Biology subjects

Interlandi, G.

Publications and source records attributed to Interlandi, G..

6 recordsLinked to original sources

bioRxiv2025

Targeting von Willebrand factor selectively under inflammatory conditions

It is challenging to develop anti-thrombotic therapeutics to treat or prevent pathological thrombus formation without increasing the risk of bleeding. Currently available anti-coagulant drugs render blood thinner irrespective of whether an inflammatory pro-thrombotic condition exists or whether clotting needs to occur because of traumatic vessel rupture. It is desirable to develop a drug that is active only under the oxidizing conditions present during inflammation. The blood protein von Willebrand factor (VWF) plays a key role in initiating blood clotting and it has been the target of anti-thrombotic therapies. It has been shown that oxidizing agents released during inflammation activate VWF by converting methionine residues within its domains to methionine sulfoxide. A previous study by us developed a method to computationally screen for drugs that inhibit VWF more strongly in the presence of oxidizing conditions. The computations suggested in particular a drug, lumacaftor, that could inhibit VWF function selectively in the presence of oxidized methionine residues. Here, we developed an enzyme-linked immunosorbent assay to test the effect of drugs on the ability of VWF to bind to the platelet surface receptor glycoprotein Ib comparing oxidizing and non-oxidizing conditions. The results indicate that lumacaftor may indeed have the desired properties of inhibiting VWF selectively when oxidized. Because of its simplicity, the assay provides a high-throughput method to efficiently screen multiple drugs against VWF in both its oxidized and unoxidized state.

biochemistry↗

bioRxiv2025

Ultra-slow conformational dynamics and catch bond formation of a Bacterial Adhesin revealed by a single-domain variant of FimH.

Bacterial adhesins such as FimH are critical for host colonization and persistence under the mechanical forces encountered at sites of infection such as the urinary tract. Despite decades of research, the molecular mechanisms by which FimH--a key virulence factor of Escherichia coli--regulates its binding through conformational switching remain incompletely understood. FimH operates across a range of conformations that includes low- (LAS), intermediate-, high-affinity (HAS) states-- and forms catch bonds which paradoxically strengthen under force. The allosteric pathways governing these transitions remain poorly defined due to experimental limitations that restrict understanding of key dynamic phenomena that underlie ligand-triggered conformational shifts and force-induced long-lived interactions. Such understanding is central to drug discovery efforts to target bacterial adhesion. Here we present a model system that fully recapitulates the conformational repertoire of FimH in the absence of its pilin domain. Our findings demonstrate that a single mutation in the lectin domain induces the LAS while allowing for ligand-binding induced conformational change to the HAS and catch bond formation, mirroring the behavior of the native FimH adhesin. We propose a dynamic allosteric mechanism that involves ultra-slow, low-frequency dynamics for the ability of FimH and the bacteria that express it, to sustain long-lived interactions with mannose under both static and force conditions. SignificanceUrinary tract infections (UTIs) are among the most common bacterial infections, and their initiation depends on the ability of uropathogenic Escherichia coli (UPEC) to adhere to bladder cells. The adhesion is mediated by FimH, a protein on the outside of UPEC that binds mannose-containing glycoprotein receptors and strengthens its grip under shear stress via a catch-bond mechanism. To investigate FimH function, we engineered a variant that can adopt both low- and high-affinity states of FimH and can form catch bonds. We discovered that FimH is governed by ultra-slow conformational dynamics that vary even among structurally similar states. These findings provide a mechanistic framework for developing anti-adhesive therapies that target FimH dynamics, offering a novel strategy to prevent and treat UTIs.

biochemistry↗

bioRxiv2024

Antibodies disrupt bacterial adhesion by ligand mimicry and allosteric interference

A critical step in infections is the attachment of many microorganisms to host cells using lectins that bind surface glycans, making lectins promising antimicrobial targets. Upon binding mannosylated glycans, FimH, the most studied lectin adhesin of type 1 fimbriae in E. coli, undergoes an allosteric transition from an inactive to an active conformation that can act as a catch-bond. Monoclonal antibodies that alter FimH glycan binding in various ways are available, but the mechanisms of these antibodies remain unclear. Here, we use cryoEM, mass spectrometry, binding assays, and molecular dynamics simulations to determine the structure-function relationships underlying antibody-FimH binding. Our study reveals four distinct antibody mechanisms of action: ligand mimicry by an N-linked, high-mannose glycan; stabilization of the ligand pocket in the inactive state; conformational trapping of the active and inactive states; and locking of the ligand pocket through long-range allosteric effects. These structures reveal multiple mechanisms of antibody responses to an allosteric protein and provide blueprints for new antimicrobial that target adhesins.

