Human African Trypanosomas [HAT] was analyzed for its repressive action against CCL2 arbitrated macrophage migration. The study delves into the binding interaction between suramin (SUR) and CCL2 monomer, elucidating the molecular and biophysical underpinnings of their interaction through various techniques, including isothermal calorimetry, fluorescence spectroscopy, fluorescence lifetime studies, CD spectroscopy, and 2D NMR spectroscopy. Additionally, in-silico mechanistic studies employing molecular dynamic simulations, MMPBSA, and decomposition analysis unravel the intricacies of CCL2-SUR interactions. The molecule is observed to be attenuating the migration of macrophages by interacting with nanomolar affinity (119 ± 11 nM) on the CCL2 with the region overlapping with the CCR2/GAG binding pocket. Thus, this study comprehensively identified suramin, as a possible GAG mimetic for scheming structure-based drug molecules exhibiting anti-inflammatory action by aiming the CCL2-CCR2-GAG axis.

Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr

Targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 with small molecules is a promising therapeutic strategy against COVID-19, but potent and safe inhibitors are lacking. HeE1-2Tyr, a nonnucleoside inhibitor of Dengue virus RdRp, was also shown to inhibit SARS-CoV-2 RdRp in vitro and to have antiviral activity in cells, but the underlying mechanism remains unclear. Here, we elucidate the molecular mechanism of HeE1-2Tyr-mediated SARS-CoV-2 RdRp inhibition. Biochemical assays confirm that HeE1-2Tyr inhibits RdRp with an IC50 of 5 µM and show that it competes with RNA binding to RdRp in vitro. Structural analysis using cryo-EM reveals that a stack of three HeE1-2Tyr molecules binds to the RNA binding site of RdRp. The identification of the conserved HeE1-2Tyr binding site and its intriguing inhibition mechanism of three stacked molecules that outcompete RNA may facilitate further development of pan-corona nonnucleoside inhibitors.

Development of Aromatic Foldamer Building Blocks Bearing Multiple Biogenic Side Chains

Aromatic oligoamides, with their intrinsic rigidity and well-defined conformations, are recognized for their potential in medical applications. Similar structures are present in several naturally occurring antibiotics and have been explored for their ability to bind to various proteins and B-DNA (canonical right-handed DNA helix). This study introduces a synthetic approach to produce quinoline amino acid monomers bearing diversified side chain combinations in positions 4, 5, and 6 of the quinoline ring, designed to enhance the side chain density on helical foldamers. By increasing the number of side chains on each monomer, we aim to mimic the dense side chain presentation of α-peptides, thus improving the potential for protein surface recognition. This synthetic strategy involves efficient functionalization through cross-coupling reactions, enabling the installation of diverse side chains at strategic positions on the quinoline ring. The process has been optimized for automated solid-phase synthesis, successfully producing a 20-unit oligoamide with good purity. This foldamer, featuring multiple cationic, anionic, polar, and hydrophobic side chains, demonstrates the potential for molecular recognition in drug discovery and therapeutic applications. The methodology described here represents a significant advancement in the construction of aromatic oligoamide foldamers, providing a robust platform for further exploration of biological systems.

Suramin enhances proliferation, migration, and tendon gene expression of human supraspinatus tenocytes

Rotator cuff tendinopathy is a common musculoskeletal disorder with limited pharmacological treatment strategies. This study aimed to investigate tenocytes' functional in vitro response from a ruptured supraspinatus tendon to suramin administration and to elucidate whether suramin can enhance tendon repair and modulate the inflammatory response to injury. Tenocytes were obtained from human supraspinatus tendons (n = 6). We investigated the effect of suramin on LPS-induced inflammatory responses and the underlying molecular mechanisms in THP-1 macrophages. Suramin enhanced the proliferation, cell viability, and migration of tenocytes. It also increased the protein expression of PCNA and Ki-67. Suramin-treated tenocytes exhibited increased expression of COL1A1, COL3A1, TNC, SCX, and VEGF. Suramin significantly reduced LPS-induced iNOS, COX2 synthesis, inflammatory cytokine TNF-α production, and inflammatory signaling by influencing the NF-κB pathways in THP-1 cells. Our results suggest that suramin holds great promise as a therapeutic option for treating rotator cuff tendinopathy.

