Favorable Regions Research Articles

QSAR, homology modeling, and docking simulation on SARS-CoV-2 and pseudomonas aeruginosa inhibitors, ADMET, and molecular dynamic simulations to find a possible oral lead candidate

BackgroundIn seek of potent and non-toxic iminoguanidine derivatives formerly assessed as active Pseudomonas aeruginosa inhibitors, a combined mathematical approach of quantitative structure-activity relationship (QSAR), homology modeling, docking simulation, ADMET, and molecular dynamics simulations were executed on iminoguanidine derivatives. ResultsThe QSAR method was employed to statistically analyze the structure-activity relationships (SAR) and had conceded good statistical significance for eminent predictive model; (GA-MLR: Q2LOO = 0.8027; R2 = 0.8735; R2ext = 0.7536). Thorough scrutiny of the predictive models disclosed that the Centered Broto-Moreau autocorrelation - lag 1/weighted by I-state and 3D topological distance-based autocorrelation—lag 9/weighted by I-state oversee the biological activity and rendered much useful information to realize the properties required to develop new potent Pseudomonas aeruginosa inhibitors. The next mathematical model work accomplished here emphasizes finding a potential drug that could aid in curing Pseudomonas aeruginosa and SARS-CoV-2 as the drug targets Pseudomonas aeruginosa. This involves homology modeling of RNA polymerase-binding transcription factor DksA and COVID-19 main protease receptors, docking simulations, and pharmacokinetic screening studies of hits compounds against the receptor to identify potential inhibitors that can serve to regulate the modeled enzymes. The modeled protein exhibits the most favorable regions more than 90% with a minimum disallowed region less than 5% and is simulated under a hydrophilic environment. The docking simulations of all the series to the binding pocket of the built protein model were done to demonstrate their binding style and to recognize critical interacting residues inside the binding site. Their binding constancy for the modeled receptors has been assessed through RMSD, RMSF, and SASA analysis from 1-ns molecular dynamics simulations (MDS) run. ConclusionOur acknowledged drugs could be a proficient cure for SARS-CoV-2 and Pseudomonas aeruginosa drug discovery, having said that extra testing (in vitro and in vivo) is essential to explain their latent as novel drugs and manner of action.

Abstract 3357: Identification and validation of novel molecular inhibitors from the DrugBank drug library

Abstract Background: The 3D crystal structure of a protein determines its overall function, and when the structure of a protein is known, small drug molecules can be designed to bind to it and inhibit its function. Target-based drug discovery, specifically for genetic products that cause a higher risk of disease (genetic targets), takes advantage of this fact in particular. This type of drug discovery is essential for combating various cancer protein targets, including ones responsible for multidrug- resistance in liver cancer, like YB-1. Methods: The RCSB protein data bank (PDB) was used to retrieve the crystal structure of YB-1, while the DrugBank database was used to obtain a list of experimental and approved drugs. A multiple sequence alignment (MSA) of YB-1 and Lin28, a known transcription factor, was then done by Clustal Omega to validate a conserved domain. Biovia Discovery Studio 2020 was used to visualize 3D models and perform a High-Throughput Virtual Screening (HTVS), including rigid docking via the LibDock extension and flexible docking via the CDocker extension pharmacokinetic profiling via an ADMET analysis. A literature search was conducted to finalize a list of potential cancer protein inhibitors. The most promising compounds were then tested in vitro on associated liver cancer cell lines and checked for expression of YB-1 related downstream target genes (including those related to multiple-drug resistance) via real-time PCR, protein expression via western blot analysis, and YB-1 translocation via immunofluorescence. Results: Utilizing this approach, we obtained a protein model with a 97.3 percentage in the most favorable region of a Ramachandran plot. Twenty-two drug candidates were identified through HTVS as potential inhibitors of a specific cancer protein target from a list of over 10,000 compounds in the DrugBank library. The best six show a decent binding ability in both rigid and flexible dockings and have been previously tested in different cancer types to some extent. The data on YB-1 stability and function and translocation efficiency modulated by the identified drugs will be presented. Conclusions: Studying protein-drug interactions is of particular importance for understanding how structural protein elements affect overall ligand affinity. By taking a bioinformatics approach to analyzing drug-protein interactions, we can drastically increase the speed with which we identify potential inhibitors for cancer protein targets. Citation Format: Omar Karkoutly, Anupam Dhasmana, Kyle Doxtater, Sudhir Kotnala, Kristopher Ezell, Sophia Leslie, Adithya Anilkumar, Samantha Lopez, Subhash Chauhan, Manish Tripathi. Identification and validation of novel molecular inhibitors from the DrugBank drug library [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3357.

