Dynamics Simulation Study Research Articles

In vitro and in silico studies of fluorinated 2,3-disubstituted thiazolidinone-pyrazoles as potential α-amylase inhibitors and antioxidant agents.

As part of our effort to identify potent α-amylase inhibitors, in the present study, a novel series of fluorinated thiazolidinone-pyrazole hybrid molecules were prepared by the condensation of 3-(aryl/benzyloxyaryl)-pyrazole-4-carbaldehydes with fluorinated 2,3-disubstituted thiazolidin-4-ones. The structures of the newly synthesized compounds were confirmed by infrared, 1 H nuclear magnetic resonance (NMR), 13 C NMR, and liquid chromatography-mass spectrometry data. All the compounds were screened for their α-amylase inhibitory and free radical scavenging activities by DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS methods. Among the tested compounds, compound 8g emerged as a promising α-amylase inhibitor with IC50 = 0.76 ± 1.23 µM, and it was found to be more potent than the standard drug acarbose (IC50 = 0.86 ± 0.81 μM). Compounds 8b and 8g showed strong free radical scavenging activity compared to the standard butylated hydroxyl anisole. The kinetic study of compound 8g revealed the reversible, classical competitive inhibition mode on the α-amylase enzyme. Molecular docking and dynamic simulations studies were performed for the most potent compound 8g, which displayed remarkable hydrogen bonding with the α-amylase protein (PDB ID: 1DHK).

Proanthocyanidin A1 promotes the production of platelets to ameliorate chemotherapy-induced thrombocytopenia through activating JAK2/STAT3 pathway

BackgroundChemotherapy-induced thrombocytopenia (CIT) is a severe adverse drug reaction, and the main reason for CIT is the destruction of megakaryocytes (MKs, precursor cells of platelet) in bone marrow by chemotherapy. Peanut skin, the seed coat of Arachis hypogaea L., is a traditional Chinese medicine commonly used to treat thrombocytopenia. However, its active compounds and the mechanisms remain unclear. PurposeThis study aims to clarify the active compounds of peanut skin to exhibit thrombogenic effects against CIT and their underlying mechanisms in vitro and in vivo. Study designThe bioassay-guided isolation based on the proliferation of MKs was used to explore the possible platelet-enhancing ingredients in peanut skin. HSCCC technique coupled with preparative HPLC was used to separate the active compounds. Dami cells and carboplatin-treated mice model were used to evaluate the thrombogenic effects of PS-1. Network pharmacology, molecular docking, dynamics simulation studies, kinase activity, surface plasmon resonance (SPR), cellular thermal shift assay (CETSA), isothermal dose-response fingerprint (ITDRFCETSA) and western blot analysis were performed to investigate the mechanisms of PS-1. ResultsProanthocyanidin A1 (PS-1) and its stereoisomers (PS-2–4) were demonstrated to promote the proliferation of MKs (Dami cells), especially PS-1 (EC50 = 8.58 μM). Further studies demonstrated that PS-1 could induce the differentiation of Dami cells in dose/time-dependent manner. Biological target analysis showed that PS-1 directly bound to JAK2 (KD = 2.06 μM) to exert potent activating effect (EC50 = 0.66 μM). Oral administration of PS-1 (25 or 50 mg/kg) significantly improved CIT, but this effect was confirmed to be inhibited by JAK2 inhibitor AG490, indicating that PS-1 exerted its efficacy through JAK2 in vivo. ConclusionProanthocyanins (PS-1–4) derived from peanut skin were first clarified as platelet-enhancing ingredients to improve CIT. The underlying mechanism of PS-1 was proved to promote the proliferation and differentiation of MKs via JAK2/STAT3 pathway both in vitro and in vivo.

Influence of Crystallization Additives on Morphology of Selected Benzoic Acids - A Molecular Dynamics (MD) Simulation Study

The possibility to modify the morphology by crystallization additives of model substances was studied using molecular dynamics simulations. For this 2,6-dimethoxybenzoic acid and 3-hydroxybenzoic acid, each having two polymorphic forms, including a form without carboxylic acid homodimers in their crystal structure were selected. For each polymorph 2-3 largest crystal faces were selected for the study and the crystal was cut along these planes by preparing a simulation box with these planes facing towards solution containing additives. In the performed study it was evaluated which additives potentially can influence the crystal morphology and possibly also polymorph obtained in the crystallization by significantly changing the growth rate of crystal by adsorbing on the surface. For the study 4-5 additives providing different intermolecular interaction possibilities were selected. Among the studied additives urea showed the most complete adsorption and the longest residence time on surfaces of both substances, with the exceptions of few specific planes.

