Design and computational evaluation of a novel multi-epitope hybrid vaccine against monkeypox virus: Potential targets and immunogenicity assessment for pandemic preparedness.

Monkeypox is a type of DNA-enveloped virus that belongs to the orthopoxvirus family, closely related to the smallpox virus. It can cause an infectious disease in humans known as monkeypox disease. Although there are multiple drugs and vaccines designed to combat orthopoxvirus infections, with a primary focus on smallpox, the recent spread of the monkeypox virus to over 50 countries have ignited a mounting global concern. This unchecked viral proliferation has raised apprehensions about the potential for a pandemic corresponding to the catastrophic impact of COVID-19. This investigation explored the structural proteins of monkeypox virus as potential candidates for designing a novel hybrid multi-epitope vaccine. The epitopes obtained from the selected proteins were screened to ensure their non-allergenicity, non-toxicity, and antigenicity to trigger T and B-cell responses. The interaction of the vaccine with toll-like receptor-3 (TLR-3) and major histocompatibility complexes (MHCs) was assessed using Cluspro 2.0. To establish the reliability of the docked complexes, a comprehensive evaluation was conducted using Immune and MD Simulations and Normal Mode Analysis. However, to validate the computational results of this study, additional in-vitro and in-vivo research is essential.

Cholecalciferol complexation with hydroxypropyl-ß-cyclodextrin (HPBCD) and its molecular dynamics simulation.

The focus of the current study is to investigate cholecalciferol (vitamin D3) solubilization by hydroxypropyl-ß-cyclodextrin (HPBCD) complexation through experimental and computational studies. Phase solubility diagram of vitamin D3 (completely insoluble in water) has an AP profile revealing a deviation from a linear regression with HPBCD concentration increase. Differential scanning calorimetry (DSC) is the best tool to confirm complex formation by disappearance of cholecalciferol exothermic peak in cholecalciferol-HPBCD complex thermogram, due to its amorphous state by entering HPBCD inner hydrophobic cavity, similarly validated by Fourier-transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). AP solubility diagram profile can be associated with cholecalciferol-HPBCD complex instability in liquid phase requiring spray drying to bring it to a solid dispersion state (always more stable) illustrated by scanning electron microscopy (SEM). Computational studies led to a deeper understanding and clarification, at molecular level, of the interactions within cholecalciferol-HPBCD complex. Thermodynamics and geometry of the complex were investigated by molecular dynamics (MD) simulation.

Impact of Reactive Oxygen and Nitrogen Species Produced by Plasma on Mdm2-p53 Complex.

The study of protein-protein interactions is of great interest. Several early studies focused on the murine double minute 2 (Mdm2)-tumor suppressor protein p53 interactions. However, the effect of plasma treatment on Mdm2 and p53 is still absent from the literature. This study investigated the structural changes in Mdm2, p53, and the Mdm2-p53 complex before and after possible plasma oxidation through molecular dynamic (MD) simulations. MD calculation revealed that the oxidized Mdm2 bounded or unbounded showed high flexibility that might increase the availability of tumor suppressor protein p53 in plasma-treated cells. This study provides insight into Mdm2 and p53 for a better understanding of plasma oncology.

Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future.

Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.

Structure-based screening of FDA-approved drugs identifies potential histone deacetylase 3 repurposed inhibitor: molecular docking and molecular dynamic simulation approaches.

Histone deacetylase 3 (HDAC3) is a member of the histone deacetylase family that has emerged as a crucial target in the quest for novel therapeutic interventions against various complex diseases, including cancer. The repositioning of FDA-approved drugs presents a promising avenue for the rapid discovery of potential HDAC3 inhibitors. In this study, we performed a structure-based virtual screening of FDA-approved drugs obtained from DrugBank. Candidate hits were selected based on their binding affinities and interactions with HDAC3. These promising hits were then subjected to a comprehensive assessment of their biological properties and drug profiles. Our investigation identified two FDA-approved drugs, Imatinib and Carpipramine, characterized by their exceptional affinity and specificity for the binding pocket of HDAC3. These molecules demonstrated a strong preference for HDAC3 binding site and formed interactions with functionally significant residues within the active site pocket. To gain deeper insights into the binding dynamics, structural stability, and interaction mechanisms, we performed molecular dynamics (MD) simulations spanning 300 nanoseconds (ns). The results of MD simulations indicated that Imatinib and Carpipramine stabilized the structure of HDAC3 and induced fewer conformational changes. Taken together, the findings from this study suggest that Imatinib and Carpipramine may offer significant therapeutic potential for treating complex diseases, especially cancer.