Evaluation of Lignin Degrading Ability and In-silico Analysis and Molecular Docking of Laccase of Schizophyllum commune with Lignin

White-rot fungi have a unique and strong ability to degrade lignin, the most abundant and the strongest natural polymer on earth. The ligninolytic enzymes of these fungi comprise of three groups of oxidative extracellular enzymes mainly, lignin peroxidase (LiP), manganese dependent peroxidase (MnP) and laccase. Fungal laccases are considered to be directly involved with the degradation of lignin. Due to the broad substrate specificity and unique ability of biodegradation, fungal laccases have a great value in industrial and biotechnological applications like bioremediation, detoxification of industrial dyes and treatment of other pollutants. The objectives of this study was to evaluate the lignin degradation ability and laccase producing ability of selected fungal isolates originated from decaying hardwoods of Dimbulagala forest reserve, Sri Lanka and to predict the three-dimensional (3D) structure of laccase from Schizophyllum commune and its binding to lignin using in silicohomology modeling and molecular docking. Ten fungal isolates originated from decaying hardwoods were screened for the lignin degradation ability by using lignin amended malt extract plate assay and laccase producing ability by using guaiacol amended PDA plates. Seven isolates showed lignin degradation ability and five of them were laccase producers. Since S. commune could produce laccase, degrade lignin and laccase protein sequence is available, it was subjected to homology modeling. Homologous templates were identified using BLASTP across Protein Data Bank from NCBI. Laccase from Cerrena sp. was selected as the template for 3D model building of laccase from S. commune using Modeller 10.1. The quality of resulted 3D model of the protein was verified by its energy and stereochemical properties. The unstable regions were selected and remodeled by loop modelling using ModLoop web server. The results of evaluation of the remodeled structure by stereochemical quality and energy was found to be improved and showed that predicted model was of good quality due to the presence of maximum residues in the favored region. Later CB-Dock server was used to perform molecular docking studies using lignin model compounds. The amino acid residues of modeled laccase of S. commune in contact with the lignin based model compounds were identified. These findings help uncovering the lignin degradation mechanisms by S. communelaccases and are useful in biofuel production and bioremediation.
 Keywords: Laccase, Homology modeling, Molecular docking, LigninAcknowledgement: Authors acknowledge the TWAS research grant (18-020 RG/BIO/AS_I), ICGEB research grant (CRP/LKA18-03) and NSF Sri Lanka (RG/2019/BT/03)

Structural, functional, phylogenetic, and molecular dynamic simulation study of PEST-containing nuclear protein: An e-science view

PEST-containing nuclear protein (PCNP) is a short-lived novel nuclear protein. It has been well evaluated that PCNP mediates the progression of several cancers, but the exact mechanisms are still under investigation. In this study, we provided an e-science view of PCNP protein from the aspects of protein structure, interactions, and bioinformatics-based analysis related to evolutionary features as well as proteomic profile. The phylogenetic relationship results reveal that PCNP is closely related to Pan troglodytes and the Bovidae family, while being distantly related to the Muridae family. The analysis of the physicochemical properties of PCNP demonstrated that it is a thermolabile protein which is slightly acidic and hydrophilic in nature. Further, coexpression and protein-protein interaction analyses were carried out, which demonstrated that the PCNP gene was remarkably expressed with MORF4LI and RSL24D1 genes and has close interactions with TRAM1, PSMC6, SRP9, PRKRIR, UHRF2, and BMI1 proteins. Gene ontology and pathway enrichment analyses showed that PCNP has a high tendency to work in cell cycle regulation. Moreover, among the four 3D structure generating tools, I-TASSER-generated structure had the highest quality factor score. The validation analysis revealed that the I-TASSER-generated structure exhibited the best quality factor score with maximum amino acids in the favored region. In addition, molecular dynamic simulation analysis approved the stable structure of the PCNP. This is the first study that highlights the usefulness of the understanding of the structural and functional analysis of the PCNP, which lays the groundwork for further experimental studies to validate the outcome.