Microbial based natural compounds as potential inhibitors for SARS-CoV-2 Papain-like protease (PLpro): a molecular docking and dynamic simulation study

COVID-19 (Coronavirus disease of 2019) pandemic is one of the largest health threats the planet has faced in recent decades. Efforts are being continuously made to design a viable drug or a vaccine. Several natural and synthetic molecules are under study for their potency to inhibit viral replication. In order to emphasize the importance of microbial-based natural components in antiviral drug discovery, an attempt has been made through this study to find potential inhibitors for SARS-CoV-2 Papain-Like protease (PLpro) molecule from microbial sources. PLpro, with its multifunctional roles like viral polypeptide proteolysis and suppression of the host's innate immune response, is acting as a potential drug target. The X-ray crystal structure of PLpro and ligand molecules were retrieved from the protein structure database and Npatlas database, respectively. The molecules were screened based on drug likeliness and the pharmacophore model created in reference to a known potent PLpro inhibitor GRL0617. Totally 3272 molecules have undergone the docking process and the complexes of top hits were subjected to 100 ns molecular dynamic simulation. The results showed that Holyrine B, Dihydroarcyriarubin C, Baraphenazine C and 3-hydroxy-3'-N-acetylholyrine A had formed a stable complex in the active site of the PLpro with significant interaction efficiency. Earlier studies showed that Holyrine B could also be a possible inhibitor of the Main protease of SARS-CoV-2, which increases its significance in the process of COVID-19 drug development. In conclusion, these microbial compounds can be considered as possible SARS-CoV-2 inhibitors for further in vitro studies. Communicated by Ramaswamy H. Sarma

Toward a treatment of antibacterial and antifungal infections: Design, synthesis and in vitro activity of novel arylhydrazothiazolylsulfonamides analogues and their insight of DFT, docking and molecular dynamic simulations

• New arylhydrazothiazolylsulfonamide derivatives 3(a-e) have been synthesized, designed and spectral characterized. • 3d displayed more potent antimicrobial activity than the antibiotics • DFT, molecular docking and dynamics simulation were performed to explore detailed binding process • Computational approach supported the in vitro results To find out effective new antibacterial agents, a series of novel aryl-hydrazothiazolyl-sulfonamide derivatives 3a-e were synthesized and well characterized by analytical and spectroscopic techniques. All the compounds were evaluated for their antibacterial and antifungal potential and the results showed excellent antimicrobial activity of 3d against all strains, especially B. cereus (MIC = 5.54 μM vs. 17.6 μM), P. aeruginosa (MIC = 7.3 μM vs.12.8 μM), E. coli (MIC = 6.4 μM vs. 21.3 μM) and C . albicans (MIC = 6.8 μM vs. 26.4 μM) in comparison to the commercial antibiotics, tetracycline and amphotericin B, respectively. The others analogues dispalyed potent to moderate antimicrobial activity. Structure-activity relationships (SARs) provides specially that incorporation of pyrimidin-2-ylsulfamoyl group at the para -phenyl position ( 3d ) is good contributor for improving the antimicrobial activity. Further, Density Functional Theory (DFT) on 3d revealed its high stability and strongest electron-donating capability. Molecular docking and dynamic simulation studies on 3d inside the active site of S. aureus tyrosyl-tRNA synthetase (PDB ID: 1JIJ), E. coli dihydropteroate synthetase (PDB ID: 1AJ0), C. albicans dihydropteroate synthetase (PDB ID: 4HOE), and C. albicans N-myristoyl transferase (PDB ID: 1IYL) showed good binding profiles with the targets proteins, in particular with 1IYL and 4HOE receptors via the involvement of hydrogen bonding and that the formed complexes were thermodynamically highly stable. Taken together, our results make 3d as a promising lead for further drugs development.

