Molecular mechanism of HIV-1 TAT peptide and its conjugated gold nanoparticles translocating across lipid membranes

Cell Membrane Perforation: Patterns, Mechanisms and Functions

Cell membrane is crucial for the cellular activities, and any disruption to it may affect the cells. It is demonstrated that cell membrane perforation is associated with some biological processes like programmed cell death (PCD) and infection of pathogens. Specific developments make it a promising technique to perforate the cell membrane controllably and precisely. The pores on the cell membrane provide direct pathways for the entry and exit of substances, and can also cause cell death, which means reasonable utilization of cell membrane perforation is able to assist intracellular delivery, eliminate diseased or cancerous cells, and bring about other benefits. This review classifies the patterns of cell membrane perforation based on the mechanisms into 1) physical patterns, 2) biological patterns, and 3) chemical patterns, introduces the characterization methods and then summarizes the functions according to the characteristics of reversible and irreversible pores, with the aim of providing a comprehensive summary of the knowledge related to cell membrane perforation and enlightening broad applications in biomedical science.

Inhibition of the RLR signaling pathway by SARS-CoV-2 ORF7b is mediated by MAVS and abrogated by ORF7b-homologous interfering peptide

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and characterized by dysregulated immune response. Studies have shown that the SARS-CoV-2 accessory protein ORF7b induces host cell apoptosis through the tumor necrosis factor alpha (TNF-α) pathway and blocks the production of interferon beta (IFN-β). The underlying mechanism remains to be investigated. In this study, we found that ORF7b facilitated viral infection and production, and inhibited the RIG-I-like receptor (RLR) signaling pathway through selectively interacting with mitochondrial antiviral-signaling protein (MAVS). MAVS439-466 region and MAVS Lys461 were essential for the physical association between MAVS and ORF7b, and the inhibition of the RLR signaling pathway by ORF7b. MAVSK461/K63 ubiquitination was essential for the RLR signaling regulated by the MAVS-ORF7b complex. ORF7b interfered with the recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) and the activation of the RLR signaling pathway by MAVS. Furthermore, interfering peptides targeting the ORF7b complex reversed the ORF7b-suppressed MAVS-RLR signaling pathway. The most potent interfering peptide V disrupts the formation of ORF7b tetramers, reverses the levels of the ORF7b-inhibited physical association between MAVS and TRAF6, leading to the suppression of viral growth and infection. Overall, this study provides a mechanism for the suppression of innate immunity by SARS-CoV-2 infection and the mechanism-based approach via interfering peptides to potentially prevent SARS-CoV-2 infection.IMPORTANCEThe pandemic coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and continues to be a threat to public health. It is imperative to understand the biology of SARS-CoV-2 infection and find approaches to prevent SARS-CoV-2 infection and ameliorate COVID-19. Multiple SARS-CoV-2 proteins are known to function on the innate immune response, but the underlying mechanism remains unknown. This study shows that ORF7b inhibits the RIG-I-like receptor (RLR) signaling pathway through the physical association between ORF7b and mitochondrial antiviral-signaling protein (MAVS), impairing the K63-linked MAVS polyubiquitination and its recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) to MAVS. The most potent interfering peptide V targeting the ORF7b-MAVS complex may reverse the suppression of the MAVS-mediated RLR signaling pathway by ORF7b and prevent viral infection and production. This study may provide new insights into the pathogenic mechanism of SARS-CoV-2 and a strategy to develop new drugs to prevent SARS-CoV-2 infection.

Research progress in nucleus-targeted tumor therapy

The nucleus is considered the most important organelle in the cell as it plays a central role in controlling cell reproduction, metabolism, and the cell cycle. The successful delivery of drugs into the nucleus can achieve excellent therapeutic effects, which reveals the potential of nucleus-targeted therapy in precision medicine. However, the transportation of therapeutics into the nucleus remains a significant challenge due to various biological barriers. Herein, we summarize the recent progress in the nucleus-targeted drug delivery system (NDDS). The structures of the nucleus and nuclear envelope are first described in order to understand the mechanisms by which drugs cross the nuclear envelope. Then, various drug delivery strategies based on the mechanisms and their applications are discussed. Finally, the challenges and solutions in the field of nucleus-targeted drug delivery are raised for developing a more efficient NDDS and promoting its clinical transformation.