In Silico Modeling and Docking Analysis of CTX-M-5, Cefotaxime-Hydrolyzing β-Lactamase from Human-Associated Salmonella Typhimurium

Objective: To computationally model the CTX-M-5 β-lactamase and establish its structure, which is exclusively present in human-associated Salmonella. Methods: The CTX-M-5 aminoacid sequence (Uniprot ID:O65975) of Salmonella enterica subsp. enterica serovar typhimurium was retrieved from UniProt database and subjected to homology modeling using MODELLER 9v7. The homology models were duly validated using RAMPAGE tool by generating Ramachandran plots, ERRAT graphs, and ProSA score. DoGSiteScorer server and ConSurf server were used to detect the cavities, pockets, and clefts to identify conserved amino acid sites in the predicted model. Subsequently, the modeled structure was docked using CLC Drug Discovery Workbench against proven drugs and known inhibitors. Results: Obtained high-quality homology model with 91.7% of the residues in favorable regions in Ramachandran plot and qualified in other quality parameters. Docking studies resulted in a higher dock score for PNK (D-benzylpenicilloic acid) molecule when compared to other reported inhibitors. Conclusion: This in silico study suggests that the compound PNK could be an efficient ligand for CTX-M-5 β-lactamase and serve as a potent inhibitor of CTX-M-5.

Multiparametric Identification of Favorable Regions for Wind or Solar Generation in the State of Pernambuco

The capacity for renewable energy generation, particularly solar and wind, tends to grow over the years. However, locating regions favorable to the development of solar and wind generation is not trivial and is subject to errors due to the social, environmental, economic, political and administrative aspects of the regions. Therefore, this article proposes an algorithm based on digital image processing, capable of performing a variable weight multi-parameter evaluation and quantifying how favorable a given territorial region is for the implantation of wind or solar plants. Maps of the region under analysis are taken as input information. The region taken as a case study is the Brazilian state of Pernambuco, due to the access to data related to the evaluated characteristics: solar radiation, solar insolation, precipitation, air humidity, temperature, electrogeography, demographic density, environmental protection areas, slope, hydrography, wind speed, urban spot and the presence of aerodromes. It was possible to list for each type generation (wind or solar, exclusively), the 15 most favorable regions for the implementation plants. Furthermore, the proposed technique presents a practical indifference to the territorial extension of the evaluated region, which can comprehend a micro-region or an entire continent, requiring only that sufficiently detailed maps of the evaluated characteristics be provided.

Comparative modeling, comparative molecular docking analyses, and revealing of potential binding pockets of MDM-2: A candidate cancer gene

MDM-2 is also known as E3 ubiquitin-protein ligase encoded by Mdm-2. MDM-2 is an important negative regulator of p53 tumor suppressor and performs key function as an inhibitor of p53 transcriptional activation and E3 ubiquitin ligase. MDM-2 also plays significant role in human cancers and therapeutic target. Hundred different structures were predicted through comparative modeling, threading and ab initio approaches followed by the evaluation of predicted structures through various evaluation tools including ERRAT, ProSa-web, Rampage, molprobidity, verify3D and Anolea. The selected 3D structure of MDM-2 showed 13 α- helix chains, 2 β-pleated sheets along with 97.4468% overall quality factor of the predicted structure. Interestingly, it was observed that only 4.5% residues were present in outlier region and the observed errors were fixed. Moreover, 91.1% residues of the selected structure were present in favored region and 8.9% in allowed region having -6.0 Z-score. High throughput virtual screening and comparative molecular docking studies was performed. Four novel compounds have been reported that showed minimum binding energy (-8.1 Kcal/mol) and maximum binding affinity against MDM-2. Molecular docking analyses revealed that Ser154, Arg155, Pro156, Ser157, Lys185, Ser186, Ser188, Ser190, Ile189, Val247, Glu257, Asp173, Glu174, Glu178, Arg161, Ard181, Lys182, Arg183 and His184 residues are significant residues for therapeutic drug targets. The reported compounds showed effective energy scores. In addition, the site-directed mutagenesis may be helpful for further analyses. The reported compounds may act like potent drug compounds against MDM-2.

