Molecular Dynamics Simulation Investigation of the Binding and Interaction of the EphA6-Odin Protein Complex

Identification of small covalent inhibitors targeting DsbA using virtual screening, covalent docking, and molecular dynamics simulations

Antimicrobial resistance (AMR) is a growing global health threat, highlighting the urgent need for new therapeutic strategies. The development of bacterial antivirulence agents and antibiotic adjuvants offers two promising strategies for combating bacterial infections. The DsbA protein is crucial for bacterial virulence and resistance, catalyzing the formation of disulfide bonds in bacterial proteins, making it an attractive target for novel antibiotics. In this study, we employed virtual screening, covalent docking, and molecular dynamics simulations to screen a library of 69,579 compounds for inhibitors targeting Cys30, a key nucleophilic residue in the CXXC catalytic motif of DsbA. We identified four small molecule covalent inhibitors that form covalent bonds with DsbA. The MM/PBSA results indicate that three covalent compounds (Cov28322, Cov16876, and Cov64052) have lower binding energies than the positive control. However, covalent binding typically offers superior target specificity and durability. These inhibitors primarily interact with key regions of DsbA, including the CXXC motif and L2 loop, suggesting their potential to disrupt DsbA's catalytic activity. This study provides a theoretical basis for designing DsbA covalent inhibitors as antibiotic adjuvants, presenting a promising strategy to combat bacterial infections and AMR.

In Silico Screening of 1,3,4-Thiadiazole Derivatives as Inhibitors of Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2)

Angiogenesis plays a pivotal role in the growth, survival, and metastasis of solid tumors, with Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) being overexpressed in many human solid tumors, making it an appealing target for anti-cancer therapies. This study aimed to identify potential lead compounds with azole moiety exhibiting VEGFR-2 inhibitory effects. A ligand-based pharmacophore model was constructed using the X-ray crystallographic structure of VEGFR-2 complexed with tivozanib (PDB ID: 4ASE) to screen the ZINC15 database. Following virtual screening, six compounds demonstrated promising docking scores and drug-likeness comparable to tivozanib. These hits underwent detailed pharmacokinetic analysis to assess their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Furthermore, Density Functional Theory (DFT) analysis was employed to investigate the molecular orbital properties of the top hits from molecular docking. Molecular dynamics (MD) simulations were conducted to evaluate the conformational stability of the complexes over a 100 ns run. Results indicated that the compounds (ZINC8914312, ZINC8739578, ZINC8927502, and ZINC17138581) exhibited the most promising lead requirements for inhibiting VEGFR-2 and suppressing angiogenesis in cancer therapy. This integrated approach, combining pharmacophore modeling, molecular docking, ADMET studies, DFT analysis, and MD simulations, provides valuable insights into the identification of potential anti-cancer agents targeting VEGFR-2.

Effect of quercetin on the protein-substrate interactions in SIRT6: Insight from MD simulations

SIRT6 is of interest for its promising effect in the treatment of aging-related diseases. Studies have shown quercetin (QUE) and its derivatives have varying degrees of effect on the catalytic effect of SIRT6. In the research, the effect of QUE on the protein-substrate interaction in the SIRT6-mediated mono-ADP ribosylation system was investigated by conventional molecular dynamics (MD) simulations combined with MM/PBSA binding free energy calculations. The results show that QUE can bind stably to SIRT6 with the binding energy of -22.8 kcal/mol and further affect the atomic interaction between SIRT6 and NAD+ (or H3K9), resulting in an increased affinity between SIRT6-NAD+ and decreased SIRT6-H3K9 binding capacity. At the same time, the binding of QUE can also alter some structural characteristics of the protein, with large shifts occurring in the residue regions involving the N-terminal (residues 1-27), Rossmann fold regions (residues 55-92), and ZBD (residues 164-179). Thus, QUE shows great potential as a scaffold for the design of novel potent SIRT6 modulators.