Discovery of first-in-class imidazothiazole-based potent and selective ErbB4 (HER4) kinase inhibitors.

This article reports on novel imidazothiazole derivatives as first-in-class potent and selective ErbB4 (HER4) inhibitors. There are no other reported selective inhibitors of this kinase in the literature, that's why they are considered as first-in-class. In addition, none of the reported non-selective ErbB4 inhibitors possesses imidazothiazole nucleus in its structure. Therefore, there is novelty in this work in both kinase selectivity and chemical structure. Compounds Ik and IIa are the most potent ErbB4 kinase inhibitor (IC50=15.24 and 17.70nM, respectively). Compound Ik showed promising antiproliferative activity. It is selective towards cancer cell lines than normal cells. Its ability to penetrate T-47D cell membrane and inhibit ErbB4 kinase inside the cells has been confirmed. Moreover, both compound Ik and IIa have additional merits such as weak potency against hERG ion channels and against CYP 3A4 and 2D6. Molecular docking and dynamic simulation studies were carried out to explain binding interactions.

In silico prediction of mozenavir as a potential drug for SARS-CoV-2 infection via binding multiple drug targets

Since the epidemic began in November 2019, no viable medicine against SARS-CoV-2 has been discovered. The typical medication discovery strategy requires several years of rigorous research and development as well as a significant financial commitment, which is not feasible in the face of the current epidemic. Through molecular docking and dynamic simulation studies, we used the FDA-approved drug mezonavir against the most important viral targets, including spike (S) glycoprotein, Transmembrane serine protease 2 (TMPRSS2), RNA-dependent RNA polymerase (RdRp), Main protease (Mpro), human angiotensin-converting enzyme 2 (ACE-2), and furin. These targets are critical for viral replication and infection propagation because they play a key role in replication/transcription and host cell recognition. Molecular docking revealed that the antiviral medication mozenavir showed a stronger affinity for SARS-CoV-2 target proteins than reference medicines in this investigation. We discovered that mozenavir increases the complex's stability and validates the molecular docking findings using molecular dynamics modeling. Furin, a target protein of COVID-19, has a greater binding affinity (-12.04 kcal/mol) than other COVID-19 target proteins, forming different hydrogen bonds and polar and hydrophobic interactions, suggesting that it might be used as an antiviral treatment against SARS-CoV-2. Overall, the present in silico results will be valuable in identifying crucial targets for subsequent experimental investigations that might help combat COVID-19 by blocking the protease furin's proteolytic activity.

Guided rational design with scaffold hopping leading to novel histamine H3 receptor ligands

During the past decades, histamine H3 receptors have received widespread attention in pharmaceutical research due to their involvement in pathophysiology of several diseases such as neurodegenerative disorders. In this context, blocking of these receptors is of paramount importance in progression of such diseases. In the current investigation, novel histamine H3 receptor ligands were designed by exploiting scaffold-hopping drug-design strategy. We inspected the designed molecules in terms of ADME properties, drug-likeness, as well as toxicity profiles. Additionally molecular docking and dynamics simulation studies were performed to predict binding mode and binding free energy calculations, respectively. Among the designed structures, we selected compound d2 and its demethylated derivative as examples for synthesis and affinity measurement. In vitro binding assays of the synthesized molecules demonstrated that d2 has lower binding affinity (Ki = 2.61 μM) in radioligand displacement assay to hH3R than that of demethylated form (Ki = 12.53 μM). The newly designed compounds avoid of any toxicity predictors resulted from extended in silico and experimental studies, can offer another scaffold for histamine H3R antagonists for further structure–activity relationship studies.