Nuclear Delivery of Nanoparticle-Based Drug Delivery Systems by Nuclear Localization Signals

Nanomedicine 2.0 refers to the next generation of nanotechnology-based medical therapies and diagnostic tools. This field focuses on the development of more sophisticated and precise nanoparticles (NPs) for targeted drug delivery, imaging, and sensing. It has been established that the nuclear delivery of NP-loaded drugs can increase their therapeutic efficacy. To effectively direct the NPs to the nucleus, the attachment of nuclear localization signals (NLSs) to NPs has been employed in many applications. In this review, we will provide an overview of the structure of nuclear pore complexes (NPCs) and the classic nuclear import mechanism. Additionally, we will explore various nanoparticles, including their synthesis, functionalization, drug loading and release mechanisms, nuclear targeting strategies, and potential applications. Finally, we will highlight the challenges associated with developing nucleus-targeted nanoparticle-based drug delivery systems (NDDSs) and provide insights into the future of NDDSs.

Functionalised penetrating peptide-chondroitin sulphate‑gold nanoparticles: Synthesis, characterization, and applications as an anti-Alzheimer's disease drug

The purpose of this study was to construct a transmembrane peptide-chondroitin sulphate‑gold nanoparticle (TAT-CS@Au) delivery system and investigate its activity as an anti-Alzheimer's disease (AD) drug. We successfully prepared TAT-CS@Au nanoparticles, investigated their anti-AD effects, and explored the possible mechanisms in in vitro models. TAT-CS@Au exhibited excellent cellular uptake and transport capacity, effectively inhibited the accumulation of Aβ_1-40, and significantly reduced Aβ_1-40-induced apoptosis in SH-SY5Y cells. Furthermore, TAT-CS@Au significantly reduced oxidative stress damage and cholinergic injury induced by Aβ_1-40 by regulating intracellular concentrations of reactive oxygen species (ROS), malondialdehyde (MDA), glutathione peroxidase (GSH-Px), and acetylcholine (ACh). Western blotting results demonstrated that TAT-CS@Au inhibited aberrant tau phosphorylation (Ser199, Thr205, Ser404, and Ser396) through GSK3β inactivation. TAT-CS@Au decreased the levels of inflammatory factors, specifically TNF-α, IL-6, and IL-1β, by inhibiting NF-κB nuclear translocation by activating MAPK signalling pathways. Overall, these results indicate that TAT-CS@Au exhibits excellent transmembrane ability, inhibits Aβ_1-40 accumulation, antagonises oxidative stress, reduces aberrant tau phosphorylation, and suppresses the expression of inflammatory factors. TAT-CS@Au may be a multi-target anti-AD drug with good cell permeability, providing new insights into the design and research of anti-AD therapeutics.

Intramembrane Nanoaggregates of Antimicrobial Peptides Play a Vital Role in Bacterial Killing

Recent developments in antimicrobial peptides (AMPs) have focused on the rational design of short sequences with less than 20 amino acids due to their relatively low synthesis costs and ease of correlation of the structure-function relationship. However, gaps remain in the understanding of how short cationic AMPs interact with the bacterial outer and inner membranes to affect their antimicrobial efficacy and dynamic killing. The membrane-lytic actions of two designed AMPs, G(IIKK)₃ I-NH₂ (G₃ ) and G(IIKK)₄ I-NH₂ (G₄ ), and previously-studied controls GLLDLLKLLLKAAG-NH₂ (LDKA, biomimetic) and GIGAVLKVLTTGLPALISWIKRKR-NH₂ (Melittin, natural) are examined. The mechanistic processes of membrane damage and the disruption strength of the four AMPs are characterized by molecular dynamics simulations and experimental measurements including neutron reflection and scattering. The results from the combined studies are characterized with distinctly different intramembrane nanoaggregates formed upon AMP-specific binding, reflecting clear influences of AMP sequence, charge and the chemistry of the inner and outer membranes. G₃ and G₄ display different nanoaggregation with the outer and inner membranes, and the smaller sizes and further extent of insertion of the intramembrane nanoaggregates into bacterial membranes correlate well with their greater antimicrobial efficacy and faster dynamic killing. This work demonstrates the crucial roles of intramembrane nanoaggregates in optimizing antimicrobial efficacy and dynamic killing.

Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations

With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.

State-of-the-art Tools to Elucidate the Therapeutic Potential of TAT-peptide (TP) Conjugated Repurposing Drug Against SARS-CoV-2 Spike Glycoproteins

BACKGROUND

In late 2019, a highly infectious and pathogenic coronavirus was recognized as Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2), which causes acute respiratory disease, threatening human health and public safety. A total of 448,327,303 documented cases and 6,028,576 deaths have been reported as of March 8th 2022. The COVID-19 vaccines currently undergoing clinical trials or already in use should provide at least some protection against SARS-CoV-2; however, the emergence of new variations as a result of mutations may lessen the effectiveness of the currently available vaccines. Since the efficacy of available drugs and vaccines against COVID-19 is notably lower, there is an urgent need to develop a potential drug to treat this deadly disease. The SARS-CoV-2 spike (SCoV-SG) is the foremost drug target among coronaviruses.

OBJECTIVE

The major objectives of the current study are to conduct a molecular docking study investigation of TAT-peptide^47-57(GRKKRRQRRRP)-conjugated remodified therapeutics such as ritonavir (RTV), lopinavir (LPV), favipiravir (FPV), remdesivir (RMV), hydroxychloroquine (HCQ), molnupiravir (MNV) and nirmatrelvir (NMV) with (SCoV-SG) structure.

METHODS

Molecular docking analysis was performed to study the interaction of repurposed drugs and drugs conjugated with the TAT-peptide with target SARS-CoV-2 spike glycoprotein (PDB ID: 6VYB) using Auto- Dock. Further docking investigation was completed with PatchDock and was visualized by the discovery of the studio visualizer 2020.

RESULTS

TAT-peptides are well-characterized immune enhancers that are used in intracellular drug delivery. The results of molecular docking analysis showed higher efficiency and significantly enhanced and improved interactions between TP-conjugated repurposed drugs and the target sites of the SCoV-SG structure.

CONCLUSION

The study concluded that TP-conjugated repurposed drugs may be effective in preventing COVID- 19, and therefore, in vitro, in vivo, and clinical trial studies are required in detail.

Molecular dynamics simulation of drug delivery across the cell membrane by applying gold nanoparticle carrier: Flutamide as hydrophobic and glutathione as hydrophilic drugs as the case studies

In this study, molecular dynamics simulation is applied to investigate drug transport in both pure state and conjugated with neutral gold nanoparticle (AuNP) as a drug carrier inside dipalmitoylphosphatidylcholine (DPPC) membrane. Flutamide (Flu) as a hydrophobic and Glutathione (GSH) as a hydrophilic anticancer drug are selected as the case studies. Dynamics of each drug including adhesion on and penetration into the cell membrane are investigated. Pure and conjugated form of drugs inside the water and near the membrane are studied. Simulation results show that the interaction between drug molecules and DPPC changes after drug conjugating with AuNP. GSH, as a hydrophilic drug, intends to remain above the membrane bilayer and after conjugating with AuNP diffuses inside DPPC. However, hydrophobic Flu molecule likes to diffuse inside DPPC, but after conjugating with AuNP, its diffusion inside the lipid bilayer decreases, and its retention time at the surface of DPPC increases. Presence of Flu-NP at the surface of DPPC could enhance its impact on blocking dihydrotestosterone binding at androgen receptors resulting in tumor cell growth arrest. In addition, the tendency of GSH-NP for diffusion to the DPPC is a positive factor for the successful transport of heavy metals such as AuNP without rapid clearance through either the hepatobiliary pathway or the renal system. In conclusion, such MD simulation results may solve problems in nanomedicine translation and turn into a bridge toward maximizing targeting and minimizing nanotoxicity of metal NPs.