The molecular mechanism of non-covalent inhibitor WU-04 targeting SARS-CoV-2 3CLpro and computational evaluation of its effectiveness against mainstream coronaviruses

There is an urgent need for highly effective therapeutic agents to interrupt the continued spread of SARS-CoV-2. As a pivotal protease in the replication process of coronaviruses, the 3CLpro protein is considered as a potential target of drug development to stop the spread and infection of the virus. In this work, molecular dynamics (MD) simulations were used to elucidate the molecular mechanism of a novel and highly effective non-covalent inhibitor, WU-04, targeting the SARS-CoV-2 3CLpro protein. The difference in dynamic behavior between the apo-3CLpro and the holo-3CLpro systems suggests that the presence of WU-04 inhibits the motion amplitude of the 3CLpro protein relative to the apo-3CLpro system, thus maintaining a stable conformational binding state. The energy calculations and interaction analysis show that the hot-spot residues Q189, M165, M49, E166, and H41 and the warm-spot residues H163 and C145 have a strong binding capacity to WU-04 by forming multiple hydrogen bonds and hydrophobic interactions, which stabilizes the binding of the inhibitor. After that, the resistance of WU-04 to the six SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Lambda, and Omicron) and two other mainstream coronavirus (SARS-CoV and MERS-CoV) 3CLpro proteins was further investigated. Excitingly, the slight difference in energy values relative to the SARS-CoV-2 system indicates that WU-04 is still highly effective against the coronaviruses, which becomes crucial evidence that WU-04 is a pan-inhibitor of the 3CLpro protein in various SARS-CoV-2 variants and other mainstream coronaviruses. The study will hopefully provide theoretical insights for the future rational design and improvement of novel non-covalent inhibitors targeting the 3CLpro protein.

The Structural Dynamics, Complexity of Interactions, and Functions in Cancer of Multi-SAM Containing Proteins

SAM domains are crucial mediators of diverse interactions, including those important for tumorigenesis or metastasis of cancers, and thus SAM domains can be attractive targets for developing cancer therapies. This review aims to explore the literature, especially on the recent findings of the structural dynamics, regulation, and functions of SAM domains in proteins containing more than one SAM (multi-SAM containing proteins, MSCPs). The topics here include how intrinsic disorder of some SAMs and an additional SAM domain in MSCPs increase the complexity of their interactions and oligomerization arrangements. Many similarities exist among these MSCPs, including their effects on cancer cell adhesion, migration, and metastasis. In addition, they are all involved in some types of receptor-mediated signaling and neurology-related functions or diseases, although the specific receptors and functions vary. This review also provides a simple outline of methods for studying protein domains, which may help non-structural biologists to reach out and build new collaborations to study their favorite protein domains/regions. Overall, this review aims to provide representative examples of various scenarios that may provide clues to better understand the roles of SAM domains and MSCPs in cancer in general.

Investigation on the interaction mechanism of different SARS-CoV-2 spike variants with hACE2: insights from molecular dynamics simulations

Since the COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), SARS-CoV-2 has evolved by acquiring genomic mutations, resulting in the recent emergence of several SARS-CoV-2 variants with improved transmissibility and infectivity relative to the original strain. An underlying mechanism may be the increased ability of the mutants to bind the receptor proteins and infect the host cell. In this work, we implemented all-atom molecular dynamics (MD) simulations to study the binding and interaction of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein singly (D614G), doubly (D614G + L452R and D614G + N501Y), triply (D614G + N501Y + E484K), and quadruply (D614G + N501Y + E484K + K417T) mutated variants with the human angiotensin-converting enzyme 2 (hACE2) receptor protein in the host cell. A combination of multiple analysis approaches elucidated the effects of mutations and the extent of molecular divergence from multiple perspectives, including the dynamic correlated motions, interaction patterns, dominant motions, free energy landscape, and charge distribution on the electrostatic potential surface between the hACE2 and all RBD variants. Moreover, free energy calculations using the MM/PBSA method evaluated the binding affinity between these RBD variants and hACE2. The results showed that the D614G + N501Y + E484K variant possessed the lowest free energy value (highest affinity) compared to the D614G + N501Y + E484K + K417T, D614G + L452R, D614G + N501Y, and D614G mutants. The residue-based energy decomposition also indicated that the energy contribution of residues at the mutation site to the total binding energy was highly variable. The interaction mechanisms between the different RBD variants and hACE2 elucidated in this study will provide some insights into the development of drugs targeting the new SARS-CoV-2 variants.