Interference of small compounds and Mg2+ with dsRNA-binding fluorophores compromises the identification of SARS-CoV-2 RdRp inhibitors

The COVID-19 pandemic highlighted the need for the rapid development of antiviral therapies. Viral RNA-dependent RNA polymerases (RdRp) are promising targets, and numerous virtual screenings for potential inhibitors were conducted without validation of the identified hits. Here we have tested a set of presumed RdRp inhibitors in biochemical assays based on fluorometric detection of RdRp activity or on the electrophoretic separation or RdRp products. We find that fluorometric detection of RdRp activity is unreliable as a screening method because many small compounds interfere with fluorophore binding to dsRNA, and this effect is enhanced by the Mg2+ metal ions used by nucleic acid polymerases. The fact that fluorimetric detection of RdRp activity leads to false-positive hits underscores the requirement for independent validation methods. We also show that suramin, one of the proposed RdRp inhibitors that could be validated biochemically, is a multi-polymerase inhibitor. While this does not hinder its potential as an antiviral agent, it cannot be considered an specific inhibitor of SARS-CoV-2 RdRp.

Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function

The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.

Small Molecule Inhibitors of Protein Kinase D: Early Development, Current Approaches, and Future Directions

Now entering its fourth decade, research on the biological function, small molecule inhibition, and disease relevance of the three known isoforms of protein kinase D, PKD1, PKD2, and PKD3, has entered a mature development stage. This mini-perspective focuses on the medicinal chemistry that provided a structurally diverse set of mainly active site inhibitors, which, for a brief time period, moved through preclinical development stages but have yet to be tested in clinical trials. In particular, between 2006 and 2012, a rapid expansion of synthetic efforts led to several moderately to highly PKD-selective chemotypes but did not yet achieve PKD subtype selectivity or resolve general toxicity and pharmacokinetic challenges. In addition to cancer, other unresolved medical needs in cardiovascular, inflammatory, and metabolic diseases would, however, benefit from a renewed focus on potent and selective PKD modulators.

High-Throughput Assay for Identifying Diverse Antagonists of the Binding Interaction between the ACE2 Receptor and the Dynamic Spike Proteins of SARS-CoV-2

SARS-CoV-2, a coronavirus strain that started a worldwide pandemic in early 2020, attaches to human cells by binding its spike (S) glycoprotein to a host receptor protein angiotensin-converting enzyme 2 (ACE2). Blocking the interaction between the S protein and ACE2 has emerged as an important strategy for preventing viral infection. We systematically developed and optimized an AlphaLISA assay to investigate binding events between ACE2 and the ectodomain of the SARS-CoV-2 S protein (S-614G: residues 1-1208 with a D614G mutation). Using S-614G permits discovering potential allosteric inhibitors that stabilize the S protein in a conformation that impedes its access to ACE2. Over 30,000 small molecules were screened in a high-throughput format for activity against S-614G and ACE2 binding using the AlphaLISA assay. A viral entry assay was used to validate hits using lentiviral particles pseudotyped with the full-length S protein of the Wuhan-1 strain. Two compounds identified in the screen, oleic acid and suramin, blocked the attachment of S-614G to ACE2 and S protein-driven cell entry into Calu-3 and ACE2-overexpressing HEK293T cells. Oleic acid inhibits S-614G binding to ACE2 far more potently than to the receptor-binding domain (RBD, residues 319-541 of SARS-CoV-2 S), potentially indicating a noncompetitive mechanism. The results indicate that using the full-length ectodomain of the S protein can be important for identifying allosteric inhibitors of ACE2 binding. The approach reported here represents a rapidly adaptable format for discovering receptor-binding inhibitors to S-proteins of future coronavirus strains.