Impact of different human walking patterns on flow and contaminant dispersion in residential kitchens: Dynamic simulation study

Impact of different human walking patterns on flow and contaminant dispersion in residential kitchens: Dynamic simulation study

Influence of lactide vs glycolide composition of poly (lactic-co-glycolic acid) polymers on encapsulation of hydrophobic molecules: molecular dynamics and formulation studies

The work demonstrates the preparation of PLGA (PLGA 50:50, PLGA 75:25) nanoparticles, to encapsulate a hydrophobic molecule (coumarin-6), using the microreactor-based continuous process. The formulations were characterized using dynamic light scattering and transmission electron microscopy to determine their size, homogeneity, zeta potential, and surface morphology. The resulting nanoparticles were safe to the CHO cells (≈80% cell survival), at the concentration of ≤600 µg/mL and were successfully taken up by the cells, as demonstrated using confocal microscopy. Moreover, imaging flow cytometry confirmed that the nanoparticles were internalized in 73.96% of the cells. Furthermore, molecular dynamics simulation and docking studies were carried out to explore the effect of polymer chain length of PLGA and lactide vs glycolide (LA:GA) ratio on their compatibility with the coumarin-6 molecules and to study the coiling and flexibility of PLGA in the presence of coumarin-6 molecules. Flory–Huggins interaction parameter (χ) was calculated for polymer chains of varying lengths and LA:GA ratio, with respect to coumarin-6. χ parameter increased with increase in polymer chain length, which indicated superior interaction of coumarin-6 with the smaller chains. Amongst all the polymeric systems, PLGA55 exhibited the strongest interaction with coumarin-6, for all the chain lengths, possibly because of their homogeneous spatial arrangements and superior binding energy. PLGA27 showed better compatibility compared to PLGA72 and PGA, whereas PLA-based polymers exhibited the least compatibility. Analysis of the radius of gyration of the polymer chains in the polymer–coumarin-6 complexes, at the end of molecular dynamics run, exhibited that the polymer chains displayed varying coiling behavior and flexibility, depending upon the relative concentrations of the polymer and coumarin-6. Factors like intra-chain interactions, spatial arrangement, inter-chain binding energies, and polymer–coumarin-6 compatibility also influenced the coiling and flexibility of polymer chains.

Diffusion study of chloride and binding of water in concrete pore by molecular dynamics simulation using LAMMPS

As for the communication between concrete and the particles, the surface shows Cl− shock and Na adsorption. With expanded particle focus, the solid adsorption capacity for Cl− is upgraded as a result of a detailed overview of the dynamic molecular simulation studies examining the chloride diffusion coefficient. Different characteristics of the diffusion process, including molecular models, system-size effects, temperature, and pressure conditions, and the type of protection, are discussed. This paper focus on Molecular Dynamic Simulation to determine the diffusion coefficient of chloride ion and water molecules in concrete. The diffusion coefficient for NaCl salt obtained 6.60178x10-10m2/s and the diffusion coefficient for CaCl2 salt obtained 7.29305x10-10m2/s. So, the average chloride diffusion coefficient 6.9475x10-10m2/s. Diffusion coefficient obtained from graph 5.562x10-10m2/s. Diffusion coefficients for water molecules for NaCl solution are 6.125x10-10m2/s, 6.85x10-10m2/s, 1.044x10-10m2/s, 8.525x10-10m2/s, 6.25x10-10m2/s. diffusion coefficient of water molecules in CaCl2 solution are 4.5x10-10m2/s, 6.725x10-10m2/s, 1.254x10-10m2/s, 7.725x10-10m2/s, 1.3x10-10m2/s. Average value obtained for water molecule diffusion are 4.545x10-10m2/s, 7.4062x10-10m2/s and 1.149x10-10m2/s. This diffusion of chloride effects the binding of water in concrete pore.

Subtractive Proteomics Supported with Rational Drug Design Approach Revealed ZINC23121280 as a Potent Lead Inhibitory Molecule for Multi-drug Resistant Francisella tularensis