Effect of biphosphate salt on dipalmitoylphosphatidylcholine bilayer deformation by Tat polypeptide

Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction of a CPP, HIV-1 Tat peptide with model dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Tat peptide has a large number of basic arginines and a couple of polar glutamines. We observe that in absence of salt, the basic residues of the polypeptide get localized in the vicinity of the membrane without altering the bilayer properties much; polypeptide induce local thinning of the bilayer membrane at the area of localization. In presence of biphosphate salt, the basic residues, dressed by the biphosphate ions, are repelled by the phosphate head groups of the lipid molecules. However, polar glutamine prefers to stay in the vicinity of the bilayer. This leads to larger local bilayer thickness at the contact point by the polar residue and non-uniform bilayer thickness profile. The thickness deformation of bilayer structure disappears upon mutating the polar residue, suggesting importance of the polar residue in bilayer deformation. Our studies point to control bilayer deformation by appropriate peptide sequence and solvent conditions.

Is It Possible to Find an Antimicrobial Peptide That Passes the Membrane Bilayer with Minimal Force Resistance? An Attempt at a Predictive Approach by Molecular Dynamics Simulation

There is still no answer to the mechanism of penetration of AMP peptides through the membrane bilayer. Several mechanisms for such a process have been proposed. It is necessary to understand whether it is possible, using the molecular dynamics method, to determine the ability of peptides of different compositions and lengths to pass through a membrane bilayer. To explain the passage of a peptide through a membrane bilayer, a method for preparing a membrane phospholipid bilayer was proposed, and 656 steered molecular dynamics calculations were carried out for pulling 7 amyloidogenic peptides with antimicrobial potential, and monopeptides (homo-repeats consisting of 10 residues of the same amino acid: Poly (Ala), Poly (Leu), Poly (Met), Poly (Arg), and Poly (Glu)) with various sequences through the membrane. Among the 15 studied peptides, the peptides exhibiting the least force resistance when passing through the bilayer were found, and the maximum reaction occurred at the boundary of the membrane bilayer entry. We found that the best correlation between the maximum membrane reaction force and the calculated parameters corresponds to the instability index (the correlation coefficient is above 0.9). One of the interesting results of this study is that the 10 residue amyloidogenic peptides and their extended peptides, with nine added residue cell-penetrating peptides and four residue linkers, both with established antimicrobial activity, have the same bilayer resistance force. All calculated data are summarized and posted on the server.

TAT-peptide conjugated repurposing drug against SARS-CoV-2 main protease (3CLpro): Potential therapeutic intervention to combat COVID-19

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that originated in Chinese city of Wuhan has caused around 906,092 deaths and 28,040,853 confirmed cases worldwide (https://covid19.who.int/, 11 September 2020). In a life-threatening situation, where there is no specific and licensed anti-COVID-19 vaccine or medicine available; the repurposed drug might act as a silver bullet. Currently, more than 211 vaccines, 80 antibodies, 31 antiviral drugs, 35 cell-based, 6 RNA-based and 131 other drugs are in clinical trials. It is therefore utter need of the hour to develop an effective drug that can be used for the treatment of COVID-19 before a vaccine can be developed. One of the best-characterized and attractive drug targets among coronaviruses is the main protease (3CL^pro). Therefore, the current study focuses on the molecular docking analysis of TAT-peptide^47–57 (GRKKRRQRRRP)-conjugated repurposed drugs (i.e., lopinavir, ritonavir, favipiravir, and hydroxychloroquine) with SARS-CoV-2 main protease (3CL^pro) to discover potential efficacy of TAT-peptide (TP) - conjugated repurposing drugs against SARS-CoV-2. The molecular docking results validated that TP-conjugated ritonavir, lopinavir, favipiravir, and hydroxychloroquine have superior and significantly enhanced interactions with the target SARS-CoV-2 main protease. In-silico approach employed in this study suggests that the combination of the drug with TP is an excelling alternative to develop a novel drug for the treatment of SARS-CoV-2 infected patients. The development of TP based delivery of repurposing drugs might be an excellent approach to enhance the efficacy of the existing drugs for the treatment of COVID-19. The predictions from the results obtained provide invaluable information that can be utilized for the choice of candidate drugs for in vitro, in vivo and clinical trials. The outcome from this work prove crucial for exploring and developing novel cost-effective and biocompatible TP conjugated anti-SARS-CoV-2 therapeutic agents in immediate future.

