Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

Flavin mononucleotide riboswitches are common among many pathogenic bacteria and are therefore considered to be an attractive target for antibiotics development. The riboswitch binds riboflavin (RBF, also known as vitamin B2), and although an experimental structure of their complex has been solved with the ligand bound deep inside the RNA molecule in a seemingly unreachable state, the binding mechanism between these molecules is not yet known. We have therefore used our Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol to analyze their binding mechanism by simulating the binding process between the riboswitch aptamer domain and the RBF, starting from the apo state of the riboswitch. Here, the refinement stage was crucial to identify the native binding configuration, as several other binding configurations were also found by McMD-based docking simulations. RBF initially binds the interface between P4 and P6 including U61 and G62, which forms a gateway where the ligand lingers until this gateway opens sufficiently to allow the ligand to pass through and slip into the hidden binding site including A48, A49, and A85.

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

The intrinsically disordered region (IDR) of Bim binds to the flexible cryptic site of Bcl-xL, a pro-survival protein involved in cancer progression that plays an important role in initiating apoptosis. However, their binding mechanism has not yet been elucidated. We have applied our dynamic docking protocol, which correctly reproduced both the IDR properties of Bim and the native bound configuration, as well as suggesting other stable/meta-stable binding configurations and revealed the binding pathway. Although the cryptic site of Bcl-xL is predominantly in a closed conformation, initial binding of Bim in an encounter configuration leads to mutual induced-fit binding, where both molecules adapt to each other; Bcl-xL transitions to an open state as Bim folds from a disordered to an α-helical conformation while the two molecules bind each other. Finally, our data provides new avenues to develop novel drugs by targeting newly discovered stable conformations of Bcl-xL.

Biochemical separation of Cetuximab-Fab from papain-digested antibody fragments and radiolabeling with 64Cu for potential use in radioimmunotheranostics

Engineered Fab fragments of monoclonal antibodies (mAbs) after radiolabeling with suitable radiometals have the potential to play a key role in personalized radioimmunotheranostics of cancer patients. In this study, we have generated Fab fragment of Cetuximab, a mAb targeting epidermal growth factor receptor (EGFR) expression and purified from the Fc and other fragments by ultrafiltration and affinity chromatography. The Cetuximab-Fab was conjugated with a suitable bifunctional chelator and radiolabeled with no-carrier-added (NCA) ⁶⁴Cu produced via ⁶⁴Zn (n, p) ⁶⁴Cu reaction in a nuclear reactor. The radioimmunoconjugate obtained after size exclusion chromatographic separation possessed >95% radiochemical purity and it retained its integrity over at least three half-lives of the radiometal. Biodistribution studies was performed in fibrosarcoma tumor bearing Swiss mice, which demonstrated the explicit need for purification of the Cetuximab-Fab from Fc fragments. Enhanced and rapid tumor uptake with decent tumor-to-background ratio with prolonged retention was observed when radiolabeled purified Cetuximab-Fab was intravenously administered in animal models. Overall, this preclinical study established the pivotal role of separation science and technology to obtain the radioimmunoconjugate with requisite purity in order to demonstrate optimal pharmacokinetics and maximized treatment efficacy.