3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules

A fast way to reconstruct and validate the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil so far in late 2021, the lineage B.1.1.28/P.1. The proposed methodology is based on the sequencing of virus proteins and that, through the incorporation of mutations in silico, which are then computationally reconstructed using an enumerative feasibility algorithm validated by the Ramachandran diagram and structural alignment, in addition to the subsequent study of structural stability through classical molecular dynamics. From the resulting structure to the ACE2-RBD complex, the valid solution presented 97.06\% of the residues in the most favorable region while the reference crystallographic structure presented 95.0\%, a difference therefore very small and revealing the great consistency of the developed algorithm. Another important result was the low RMSD alignment between the best solution by the BP algorithm and the reference structure, where we obtained 0.483 A. Finally, the molecular dynamics indicated greater structural stability in the ACE2-RBD interaction with the P.1 strain, which could be a plausible explanation for convergent evolution that provides an increase in the interaction affinity with the ACE2 receptor.

Image Recognition–Based Identification of Multifractal Features of Faults

Geologists have made several advances in applying multifractal theory in geology; however, some questions such as a large statistical workload and low efficiency remain unanswered. Thus, this study proposes an image recognition–based method for calculating fault multifractality. First, grayscale processing and binarization of the fault distribution map were performed. The image was then gridded, and the grids were numbered. Subsequently, computer image recognition technology was used to count the number of faults in each grid as a replacement for manual counting. Finally, the fractal dimensions of the faults were calculated using a multifractal box-counting algorithm. This method was successfully applied to fracture studies of the Maokou Formation in southeast Sichuan. Compared to the conventional approach, the proposed method demonstrated considerably improved work efficiency and accuracy. The results showed that the faults in the study area exhibited good statistical self-similarity in the scale range, indicating fractal characteristics. The fractal dimensions of faults with different orientations and the planar distribution of the fractal dimension contours indicate tectonic stages and stress magnitude in the study area. The results indicate that the tectonic setting of southeast Sichuan was formed primarily during the Indosinian, Yanshanian, and Himalayan periods. From the Indosinian to the early Yanshanian periods, NE-trending faults with relatively large fractal dimensions developed under NW–SE compressional tectonic stress. From the Late Yanshanian to Early Himalayan, EW-trending faults were formed by relatively weak N–S compressional stress and had the lowest fractal dimensions. The NW-trending faults formed by intense NE–SW compressional tectonic stress in the Late Himalayan region had the highest fractal dimensions. To promote oil and gas migration and ensure that faults do not destroy the caprock, oil and gas reservoirs must be in a relatively mild tectonic environment. Thus, the fractal dimensions of faults in favorable areas should be neither too high nor too low. The relationship between the fractal dimensions of faults and well test results in southeast Sichuan indicates that the region along the wells “ls1–xia14–guan3” (with fractal dimensions of 1.49–1.57) in the study area is a relatively favorable region for oil and gas preservation.

Generation of wild-type rat Glucocerebrosidase homology modeling: Identification of putative interactions site and mechanism for chaperone using combined in-silico and in-vitro studies

Disease-modifying treatment strategy for Parkinson’s disease (PD) by stabilization of Glucocerebrosidase (GCase) enzyme by chaperones is of particular interest. Wild-type rat is a widely used animal model for PD; however, the in-silico model to elucidate the nature of rat GCase (rGCase)-chaperone interactions, mechanisms, and structural stability is still unavailable. Hence, we have developed pH-dependent rGCase homology models, in-silico (docking and molecular dynamics), and in-vitro techniques (enzyme kinetics and thermal stability) to address this gap. The homology modeling results revealed ≥ 90% rGCase residues were in the favored regions, representing adequate models quality. In-silico studies showed an interaction between chaperone (Ambroxol, AMB) and the active site residues TYR 331, TYR 263, GLN 266, and GLU 358 with the higher affinity at neutral pH than acidic pH. In-vitro studies showed higher inhibitory activity (IC50) and binding affinity (Ki) of AMB at neutral pH (IC50: 8.2 ± 2.6 µM and Ki: 4.3 ± 1.2 µM) than acidic pH (IC50 and Ki: not identified). AMB improved rGCase thermostability was confirmed by thermal denaturation assay. We have developed the homology model for rGCase, which provides a perspective for designing and screening the chaperones at the initial phases of drug discovery to ameliorate PD.

