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.

Computational Modeling of the Interactions between DPP IV and Hemorphins.

Type 2 diabetes is a chronic metabolic disorder characterized by high blood glucose levels due to either insufficient insulin production or ineffective utilization of insulin by the body. The enzyme dipeptidyl peptidase IV (DPP IV) plays a crucial role in degrading incretins that stimulate insulin secretion. Therefore, the inhibition of DPP IV is an established approach for the treatment of diabetes. Hemorphins are a class of short endogenous bioactive peptides produced by the enzymatic degradation of hemoglobin chains. Numerous in vitro and in vivo physiological effects of hemorphins, including DPP IV inhibiting activity, have been documented in different systems and tissues. However, the underlying molecular binding behavior of these peptides with DPP IV remains unknown. Here, computational approaches such as protein-peptide molecular docking and extensive molecular dynamics (MD) simulations were employed to identify the binding pose and stability of peptides in the active site of DPP IV. Findings indicate that hemorphins lacking the hydrophobic residues LVV and VV at the N terminal region strongly bind to the conserved residues in the active site of DPP IV. Furthermore, interactions with these critical residues were sustained throughout the duration of multiple 500 ns MD simulations. Notably, hemorphin 7 showed higher binding affinity and sustained interactions by binding to S1 and S2 pockets of DPP IV.

Interaction of hemorphins with ACE homologs.

Hemorphins, short bioactive peptides produced by enzymatic cleavage of ß-hemoglobin, exhibit antihypertensive properties by inhibiting angiotensin-1 converting enzyme (ACE1). ACE1 is a key player in the renin-angiotensin system (RAS) and regulates blood pressure. ACE1 and its homolog, ACE2, which exhibit opposing activities in the RAS, share considerable similarity in their catalytic domains. The primary objective of this study was to identify and contrast the molecular mechanisms underlying the interaction of hemorphins of camels and that of other mammals with the two ACE homologs. In silico docking and molecular dynamics simulations were performed for ACE1 and ACE2, along with in vitro confirmatory assays for ACE1. The C-domain of ACE1, primarily involved in regulating blood pressure, was used along with the N-terminal peptidase domain of ACE2. The findings revealed conserved hemorphin interactions with equivalent regions of the two ACE homologs and differential residue-level interactions reflecting the substrate preferences of ACE1 and ACE2 considering their opposing functions. Therefore, conserved residue-level associations and implications of poorly conserved regions between the two ACE receptors may potentially guide the discovery of selective domain-specific inhibitors. The findings of this study can provide a basis for the treatment of related disorders in the future.

Novel Plant-Protein (Quinoa) Derived Bioactive Peptides with Potential Anti-Hypercholesterolemic Activities: Identification, Characterization and Molecular Docking of Bioactive Peptides.

Hypercholesterolemia remains a serious global public health concern. Previously, synthetic anti-hypercholesterolemic drugs were used for ameliorating this condition; however, long-term usage presented several side-effects. In this regard, natural products as an adjunct therapy has emerged in recent times. This study aimed to produce novel bioactive peptides with anti-hypercholesterolemic activity (cholesterol esterase (CEase) and pancreatic lipase (PL)) from quinoa protein hydrolysates (QPHs) using three enzymatic hydrolysis methods (chymotrypsin, protease and bromelain) at 2-h hydrolysis intervals (2, 4, and 6 h). Chymotrypsin-generated hydrolysates showed higher CEase (IC50: 0.51 mg/mL at 2 h) and PL (IC50: 0.78 mg/mL at 6 h) inhibitory potential in comparison to other derived hydrolysates and intact quinoa proteins. Peptide profiling by LC-MS QTOF and in silico interaction with target enzymes showed that only four derived bioactive peptides from QPHs could bind in the active site of CEase, whereas twelve peptides could bind in the active site of PL. Peptides QHPHGLGALCAAPPST, HVQGHPALPGVPAHW, and ASNLDNPSPEGTVM were identified to be potential CEase inhibitors, and FSAGGLP, QHPHGLGALCAAPPST, KIVLDSDDPLFGGF, MFVPVPH, and HVQGHPALPGVPAHW were identified as potential PL inhibitors on the basis of the maximum number of reactive residues in these bioactive peptides. In conclusion, QPHs can be considered as an alternative therapy for the treatment of hypercholesterolemia.

Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2.

Background: The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods: To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein's receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics-generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results: Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2's N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.

Characterization of peptide binding to the SARS-CoV-2 host factor neuropilin.

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global health concern. It is now well established that the spike (S) protein of SARS-CoV-2 interacts with its primary host receptor, the angiotensin converting enzyme 2 (ACE2). Additionally, the interaction of S with the neuropilin (NRP) receptor has been reported to facilitate viral entry. SARS-CoV-2 S protein binds to neuropilin-1 (NRP1) by virtue of a CendR motif which terminates with either an arginine or lysine. Furthermore, a number of different peptide sequences have been reported to bind to the same site in NRP1 including vascular endothelial growth factor A and other viral proteins. To gain a deeper understanding of additional factors besides the C-terminal arginine that may favour high NRP1 binding, several modelled peptides were investigated using triplicate 1 µs molecular dynamics simulations. A C-end histidine failed to exhibit strong NRP1 affinity. Some previously reported factors that increase binding affinity and secure NRP1 receptor activation was observed in the NRP1-peptide complexes studied and such complexes had higher molecular mechanics-generalized Born surface area based free energy of binding. Additionally, the results also highlight the relevance of an exposed arginine at its canonical location as capping it blocked arginine from engaging key residues at the NRP1 receptor site that are indispensable for functional binding; and that the presence of proline reinforces the C-terminal arginine. Given that stable NRP1 binding is crucial for viral uptake, stable interactions should be accounted for in the design of potential drugs and treatment routes to target or disrupt this interface, considering the S1-NRP1 interaction as well as its endogenous VEGF-A ligand that is associated with nociception.

Neuropilins: C-end rule peptides and their association with nociception and COVID-19.

Viral internalization is aided by host cell surface receptors. In the case of SARS-CoV-2 and SARS-CoV, the primary host receptor is the angiotensin-converting enzyme 2 (ACE2). Considering the disparities in the transmission rate and viral tropism of the two coronaviruses, additional host factors were suspected. Recently, a novel host factor for SARS-CoV-2 entry, neuropilin-1 (NRP-1) has been identified. These receptors potentiate viral infection in the presence of other host factors like ACE2. Through its C-end rule (CendR) motif exposed following furin processing, the SARS-CoV-2 spike protein binds to the CendR pocket of NRP-1 and achieves cell entry through endocytosis. The binding of SARS-CoV-2 spike protein to the NRP-1 receptor interferes with the docking of its endogenous ligand VEGF-A, signaling that would otherwise promote nociception. This review looks at the function of neuropilins and how it contributes to SARS-CoV-2 infection and nociception.