immunology↗

bioRxiv2024

Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations

The blood protein von Willebrand factor (VWF) is a large multimeric protein that, when activated, binds to blood platelets tethering them to the site of vascular injury initiating blood coagulation. This process is critical for the normal haemostatic response, but especially under inflammatory conditions it is thought to be a major player in pathological thrombus formation. For this reason, VWF has been the target for the development of anti-thrombotic therapeutics. However, it is challenging to prevent pathological thrombus formation while still allowing normal physiological blood coagulation as currently available anti-thrombotic therapeutics are known to cause unwanted bleeding in particular intracranial haemorrhage. This work explores the possibility of inhibiting VWF selectively under the inflammatory conditions present during pathological thrombus formation. In particular, the A2 domain of VWF is known to inhibit the neighboring A1 domain from binding to the platelet surface receptor GpIb and this auto-inhibitory mechanism has been shown to be removed by oxidizing agents released during inflammation. Hence, finding drug molecules that bind at the interface between A1 and A2 only under oxidizing conditions could restore such auto-inhibitory mechanism. Here, by using a combination of computational docking, molecular dynamics simulations and free energy perturbation calculations, a ligand from the ZINC15 database was identified that binds at the A1A2 interface with the interaction being stronger under oxidizing conditions. The results provide a framework for the discovery of drug molecules that bind to a protein selectively in inflammatory conditions.

biophysics↗

bioRxiv2019

Oxidation shuts down an auto-inhibitory mechanism of von Willebrand factor

The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. In particular, oxidation of methionine residues in specific domains of VWF due to the release of oxidants in inflammatory conditions has been linked to an increased platelet-binding activity. However, the atomistic details how methionine oxidation activates VWF have not been elucidated to date. Yet understanding the activation mechanism of VWF under oxidizing conditions can lead to the development of novel therapeutics that target VWF selectively under inflammatory conditions in order to reduce its thrombotic activity while maintaining its haemostatic function. In this manuscript, we used a combination of a dynamic flow assay and molecular dynamics (MD) simulations to investigate how methionine oxidation removes an auto-inhibitory mechanism of VWF. Results from the dynamic flow assay revealed that oxidation does not directly activate the A1 domain, which is the domain in VWF that contains the binding site to the platelet surface receptor glycoprotein Ib (GpIb), but rather removes the inhibitory function of the neighboring A2 and A3 domains. Furthermore, the MD simulations combined with free energy perturbation calculations suggested that methionine oxidation may destabilize the binding interface between the A1 and A2 domains leading to unmasking of the GpIb-binding site in the A1 domain.

bioengineering↗

bioRxiv2018

Effects of inflammation-induced oxidation on the dimerization of fibrinogen αC domain

Upon activation, fibrinogen is converted to insoluble fibrin, which assembles into long strings called protofibrils. These aggregate laterally to form a fibrin matrix that stabilizes a blood clot. Lateral aggregation of protofibrils is mediated by the C domain, a partially structured fragment located in a disordered region of fibrinogen. Polymerization of C domains links multiple fibrin molecules with each other enabling the formation of thick fibrin fibers and a fibrin matrix that is stable but can also be digested by enzymes. How-ever, oxidizing agents produced during the inflammatory response have been shown to cause thinner fibrin fibers resulting in denser clots, which are harder to proteolyze and pose the risk of deep vein thrombosis and lung embolism. It has been postulated that oxidation of Met476 located within the C domain hinders its ability to polymerize disrupting the lateral aggregation of protofibrils and leading to the observed thinner fibers. How C domains assemble into polymers is still unclear and yet this knowledge would shed light on the mechanism through which oxidation weakens the lateral aggregation of protofibrils. This study used temperature replica exchange molecular dynamics simulations to investigate the C-domain dimer and how this is affected by oxidation of Met476. The results suggest that multiple binding modes between two alphaC domains can occur and that oxidation decreases the likelihood of dimer formation. Furthermore, the side chain of Met476 acts as a docking spot between C domains and this function is abrogated by its conversion to methionine sulfoxide.

biochemistry↗