Effect of annealing treatment on microstructure evolution and deformation behavior of 304 L stainless steel made by laser powder bed fusion

This paper focuses on the microstructural evolution of 304 L austenitic stainless steel (SS) manufactured by laser powder bed fusion (LPBF) after stress-relieving annealing (650 °C) and solution annealing (1050 °C). Multiple advanced characterizations were adopted to disclose the microstructural characteristics and investigate the annealing-driven dislocation migration process. At 650 °C, the dislocation density of cellular walls decreased slightly, associated with a slight decrease of strength. At 1050 °C, the dislocations of cellular walls migrated to more energetically favorable regions, forming subgrain boundaries with higher dislocation density and resulting in a strength-ductility trade-off. The temperature of 1050 °C could slightly increase the recrystallization volume fraction and induce the coalescence of multi-oriented fine-grained tribes into single-oriented grains. The nano-scale characterization indicated that the as-built samples and annealed samples at 650 °C contained the square lattice distortion networks composed of orthogonal strain ripples. However, after annealing at 1050 °C, only unidirectional strain ripples in square lattice distortion networks were retained due to unidirectional dislocation migration. Direct experimental results were provided that the local misorientation ranges of cellular interior, cellular walls, and newly formed subgrain boundaries were <0.2°, 0.2°-0.5°, and 0.5°-2°, respectively. After tensile deformation, interacting deformation twins occurred in <111> and 〈101〉 oriented grains of as-built and annealed specimens at 650 °C, while the twins occurred in all oriented grains of annealed specimens at 1050 °C due to the disappearance of cellular substructure and the increase of tensile elongation. This work yields new insights into misorientation across the cellular walls, dislocation migration process during annealing, strengthening mechanisms, and work hardening behaviors, which can be used to design and optimize future annealing routines for LPBF materials.

Indazole Derivatives Effective against Gastrointestinal Diseases.

In this fast-growing lifestyle, humans are in the race against time to cope up with busy schedule. Less exercise, consumption of high calorie-low fiber food and stress take us one step closer towards digestive dysfunction. Dysfunctional digestive system causes various gastrointestinal disorders like constipation, IBS, UC, diarrhea, gastrointestinal tract immobility, hyperglycemia, hemorrhoids, fistula, anal fissures, stomach cancer, hepatocellular carcinoma, pancreatic cancer, colon cancer and metabolic syndrome. Amongst various natural and synthetic indazole derivatives nigellicine, nigellamine, nigellidine, zanubrutinib and SCH772984 showed prominent results to cure various gastrointestinal disorders. In this manuscript, we focus on the importance of indazole derivatives in the treatment of various gastrointestinal diseases. In the treatment of IBS, four positions (R1, R2, R3 and R4) of indazole were mainly substituted with aromatic aldehyde/substituted methyl, aromatic acid/formamide, benzamide/ sulfonamide and methyl groups, respectively. In case of diarrhea and metabolic syndrome treatment, substitutions with benzyl/isopropyl/acetaldehyde (R1 position) and carboxamide/ formamide (R2 position) of indazole play a critical role. Also, in the treatment of diabetes melitus, all six positions of indazole derivative were substituted with substituted aryl/alkyl/aromatic acid, substituted formamide, substituted acetamide/hydrazide group, halo aryl, substituted aryl/aromatic acid and a long chain of alkyl-aryl alcohol groups, respectively. In the treatment of gastrointestinal cancers, all six positions of indazole derivative were substituted with benzylamide (R1), octanediamide/ benzamide/formamide (R2), carbaldehyde (R4) and substituted phenyl (R5 and R6) groups, respectively. Six receptors (6NP0, 2YME, 4EFU, 4WZ8, 5U4W and 7KKP) associated with GI disorders (co-crystallized with indazole derivative) were identified. Analysis of the receptors showed that co-crystalized ligand molecules were well-interacted with receptors via pie-pie interaction, coordinate and sigma bonding within 4 Å distance. As per Ramachandran plot analysis, more than 90% of the amino acid residues were present in the most favored region. So, if sufficient focuses are imposed on the development of newer indazole derivatives to treat gastrointestinal diseases, it will work as a boon to society.