Revealing the interaction mechanism between bovine serum albumin (BSA) and a fluorescent coumarin derivative: A multispectroscopic and in silico approach.

The interaction of biomacromolecules with each other or with the ligands is essential for biological activity. In this context, the molecular recognition of bovine serum albumin (BSA) with 4-(Benzo[1,3]dioxol-5-yloxymethyl)-7-hydroxy-chromen-2-one (4BHC) is explored using multispectroscopic and computational techniques. UV-Vis spectroscopy helped in predicting the conformational variations in BSA. Using fluorescence spectroscopy, the quenching behaviour of the fluorophore upon interaction with the ligand is examined, which is found to be a static type of quenching; fluorescence lifetime studies further verify this. The binding constant is discovered to be in the range of 104 M-1, which indicates the moderate type of association that results in reversible binding, where the transport and release of ligands in the target tissue takes place. Fourier-transform infrared spectroscopy (FT-IR) measurements validate the secondary structure conformational changes of BSA after complexing with 4BHC. The thermodynamic factors obtained through temperature-dependent fluorescence studies suggest that the dominant kind of interaction force is hydrophobic in nature, and the interaction process is spontaneous. The alterations in the surrounding microenvironment of the binding site and conformational shifts in the structure of the protein are studied through 3D fluorescence and synchronous fluorescence studies. Molecular docking and molecular dynamics (MD) simulations agree with experimental results and explain the structural stability throughout the discussion. The outcomes might have possible applications in the field of pharmacodynamics and pharmacokinetics.

Molecular interaction analysis of anti-IL-8 scFv-10F8-6His against IL-8 monomer through molecular docking and molecular dynamic simulations.

Elevated interleukin 8 (IL-8) expression has been linked to unfavorable outcomes in a range of inflammatory conditions, such as rheumatoid arthritis, psoriasis, and cancer. The human monoclonal antibody (HuMab) 10F8 and the hybridoma 35B11-B bind to an epitope on human IL-8, respectively. 10F8 inhibited interaction between IL-8 and neutrophils in eczema and pustulosis palmoplantaris patients while 35B11-B decreased size lesion in rat model. The binding interaction of monoclonal antibodies and IL-8, especially how complementarity-determining region (CDR) loops could bind the N-terminal of IL-8, has not been fully deliberated at molecular-level. Here, we used a combination of molecular docking, heated and long coarse-grained molecular dynamics simulations to identify key residues of established interaction. Based on heated MD simulation, docked pose of complexes generated by ClusPro showed good binding stability throughout of 70 ns simulation. Based on long molecular dynamic simulations, key residues for the binding were identified throughout of 1000 ns simulation. TYR-53, ASP-99, and ARG-100 of heavy chain CDR together with TYR-33 of light chain CDR are among the highest contributing energy residues within the binding interaction. Meanwhile, LYS11 and TYR13 of IL-8 are important for the determination of overall binding energy. Furthermore, the result of decomposition residues analysis is in good agreement with the interaction analysis data. Current study provides a list of important interacting residues and further scrutiny on these residues is essential for future development and design of a new and stable recombinant antibody against IL-8.Communicated by Ramaswamy H. Sarma.

Effect of ligand conjugation site on the micellization of Bio-Targeted PLGA-Based nanohybrids: A computational biology approach.

