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Human α-defensin 5 (HD5) is one of cationic antimicrobial peptides which plays a crucial role in an innate immune system in human body. HD5 shows the killing activity against a broad spectrum of pathogenic bacteria by making a pore in a bacterial membrane and penetrating into a cytosol. Nonetheless, its pore-forming mechanisms remain unclear. Thus, in this work, the constant-velocity steered molecular dynamics (SMD) simulation was used to simulate the permeation of a dimeric HD5 into a gram-negative lipopolysaccharide (LPS) membrane model. Arginine-rich HD5 is found to strongly interact with a LPS surface. Upon arrival, arginines on HD5 interact with lipid A head groups (a top part of LPS) and then drag these charged moieties down into a hydrophobic core resulting in the formation of water-filled pore. Although all arginines are found to interact with a membrane, Arg13 and Arg32 appear to play a dominant role in the HD5 adsorption on a gram-negative membrane. Furthermore, one chain of a dimeric HD5 is required for HD5 adhesion. The interactions of arginine-lipid A head groups play a major role in adhering a cationic HD5 on a membrane surface and retarding a HD5 passage in the meantime., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Cordycepin (3'-deoxyadenosine, abbreviated as COR) from Cordyceps shows a wide range of pharmacological activities, including antioxidant and anticancer effects, therefore representing a potential alternative medicine. However, COR has a short half-life in the human body, where it is metabolized by adenosine deaminase 1 (ADA1). ADA1 helps regulate adenosine levels by deaminating excess adenosine (ADE) and its derivatives, such as 2'-deoxyadenosine (DEO). Understanding binding mechanisms of ADA1 with COR in comparison with its other substrates will play a vital role in improving the bioactivity and lifetime of COR for commercial medicinal use. Recently, the first structure of human ADA1 in complex with DEO was solved. We therefore employed molecular dynamics (MD) simulations to predict structures and dynamics of ADA1 complexing with ADE, DEO, and COR in comparison to a ligand-free (LF) structure. Our data reveal that a large and highly water-exposed binding pocket of ADA1 is responsible for ligand translocation and reorientation. Two possible binding locations (site1 and site2) are identified. The binding affinities of the ligands are ADE > COR > DEO. Furthermore, the movements of two loop regions at the binding pocket entrance, residues 183-193 and 215-230, contribute to gating activity.

Human α-defensin 5 (HD5) is one of the important antimicrobial peptides (AMPs) used against a broad-spectrum of pathogens, especially Gram-negative bacteria. HD5 kills by disrupting and making a pore in the bacterial membrane. The presence of lipopolysaccharide (LPS), located on a membrane surface, is found to have an impact on HD5's activity, where such binding mechanism in microscopic detail remains unclear. In this work, we therefore employed molecular dynamics (MD) simulations to investigate the binding mechanisms of HD5 on LPS in comparison to a bare DMPC lipid membrane. Two oligomers, dimer and tetramer, are studied here. Apparently, the membrane structure influences the protein binding affinity. HD5 binds tighter to a lipid membrane than LPS. Both dimeric and tetrameric HD5 can penetrate deeply into a phosphate layer in a lipid membrane, whereas only facial contacts are observed for LPS systems. The proteins appear to stay in the polar area instead of diving into a hydrophobic region. Furthermore, it happens in all cases that residues in the active region (A1, T2, R6, R13, R32) contribute to the membrane adsorption. The breakdown of tetramer into two dimers is also found. This implies that the dimer is more favorable for membrane binding. Moreover, both dimeric and tetrameric HD5 can significantly disrupt a LPS layer, whilst no serious distortion of lipid membrane is obtained. This emphasizes the importance of LPS on HD5 activity.

Pseudomonas aeruginosa is an important nosocomial human pathogen. The major difficulty in the fight against this pathogen is the relative impermeability of its outer membrane (OM). Only specific substrates can penetrate through the OM of P. aeruginosa via substrate-specific porins, so this has become one of the most problematic drug-resistant pathogens. Carbapenems are the most effective drugs for treating P. aeruginosa infections. One such carbapenem that is applied in cases of P. aeruginosa infection is imipenem (IMI), which uses outer membrane carboxylate channel D1 (OccD1) as a point of entry into the pathogen. Unlike IMI, ertapenem (ERTA, another carbapenem) shows only weak activity towards P. aeruginosa, as it is blocked from penetrating through the OM. However, it is currently unclear as to why IMI is allowed to pass through the OM while ERTA is not. Therefore, we conducted molecular dynamics (MD) simulations to elucidate the behavior of these drugs inside OccD1 as compared to the ligand-free state. We discovered another possible binding site in the constriction region close to the side-pore opening. Both drugs employ the core lactam part to tether themselves to the binding site, whereas the tail governs the direction of permeation. L132 and F133 appear to be involved in interactions that are key to core attachment. At least four hydrogen bonds are required for drug binding. The direction of motion of L2 also plays a role: inward flipping traps IMI in the constriction area, while a shift of L2 towards the membrane brings ERTA into contact with more water, which prompts the expulsion of ERTA to the mouth of the channel protein. The opening of L2 seems to facilitate the rejection of ERTA.