Efficient drug delivery by novel cell-penetrating peptide derived from Midkine, with two heparin binding sites braced by a length-specific helix

Cell-penetrating peptides (CPPs) have been regarded as potential drug carriers for cancer therapy. However, most well-studied CPPs fail to deliver exogenous drugs efficiently and selectively. In this study, a tumour-targeted CPP with high efficiency derived from heparin-binding domain (HBD) of Midkine (named HMD) was discovered. HMD exhibited higher delivery efficiency than classic CPPs (TAT and R9) and manifested selectivity in tumour cells. Normally, the positive charge is the key factor for the transmembrane activity of CPPs such as TAT and R9. Here, the length of α-helix inside CPP was found also important for in the recognition of heparan sulphate proteoglycans (HSPGs). Subsequently, the introduction of HMD enhanced the inhibitory effect of Momordica antiviral protein of 30 kDa (MAP30) on tumour cells, resulting in a 6.07-fold and 5.42-fold increase in HeLa cells and MGC80-3 cells respectively without enhanced cytotoxicity in normal cells. These results show that HMD possesses high efficiency and good tumour specificity and can be utilised as a promising agent for the tumour-targeted delivery of drug. This study is also a supplement to the existing theories about the biological activities of the α-helix in CPPs.

The interplay between surface-functionalized gold nanoparticles and negatively charged lipid vesicles

The comprehensive understanding of the interactions between gold nanoparticles (AuNPs) and phospholipid vesicles has important implications in various biomedical applications; however, this is not yet well understood. Here, coarse-grained molecular dynamics (CGMD) simulations were performed to study the interactions between functionalized AuNPs and negatively charged lipid vesicles, and the effects of the surface chemistry and surface charge density (SCD) of AuNPs were analyzed. It is revealed that AuNPs with different surface ligands adhere to the membrane surface (anionic AuNPs) or get into the vesicle bilayer (hydrophobic and cationic AuNPs). Due to the loose arrangement of lipid molecules, AuNPs penetrate curved vesicle membranes more easily than planar lipid bilayers. Cationic AuNPs present three different interaction modes with the vesicle, namely insertion, partial penetration and complete penetration, which are decided by the SCD difference. Both hydrophobic interaction and electrostatic interaction play crucial roles in the interplay between cationic AuNPs and lipid vesicles. For the cationic AuNP with a low SCD, it gets into the lipid bilayer without membrane damage through the hydrophobic interaction, and it is finally stabilized in the hydrophobic interior of the vesicle membrane in a thermodynamically stable "snorkeling" configuration. For the cationic AuNP with a high SCD, it crosses the vesicle membrane and gets into the vesicle core through a membrane pore induced by strong electrostatic interaction. In this process, the membrane structure is destroyed. These findings provide a molecular-level understanding of the interplay between AuNPs and lipid vesicles, which may further expand the application of functional AuNPs in modern biomedicine.

Genetic Fusion of Transacting Activator of Transcription Peptide to Cyclized Green Fluorescence Protein Improves Stability, Intracellular Delivery, and Tumor Retention

