Structural and Energetic Affinity of Annocatacin B with ND1 Subunit of the Human Mitochondrial Respiratory Complex I as a Potential Inhibitor: An In Silico Comparison Study with the Known Inhibitor Rotenone

Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models

G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.

Study of the Rv1417 and Rv2617c Membrane Proteins and Their Interactions with Nicotine Derivatives as Potential Inhibitors of Erp Virulence-Associated Factor in Mycobacterium tuberculosis: An In Silico Approach

The increasing emergence of Mycobacterium tuberculosis (Mtb) strains resistant to traditional anti-tuberculosis drugs has alarmed health services worldwide. The search for new therapeutic targets and effective drugs that counteract the virulence and multiplication of Mtb represents a challenge for the scientific community. Several studies have considered the erp gene a possible therapeutic target in the last two decades, since its disruption negatively impacts Mtb multiplication. This gene encodes the exported repetitive protein (Erp), which is located in the cell wall of Mtb. In vitro studies have shown that the Erp protein interacts with two putative membrane proteins, Rv1417 and Rv2617c, and the impairment of their interactions can decrease Mtb replication. In this study, we present five nicotine analogs that can inhibit the formation of heterodimers and trimers between these proteins. Through DFT calculations, molecular dynamics, docking, and other advanced in silico techniques, we have analyzed the molecular complexes, and show the effect these compounds have on protein interactions. The results show that four of these analogs can be possible candidates to counteract the pathogenicity of Mtb. This study aims to combine research on the Erp protein as a therapeutic target in the search for new drugs that serve to create new therapies against tuberculosis disease.

Structural insights into the binding of zoledronic acid with RANKL via computational simulations

Zoledronic acid (ZOL) inhibits receptor activator of nuclear factor-κB ligand (RANKL) and reduces bone turnover. This plays an important role in the development of bisphosphonate-related osteonecrosis of the jaw (BRONJ). Previous reports have shown that ZOL binds to the enzyme farnesyl pyrophosphate synthase (FPPS) to block its activity. However, the mechanism of action of ZOL and its interaction with RANKL is still unclear. In this study, we confirmed that ZOL significantly suppressed the bone remodeling in ZOL-treated rats, investigated whether ZOL could bind to RANKL and examined the interactions between these molecules at the atomic level. Surface plasmon resonance (SPR) assay was performed to validate that ZOL could directly bind to RANKL in a dose dependent manner, and the equilibrium constant was calculated (K_D = 2.28 × 10⁻⁴ M). Then, we used molecular docking simulation to predict the binding site and analyze the binding characteristics of ZOL and RANKL. Through molecular dynamics simulation, we confirmed the stable binding between ZOL and RANKL and observed their dynamic interactions over time. Binding free energy calculations and its decomposition were conducted to obtain the binding free energy −70.67 ± 2.62 kJ/mol for the RANKL–ZOL complex. We identified the key residues of RANKL in the binding region, and these included Tyr217(A), Val277(A), Gly278(A), Val277(B), Gly278(B), and Tyr215(C). Taken together, our results demonstrated the direct interaction between ZOL and RANKL, indicating that the pharmacological action of ZOL might be closely related to RANKL. The design of novel small molecules targeting RANKL might reduce the occurrence of BRONJ.