In this study, the effect of ligand binding position on the polymeric nanoparticles (NPs) is based on poly(lactic-co-glycolic acid) (PLGA) with two different polymer chain length at the atomistic level was presented. We explored the conjugation of riboflavin (RF) ligand from the end of the ribityl chain (N-10) to the polymer strands as well as from the amine group on the isoalloxazine head (N-3). The energy interactions for all samples revealed that the NPs containing ligands from N-10 positions have higher total attraction energies and lower stability in comparison with their peers conjugated from N-3. As NPs containing RF conjugated from N-3 exhibit the lower energy level with 20% and 10% of RF-containing composition for lower and higher. The introduction of RF from the N-10 position in any composition has increased the energy level of nanocarriers. The results of Gibb's free energy confirm the interatomic interaction energies trend where the lowest Gibbs free energy level for N-3 NPs occurs at 20 and 10% of RF-containing polymer content for PLGA10- and PLGA11- based NPs. Furthermore, with N-10 samples based on both polymers, non-targeted models form the stablest particles in each category. These findings are further confirmed with molecular docking analysis which revealed affinity energy of RF toward polymer chain from N-3 and N-10 are -981.57 kJ/mole and -298.23 kJ/mole, respectively. This in-silico study paves the new way for molecular engineering of the bio-responsive PLGA-PEG-RF micelles and can be used to nanoscale tunning of smart carriers used in cancer treatment.Communicated by Ramaswamy H. Sarma.

Inhibition performances of graphene oxide/silver nanostructure for the microbial corrosion: molecular dynamic simulation study.

Steel is one of the mainly used materials in the oil and gas industry. However, it is susceptible to the marine corrosion, which 20% of the total marine corrosion is caused by microbiologically influenced corrosion (MIC). The economic and environmental impacts of corrosion are significant, and it is crucial to fight against corrosion in a proper sustainability context and environmental-friendly methods. In this study, the graphene oxide/silver nanostructure (GO-Ag) inhibitory effect on the corrosion of steel in the presence of sulfate reducing bacteria (SRB) was investigated, via weight loss (WL) and Tafel polarization measurements. Moreover, molecular dynamic (MD) simulations were performed to obtain a deep understanding of the corrosion inhibition effect of GO-Ag. GO-Ag showed a significant antibacterial effect at 80 ppm. Moreover, WL and Tafel polarization measurements illustrated a great inhibition efficiency, which reached up to 84% reduction of WL and 98% reduction of corrosion current density (Icorr) after 7 days of incubation with GO-Ag. Based on MD simulations, bonding energy reached to the larger value in the presence of GO-Ag, which indicated the ability of graphene oxide nanosheets to be adsorbed on the steel surface and prevent the access of corrosive agents to the steel surface. The radial distribution function (RDF) results implied distance between corrosive agent (water and SRB) and steel surface (Fe atoms), which indicated protection of the steel surface due to the effective adsorption of GO nanosheets through the active sites of the steel surface. The mean square displacement (MSD) result showed smaller displacement of the corrosive particles on the surface of steel, resulting that the GO-Ag molecules bonded with Fe molecules on the surface of steel.

Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs.

Calcineurin is a critical enzyme in fungal pathogenesis and antifungal drug tolerance and, therefore, an attractive antifungal target. Current clinically accessible calcineurin inhibitors, such as FK506, are immunosuppressive to humans, so exploiting calcineurin inhibition as an antifungal strategy necessitates fungal specificity in order to avoid inhibiting the human pathway. Harnessing fungal calcineurin-inhibitor crystal structures, we recently developed a less immunosuppressive FK506 analog, APX879, with broad-spectrum antifungal activity and demonstrable efficacy in a murine model of invasive fungal infection. Our overarching goal is to better understand, at a molecular level, the interaction determinants of the human and fungal FK506-binding proteins (FKBP12) required for calcineurin inhibition in order to guide the design of fungus-selective, nonimmunosuppressive FK506 analogs. To this end, we characterized high-resolution structures of the Mucor circinelloides FKBP12 bound to FK506 and of the Aspergillus fumigatus, M. circinelloides, and human FKBP12 proteins bound to the FK506 analog APX879, which exhibits enhanced selectivity for fungal pathogens. Combining structural, genetic, and biophysical methodologies with molecular dynamics simulations, we identify critical variations in these structurally similar FKBP12-ligand complexes. The work presented here, aimed at the rational design of more effective calcineurin inhibitors, indeed suggests that modifications to the APX879 scaffold centered around the C15, C16, C18, C36, and C37 positions provide the potential to significantly enhance fungal selectivity. IMPORTANCE Invasive fungal infections are a leading cause of death in the immunocompromised patient population. The rise in drug resistance to current antifungals highlights the urgent need to develop more efficacious and highly selective agents. Numerous investigations of major fungal pathogens have confirmed the critical role of the calcineurin pathway for fungal virulence, making it an attractive target for antifungal development. Although FK506 inhibits calcineurin, it is immunosuppressive in humans and cannot be used as an antifungal. By combining structural, genetic, biophysical, and in silico methodologies, we pinpoint regions of the FK506 scaffold and a less immunosuppressive analog, APX879, centered around the C15 to C18 and C36 to C37 positions that could be altered with selective extensions and/or deletions to enhance fungal selectivity. This work represents a significant advancement toward realizing calcineurin as a viable target for antifungal drug discovery.