Therapeutic proteins such as enzymes, hormones, and cytokines suffer from poor stability, inefficient cellular penetration, and rapid clearance from circulation. Conjugation with polymers (such as poly(ethylene glycol)) and fusion with long-acting proteins (such as albumin and Fc fragments) have been utilized to partially address the delivery issues, but these strategies require the introduction of new macromolecular substances, resulting in potential immunogenicity and toxicity. Herein, we report an easy strategy to increase the intracellular delivery efficiency and stability of proteins by combining of sortase-mediated protein cyclization and cell-penetrating peptide (CPP)-mediated intracellular delivery. We, for the first time, genetically constructed a green fluorescence protein (GFP) fused with a CPP, a transacting activator of transcription (TAT) peptide, at its C-terminus for intracellular internalization, and two sortase recognition sequences, pentaglycine and LPETG, at its N- and C-termini for cyclization. Notably, the cyclized GFP-TAT (cGFP-TAT) not only highly retained the photophysical properties of the protein but also significantly improved the in vitro stability compared with the native linear GFP (lGFP) and linear TAT peptide-fused GFP (lGFP-TAT).Moreover, cGFP-TAT showed better cellular internalization ability compared with lGFP. In C26 tumor-inoculated mice, cGFP-TAT exhibited enhanced in vivo tumor retention, with increases of 7.79- and 6.52-fold relative to lGFP and lGFP-TAT in tumor retention 3 h after intratumor administration. This proof-of-concept study has provided an easy strategy to increase the in vitro stability, intracellular delivery efficiency, and in vivo tumor retention of GFP, which would be applicable to numerous therapeutic proteins and peptides for clinical practice.

Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations

The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.

Antiviral Drug Targets of Single-Stranded RNA Viruses Causing Chronic Human Diseases

Ribonucleic acid (RNA) viruses associated with chronic diseases in humans are major threats to public health causing high mortality globally. The high mutation rate of RNA viruses helps them to escape the immune response and also is responsible for the development of drug resistance. Chronic infections caused by human immunodeficiency virus (HIV) and hepatitis viruses (HBV and HCV) lead to acquired immunodeficiency syndrome (AIDS) and hepatocellular carcinoma respectively, which are one of the major causes of human deaths. Effective preventative measures to limit chronic and re-emerging viral infections are absolutely necessary. Each class of antiviral agents targets a specific stage in the viral life cycle and inhibits them from its development and proliferation. Most often, antiviral drugs target a specific viral protein, therefore only a few broad-spectrum drugs are available. This review will be focused on the selected viral target proteins of pathogenic viruses containing single-stranded (ss) RNA genome that causes chronic infections in humans (e.g. HIV, HCV, Flaviviruses). In the recent past, an exponential increase in the number of available three-dimensional protein structures (>150000 in Protein Data Bank), allowed us to better understand the molecular mechanism of action of protein targets and antivirals. Advancements in the in silico approaches paved the way to design and develop several novels, highly specific small-molecule inhibitors targeting the viral proteins.

Gold nanoparticles-biomembrane interactions: From fundamental to simulation

Gold Nanoparticles (AuNPs) are a class of promising nanomaterial for biomedical applications ranging from bioimaging, drug delivery to phototherapy because of their biocompatibility, easily tunable size and shape, and versatile surface modifications. In recent years, the rapid development of AuNPs in nanomedicine has made it imperative to seek fundamental understanding on their nano-biointeractions to minimize adverse effects and improve targeting/imaging efficiency. In this review, we summarize the different pathways of NPs-biomembrane interactions with a focus on AuNPs, follow by an analysis on how the physiochemical properties (size, surface charge, shape, surface ligands, and hydrophobicity etc.) of AuNPs can be involved in the mechanisms of cellular uptake. Finally, some recent advances on simulation modelling of AuNPs-biomembrane interactions and a brief outlook in the field are discussed.

Energy Landscapes of a Pair of Adsorbed Peptides

The wide relevance of peptide adsorption in natural and synthetic contexts means it has attracted much attention. Molecular dynamics (MD) simulation has been widely used in these endeavors. Much of this has focused on single peptides due to the computational effort required to capture the rare events that characterize their adsorption. This focus is, however, of limited practical relevance as in reality, most systems of interest operate in the nondilute regime where peptides will interact with other adsorbed peptides. As an alternative to MD simulation, we have used energy landscape mapping (ELM) to investigate two met-enkephalin molecules adsorbed at a gas/graphite interface. Major conformations of the adsorbed peptides and the connecting transition states are elucidated along with the associated energy barriers and rates of exchange. The last of these makes clear that MD simulations are currently of limited use in probing the co-adsorption of two peptides, let alone more. The constant volume heat capacity as a function of temperature is also presented. Overall, this study represents a significant step toward characterizing peptide adsorption beyond the dilute limit.