Controlling cell proliferation by targeting cyclin-dependent kinase 6 using drug repurposing approach

Cyclin-dependent kinase 6 (CDK6) is an essential kinase in cell cycle progression, which is a viable target for inhibitors in various malignancies, including breast cancer. This study aimed to virtually screen efficient compounds as new leads in treating breast cancer using a drug repurposing approach. Apoptosis regulatory compounds were taken from the seleckchem database. Molecular docking experiments were carried out in the presence of abemaciclib, a routinely used FDA drug. Compared to conventional drugs, the two compounds demonstrated a higher binding affinity for CDK6. Compounds (N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-(naphthalen-1-ylmethyl)-4,7-dioxo-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide) and (1'-[4-[1-(4-fluorophenyl)indol-3-yl]butyl]spiro[1H-2-benzofuran-3,4'-piperidine]) were discovered to have an inhibitory effect against CDK6 at -8.49 and -6.78kcal/mol, respectively, compared to -8.09kcal/mol of the control molecule, the interacting residues of these two new compounds were found to fall within the binding site of the CDK6 molecule. Both compounds exhibited equal ADME features compared with abemaciclib and would be well distributed and metabolized by the body with an appropriate druglikeness range. Lastly, molecular dynamics was initiated for 200ns for the selected potent inhibitors and abemaciclib as complexed with CDK6. The RMSD, RMSF, Rg, H-Bond interactions, SASA, PCA, FEL, and MM/PBSA analysis were performed for the complexes to assess the stability, fluctuations, radius of gyration, hydrogen bond interaction, solvent accessibility, essential dynamics, free energy landscape, and MM/PBSA. The selected two compounds are small molecules in the appropriate druglikeness range. The results observed in molecular docking and molecular dynamics simulations were most promising for two compounds, suggesting their potent inhibitory effect against CDK6. We propose that these candidate compounds can undergo in vitro validation and in vivo testing for their further use against cancer.

Computational Design of Miniprotein Inhibitors Targeting SARS-CoV-2 Spike Protein

The ongoing pandemic of COVID-19 caused by SARS-CoV-2 has become a global health problem. There is an urgent need to develop therapeutic drugs, effective therapies, and vaccines to prevent the spread of the virus. The virus first enters the host cell through the interaction between the receptor binding domain (RBD) of spike protein and the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2). Therefore, blocking the binding of RBD and ACE2 is a promising strategy to inhibit the invasion and infection of the virus in the host cell. In the study, we designed several miniprotein inhibitors against SARS-CoV-2 by single/double/triple-point mutant, based on the initial inhibitor LCB3. Molecular dynamics (MD) simulations and trajectory analysis were performed for an in-depth analysis of the structural stability, essential protein motions, and per-residue energy decomposition involved in the interaction of inhibitors with the RBD. The results showed that the inhibitors have adapted the protein RBD in the binding interface, thereby forming stable complexes. These inhibitors display low binding free energy in the MM/PBSA calculations, substantiating their strong interaction with RBD. Moreover, the binding affinity of the best miniprotein inhibitor, H6Y-M7L-L17F mutant, to RBD was ∼45 980 times (ΔG = RT ln Ki) higher than that of the initial inhibitor LCB3. Following H6Y-M7L-L17F mutant, the inhibitors with strong binding activity are successively H6Y-L17F, L17F, H6Y, and F30Y mutants. Our research proves that the miniprotein inhibitors can maintain their secondary structure and have a highly stable blocking (binding) effect on SARS-CoV-2. This study proposes novel miniprotein mutant inhibitors with enhanced binding to spike protein and provides potential guidance for the rational design of new SARS-CoV-2 spike protein inhibitors.