Francisella tularensis is a Gram-negative bacterium and is the etiological agent of taluremia. The prolonged use of antibiotics is the reason for pathogen resistance to antibiotics such as beta-lactams and macrolides. This leads to the search to explore novel drug targets for F. tularensis to inhibit its growth. Subtractive proteomics revealed Glucose-1-phosphate thymidylyltransferase (G1PTT) as the most promising protein as a drug target. A pharmacophore model was generated for virtual screening of a druglike library comprised of 1,000,000 drug molecules. Based on a pharmacophore-based search, a set of 152 compounds was predicted as the most potent inhibitors against this enzyme. The screened hits were docked with the target enzyme; which unveiled ZINC23121280 as the best-docked inhibitor having Autdock Vina binding energy of -7.2 kcal/mol and the GOLD score of 64.06. Moreover, the timedependent dynamic behavior of the complex was analyzed using Molecular Dynamics (MD) simulation studies that revealed a stable system with a Root Mean Square Deviation (RMSD) average value of 2.25 Å and Root Mean SquareFluctuations (RMSF) of 1.16 Å. Radial Distribution Function (RDF) predicted strong hydrogen interactions between the ligand and Trp221 from the enzyme active pocket. The higher affinity of the antagonist for the enzyme was further supported by Molecular Mechanics Energies combined with the Poisson–Boltzmann and Surface Area (MMPBSA) and or Generalized Born and Surface Area (MMGBSA) with the estimated binding free energy of −1.07 kcal/mol and −29.59 kcal/mol, respectively. Findings from this present computational framework may provide the foundation for future drug discovery against F. tularensis.

Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance.

Antimicrobial resistance (AMR) in bacterial pathogens is a major global distress. Due to the slow progress of antibiotics development and the fast pace of resistance acquisition, there is an urgent need for effective vaccines against such bacterial pathogens. In-silico approaches including pan-genomics, subtractive proteomics, reverse vaccinology, immunoinformatics, molecular docking, and dynamics simulation studies were applied in the current study to identify a universal potential vaccine candidate against the 18 multi-drug resistance (MDRs) bacterial pathogenic species from a WHO priority list. Ten non-redundant, non-homologous, virulent, and antigenic vaccine candidates were filtered against all targeted species. Nine B-cell-derived T-cell antigen epitopes which show a great affinity to the dominant HLA allele (DRB1*0101) in the human population were screened from selected vaccine candidates using immunoinformatics approaches. Screened epitopes were then used to design a multi-epitope peptide vaccine construct (MEPVC) along with β-defensin adjuvant to improve the immunogenic properties of the proposed vaccine construct. Molecular docking and MD simulation were carried out to study the binding affinity and molecular interaction of MEPVC with human immune receptors (TLR2, TLR3, TLR4, and TLR6). The final MEPVC construct was reverse translated and in-silico cloned in the pET28a(+) vector to ensure its effectiveness. This in silico construct is expected to be helpful for vaccinologists to assess its immune protection effectiveness in vivo and in vitro to counter rising antibiotic resistance worldwide.

Probing the effect of newly synthesized phenyltrimethylammonium tetrachloroaluminate ionic liquid as an inhibitor for carbon steel corrosion

The corrosion protection effect of phenyltrimethylammoniumtetrachloroaluminate[PTMA]+[AlCl4]−as an inhibitor was explored in the present work. In this paper, the authors have explored a non-heterocyclicbased ionic liquid as a corrosion inhibitor for metal protection in the acid cleaning process of metal. In particular, a negative ion is designed based onthe lewis acid concept by which it could cover the maximum surface by the bigger molecule size. The inhibition efficiency was found to be steadily increasing as the concentration of the [PTMA]+[AlCl4]− ionic liquids increased.These studies revealed thatthe inhibitor exhibited a remarkable potential for corrosion protection on carbon steel in 1 N HCl solution. Stable corrosion protection efficiency (96%) was achieved for 1.3 mMof inhibitor. The adsorption of the inhibitive molecule was studied by Langmuir adsorption isotherm. The anti-corrosion effect of ionic liquid on the surface protection was revealed by scanning electron microscope (SEM)and lower surface roughness attained at an optimum concentration of inhibitor in atomic force microscope (AFM) analysis. In this study, with the view of the experimental and theoretical investigation (gaseous and aqueous forms of [PTMA]+[AlCl4]− ionic liquid in presence of HCl)was investigated, and finding deduced that the ionic liquid offered maximum dispenses with the heterocyclic group. In addition, to validate the experimental result, dynamic simulation studies were performed in both gaseous and liquid stimulation conditions.