Potent novel inhibitors against hepatitis C virus NS3 (HCV NS3 GT-3a) protease domain.

HCV NS3, a non-structural hepatitis C viral protein is used as one of the potential targets for inhibition by direct-acting antivirals. It is known that the success rate for HCV genotype-1 treatment remained very high, however, treatment of genotype-3a (GT-3a), is still quite challenging. In the current study, the HCV GT-3a full-length NS3 gene was amplified and sequenced. The complete nucleotide sequence was translated into the amino acid sequence and homology models of HCV-NS3 GT-3a were generated by HCV-NS3 genotype-1b as a template. The objective of the study was to screen novel therapeutic hits from large databases. For this aim, various small molecule databases including, BindingDB (∼45.000 compounds), NCI (∼265.000 compounds), and Specs-SC (∼212.000 compounds) were used. Firstly, all of the compounds were screened using binary-QSAR models from the MetaCore/MetaDrug server, and compounds were filtered based on therapeutic activity predictions by the anti-viral QSAR model. Filtered molecules were used in 26 different toxicity QSAR models and active non-toxic compounds were identified. These selected molecules were then used in docking and molecular dynamics (MD) simulations studies at the binding cavities of the NS3 protease domain of the GT-3a. Results were compared with known inhibitors and novel molecules are proposed against HCV-NS3 GT-3a. These molecules have high ligand efficiencies as compared to the reference molecules suggesting a better alternate to the existing suite of inhibitors. Thus, this study will be a step ahead in the development of new potential compounds as antiviral drugs for the GT-3a target.

Nanoparticle assembly under block copolymer confinement: The effect of nanoparticle size and confinement strength.

We investigate the self-assembly of cylinder-forming polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) block copolymers (BCP) mixed with metal nanoparticles (NP) coated with short-chain polystyrene (PS) ligands. The NP formed hierarchical superstructures under confinement of cylindrical PS domains of PS-b-P4VP BCP. The complexity of NP superstructures was found to depend on the ratio between PS cylindrical domain size and NP size (DC/DNP). As the DC/DNP ratio increased, the number of NP layers normal to the cylinder axis also increased. However, the packing density of the NP decreased at higher DC/DNP. Furthermore, the morphology of the structures obtained during different solvent casting conditions revealed that the initial clustering of NP and micellization around these clusters act as a precursor for the subsequent formation of closely packed structures of NP in cylinders. The experimental results were further supported by modeling results obtained from molecular dynamics (MD) simulation. Based on MD simulations, we constructed structural phase diagram of nanoparticle assemblies in the presence of asymmetric diblock copolymers comprising short NP-attractive blocks. The MD simulation results indicate that NP undergo transition from spherical to cylindrical assemblies depending on the NP size, the overall concentration of components and the degree of affinity of the minor block to NP.

Co-amorphous solid dispersion systems of lacidipine-spironolactone with improved dissolution rate and enhanced physical stability.

Co-amorphous solid dispersion (C-ASD) systems have attracted great attention to improve the solubility of poorly soluble drugs, but the selection of an appropriate stabilizer to stabilize amorphous forms is still a huge challenge. Herein, C-ASD system of two clinical combined used drugs (lacidipine (LCDP) and spironolactone (SPL)) as stabilizers to each other, was prepared by solvent evaporation method. The effects of variation in molar ratio of LCDP and SPL (3:1, 1:1, 1:3, 1:6, and 1:9) on the drug release characteristics were explored. Polarized light microscopy (PLM), powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were employed to evaluate the solid states. Prepared C-ASDs were further studied for their stability under the high humidity (RH 92.5%). Further analysis of C-ASDs via Fourier-transform infrared spectroscopy (FTIR) and Raman spectroscopy confirmed that hydrogen bond interactions between the two drugs played a significant role in maintaining the stability of the C-ASDs systems. Moreover, molecular dynamic (MD) simulations provided a clear insight into the stability mechanism at the molecular level. This study demonstrated the novel drug-drug C-ASDs systems is a promising formulation strategy for improved dissolution rate and enhanced physical stability of poorly soluble drugs.