Molecular docking and dynamics studies of Nicotinamide Riboside as a potential multi-target nutraceutical against SARS-CoV-2 entry, replication, and transcription: A new insight

The highly contagious Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is a newborn infectious member of the dangerous beta-coronaviruses (β-CoVs) following SARS and MERS‐CoVs, can be regarded as the most significant issue afflicting the whole world shortly after December 2019. Considering CoVs as RNA viruses with a single-stranded RNA genome (+ssRNA), the critical viral enzyme RNA dependent RNA polymerase (RdRp) is a promising therapeutic target for the potentially fatal infection COVID-19. Nicotinamide riboside (NR), which is a naturally occurring analogue of Niacin (vitamin B3), is expected to have therapeutic effects on COVID-19 due to its super close structural similarity to the proven RdRp inhibitors. Thus, at the first phase of the current molecular docking and dynamics simulation studies, we targeted SARS-CoV-2 RdRp. On the next phase, SARS-CoV RdRp, human Angiotensin-converting enzyme 2, Inosine-5’-monophosphate dehydrogenase, and the SARS-CoV-2 Structural Glycoproteins Spike, Nonstructural viral protein 3-Chymotrypsin-like protease, and Papain-like protease were targeted using the docking simulation to find other possible antiviral effects of NR serendipitously. In the current study, the resulted scores from molecular docking and dynamics simulations as the primary determinative factor as well as the observed reliable binding modes have demonstrated that Nicotinamide Riboside and its active metabolite NMN can target human ACE2 and IMPDH, along with the viral Spro, Mpro, PLpro, and on top of all, RdRp as a potential competitive inhibitor.

Strategic analyses to identify key structural features of antiviral/antimalarial compounds for their binding interactions with 3CLpro, PLpro and RdRp of SARS-CoV-2: in silico molecular docking and dynamic simulation studies

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel member of the betacoronavirus family is a single-stranded RNA virus that has spread worldwide prompting the World Health Organization to declare a global pandemic. This creates an alarming situation and generates an urgent need to develop innovative therapeutic agents. In this context, an in silico molecular docking and molecular dynamics (MD) simulation study on the existing 58 antiviral and antimalarial compounds was performed on 3CLpro, PLpro and RdRp SARS-CoV-2 proteins. The antiviral compounds are best fitted in the binding pockets and interact more profoundly with the amino acid residues compared to antimalarial compounds. An HIV protease inhibitor, saquinavir showed a good dock score and binding free energy with varied binding interactions against 3CLpro and PLpro. While, adefovir, a nucleotide HBV DNA polymerase inhibitor exhibited good dock score and binding interactions against RdRp. Although, the antimalarial compounds showed relatively less dock score but were found to be crucial in displaying essential binding interactions with these proteins. The MD simulation runs for 100 ns on 3CLpro–saquinavir, PLpro–saquinavir and RdRp–adefovir complexes using Desmond revealed fairly stable nature of interactions. This study helped in understanding the key interactions of the vital functionalities that provide a concrete base to develop lead molecules effective against SARS-CoV-2.

Solvatochromism of a D205 indoline dye at the interface of a small TiO2-anatase nanoparticle in acetonitrile: a combined molecular dynamics simulation and DFT calculation study

ABSTRACT A combined molecular dynamics (MD) simulation and density functional theory (DFT) calculations were used to investigate the effect of the acetonitrile (ACN) solution on the absorption and the charge transfer in a D205 indoline dye at the interface of a TiO2 nanoparticle. DFT calculations were carried out to estimate the equilibrium geometry of a small Ti30O62H4-anatase nanoparticle and to derive interaction parameters for bidentate binding of a D205 dye to TiO2. A series of the D205 dye configurations anchored to Ti30O62H4 were generated from the MD simulations and used as input for the time-dependent DFT (TD-DFT) calculations. We found that the immersion of the D205-Ti30O62H4 composite system into the polar ACN environment results in conformational changes of the dye moiety, which are accompanied by the solvatochromic redshift of its long-wavelength absorption band up to 1900 cm-1. Our results show that the HOMO and LUMO energy level alignment of the dye and the nanoparticle suggests a favourable driving force for charge transfer from the dye to TiO2. The MD/TD-DFT-estimated solvatochromic shift for the D205 dye at the TiO2/ACN interface is in good agreement with the experiment, showing that such computational approach enables reliable predictions of optical properties of other dye-TiO2 composites in solution.