Hexagonal boron nitride nanosheet as novel drug delivery system for anticancer drugs: Insights from DFT calculations and molecular dynamics simulations.

Density functional theory (DFT) calculations and molecular dynamic (MD) simulations were accomplished to comprehend the nature of the interactions between 5-fluorouracil (FU)/6-mercaptopurine (MP)/6-thioguanine (TG) anticancer drugs and hexagonal boron nitride (BN) nanosheet as a drug delivery system. It is found from the calculations that the adsorption process of drug molecules on the BN nanosheet is exothermic and occurs spontaneously. The polarity for the drug loaded complexes, offers the possibility of improving the condition of solubility, which is favorable for drug delivery in biological media. Orbital energy and density of state (DOS) calculations show that HOMO-LUMO energy gap of BN nanosheet decreases upon the adsorption of drug molecules. The quantum molecular descriptors show that the absorption of drugs on BN nanosheet increases the chemical reactivity. The results of the energy decomposition analysis (EDA) indicated that the dispersion interaction plays a predominant role in the stabilization of the drug-BN complexes. The intermolecular interactions were also investigated by the noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. The MD results showed that the average of the interaction energy values in acidic conditions are lower (absolute values) than corresponding values obtained at neutral pH, which indicated the drug could be released within the target cancer cells. These findings contribute to the development of drug delivery systems based on BN nanosheet for delivery of anticancer drugs.

Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline.

Appropriate therapeutic solutions against Staphylococcal infections are currently limited. To work out the complex task of challenging drug resistance in Staphylococcus aureus, new compounds with novel modes of action are required. In this study, we performed target-driven virtual screening to filter exhaustive phytochemical libraries that can inhibit the activity of S. aureus DNA Gyrase B (Gyr B). Three top-ranked hit molecules (Mangostenone E, Candenatenin A and 2,4,4'-trihydroxydihydrochalcone) were identified from comprehensive molecular docking studies based on their strong spatial affinity with key catalytic residues of the binding pocket of DNA GyrB, especially with the well-known crucial residue Asp81. Molecular dynamics (MD) simulations were performed for these identified hit molecules for better understanding of their dynamical and structural profiles throughout the MD simulations. These compounds can be explored as future lead optimization molecules to discover a new class of antibiotics against resistant Staphylococcus aureus strains.

Interactions between poly-(phthalazinone ether sulfone ketone) (PPESK) and TNT or TATB in polymer bonded explosives: a molecular dynamic simulation study.

The glass transition temperature (T g) and density of poly-(phthalazinone ether sulfone ketone) (PPESK A) were estimated by molecular dynamic (MD) simulation. A novel poly-(phthalazinone ether sulfone ketone) (PPESK B) was constructed by introducing nitrol and amini energetic groups into PPESK A, and T g and density were also simulated for PPESK B. The estimated T g values of PPESK A were very close to experimental results, while for PPESK B three estimated values differed by < 5 K. The interactions between explosives and polymer binders of polymer bonded explosives (PBXs) were simulated by MD. Comparison of the cohesive energy densities (CED) and solubility parameter (δ) values of PBXs, polymer binders, and mono-explosives indicate that, upon introducing polymer binders, the CED and δ values of PBXs decreased compared with those of corresponding mono-explosives. The binding energies (E bind) imply that 2,4,6-trinitrotoluene-based PBXs are more stable than 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)-based PBXs. The mechanical properties, Young's modulus E, shear modulus G, bulk modulus K, Poisson's ratio γ and Cauchy pressure (C 12 -C 44) of the PBXs were assessed. The rigidity of the PBXs was found to be lower than that of mono-explosives. All K/G values were positive, indicating that PBXs are flexible. Based on these mechanical properties results, PBXs using PPESK B as a binder are superior to those using PPESK A as a binder. Due to the low C 12 -C 44 values of the PBXs, the ductility of the materials of the fracture surface is poorer, especially for TATB-based PBXs.