Shading devices applied to sun control in occupied spaces in summer conditions

This work presents a study of a numerical building dynamic simulation in the development of a horizontal shading device passive solution applied in a university canteen. The used building dynamic simulation software, that simulates simultaneously a building or groups of buildings with complex topologies, in transient conditions, considers the solar radiation, the HVAC system, glass radiative proprieties, radiative heat exchanges, thermal solutions, thermal comfort of occupants, indoor air quality, among others properties. The development of efficient external horizontal shading devices is made by a numerical model that uses the sun's trajectory and its position in relation to the windows where it falls. The canteen is constituted by three levels and is divided in 37 spaces. In the numerical simulation, 100 transparent surfaces and 773 opaque surfaces are considered. Special attention is given in the students’ main canteen, professors’ main canteen, specialized canteen and university bar. The simulation is made, in summer conditions, considered the selected spaces without and with horizontal shading devices placed above their windows. In the simulation, the occupancy and the implemented ventilation system are considered. Regarding to the obtained results the use of horizontal shading devices can reduce the air temperature range and improve the thermal comfort level that the occupants are subjected in some of the analyzed spaces.

Computational Screening of FDA Approved Drugs from ZINC Database for Potential Inhibitors of Zika Virus NS2B/NS3 Protease: A Molecular Docking and Dynamics Simulation Study

Zika virus is a mosquito borne pathogen with a single strand RNA genome. Human infection with this virus is usually asymptomatic, however outbreaks reported in both Pacific region and Latin America have been associated with increase in frequency of microcephaly in newborns and fetuses of infected mothers. Also, the incidence of Guillain-Barré syndrome had also increased among adults with Zika virus infection. Currently, neither vaccine nor antiviral drug has been developed against Zika virus. Structure based virtual screening can be employed, through drug repurposing strategy, to accelerate the identification of potential anti-Zika virus candidates. As such, virtual screening of approved drugs against Zika virus NS2B/NS3 protease can help to recognize new hits capable of hindering viral ability to replicate and evade immune system of the host. In this computational study, we have screened 1615 FDA approved drugs against NS2B/NS3 protease enzyme of Zika virus by using both molecular docking and dynamics simulation. Our virtual screening results indicate that the anti-muscarinic agent Darifenacin and the anti-diarrheal agent Loperamide may have a promising capacity to inhibit Zika virus NS2B/NS3 protease. According to molecular docking and dynamics simulation, these two approved drugs have good binding capacity to NS2B/NS3 as reported by docking energy of binding and MM-PBSA binding energy. In addition, both Darifenacin and Loperamide were able to maintain close proximity to protease crystal throughout simulation period. However, invitro evaluation of these two drugs against Zika virus NS2B/NS3 protease is required to confirm these computational results.

Identification of plant-based hexokinase 2 inhibitors: combined molecular docking and dynamics simulation studies

Cancer cells ferment glucose, even under aerobic conditions, following a phenomenon known as the ‘Warburg effect.’ Hexokinase 2 (HK2) catalyzes the crucial step of phosphorylation of glucose for subsequent utilization in glycolysis and other pathways. HK2 has been proposed as a potential therapeutic target for anti-cancer therapy because of its enhanced expression in glucose-dependent tumors. Here, we have employed structure-based virtual screening using in-house library to identify potential phytoconstituents which could inhibit the HK2 activity. The initial hits were selected based on their binding affinity towards HK2 using the molecular docking approach. Subsequently, the filters for physicochemical properties, PAINS patterns and PASS evaluation were applied to find potential hits against HK2. Finally, we have identified epigallocatechin gallate (EGCG) and quercitrin, two natural compounds with appreciable binding affinity, efficiency and specificity towards the HK2 binding pocket. Both compounds were found to be binding preferentially to the HK2 active site and showed a decent set of drug-like properties. All-atom molecular dynamics (MD) simulations for 100 ns were carried out to see the conformational dynamics, complexes stability and interaction mechanism of HK2 with EGCG and quercitrin. MD simulation results showed that HK2 forms stable protein-ligand complexes with EGCG and quercitrin with consistency throughout the trajectory. Overall, these findings suggest that EGCG and quercitrin might be further exploited as promising scaffolds in the drug development process against HK2.. Communicated by Ramaswamy H. Sarma