In silico evaluation of inhibitors of Plasmodium falciparumAP2‐I transcription factor

Recent treatment failures observed for Artemisinin‐based combination therapy (ACT) have raised concerns about the efficacy of the front‐line drug to treat malaria and the need to develop a new antimalarial drug regimen. Plasmodium falciparum Apicomplexan Apetala 2 Invasion (PfAP2‐I) transcription factor (TF) is a protein that regulates the expression of a subset of gene families involved in Plasmodium falciparum red blood cell (RBC) invasion. Inhibiting PfAP2‐I TF with small molecules represents a potential new antimalarial therapeutic target to combat drug resistance, which is the aim of this study. The 3D model structure of PfAP2‐I was predicted ab initio using ITASSER and ROBETTA prediction tools and was validated using Errat and Procheck from the Save server 6.0. Computed Atlas of Surface Topography of proteins (CASTp) 3.0 and ConCavity were used to predict the active sites of the PfAP2‐I 3D7 modeled structure. Pharmacophore modeling of the control ligand (3W7 from COACH server) and modeled 3D structure of PfAP2‐I was carried out using the Pharmit server to obtain several compounds for docking analysis. Chimera software was used to remove the complexed ligands, and the modeled protein structure was defined as a receptor. Virtual screening and post‐screening studies were conducted using AutoDock vina and LigPlot. The designed ligands’ toxicity predictions and in silico drug‐likeness were performed using the Swiss ADME predictor and OSIRIS Property Explorer. The modeled protein from the ROBETTA prediction tool was prioritized based on structure validation results of 96.827 for ERRAT and 90.2% of the amino acid residues in the most favored region for the Ramachandran plot. A total of 8656 compounds obtained from six (6) databases on the Pharmit server were used to prepare the ligand library and screened against the prepared 3D model structure of PfAP2‐I, considering the active sites predicted from CASTp and ConCavity. Six (6) best hits were selected based on the binding affinity to the active site PfAP2‐I and were considered for post‐screening analyses. The six compounds exhibited dock score values (between ‐9.9 to ‐10.2 kcal/mol), having lower binding energies than the standard drug ‐ Chloroquine (‐5.10 kcal/mol). The best dock score was compound ZINC97139187 (‐10.2 kcal/mol). For the ADMET properties, compound ZINC97139187 had the highest drug score of 0.63, followed by compound 154861216 with a drug score of 0.58 (both higher than that of the standard drug ‐ chloroquine of 0.25). The good, estimated binding energies and drug score values observed for compound ZINC97139187 and compound 154861216 suggest that they can be considered possible PfAP2‐I inhibitors. Further pre‐clinical experimental validations should be carried out to ascertain the efficacy of these predicted best hits.

Characterization of sulfated polysaccharide activity against virulent Plasmodium falciparum PHISTb/RLP1 protein.

Background: The emergence of artemisinin resistance in South East Asia calls for urgent discovery of new drug compounds that have antiplasmodial activity. Unlike the classical compound screening drug discovery methods, the rational approach involving targeted drug discovery is less cumbersome and therefore key for innovation of new antiplasmodial compounds. Plasmodium falciparum (Pf) utilizes the process of host erythrocyte remodeling using Plasmodium-helical interspersed sub-telomeric domain (PHIST) containing proteins, which are amenable drug targets. The aim of this study is to identify inhibitors of PHIST from sulfated polysaccharides as new antimalarials. Methods: 251 samples from an ongoing study of epidemiology of malaria and drug resistance sensitivity patterns in Kenya were sequenced for PHISTb/RLP1 gene using Sanger sequencing. The sequenced reads were mapped to the reference Pf3D7 protein sequence of PHISTb/RLP1 using CLC Main Workbench. Homology modeling of both reference and mutant protein structures was achieved using the LOMETs tool. The models were refined using ModRefiner for energy minimization. Ramachandran plot was generated by ProCheck to assess the conformation of amino acids in the protein model. Protein binding sites predictions were assessed using FT SITE software. We searched for prospective antimalarials from PubChem. Docking experiments were achieved using AutoDock Vina and analysis results visualized in PyMOL. Results: Sanger sequencing generated 86 complete sequences. Upon mapping of the sequences to the reference, 12 non-synonymous single nucleotide polymorphisms were considered for mutant protein structure analysis. Eleven drug compounds with antiplasmodial activity were identified. Both modeled PHISTb/RLP1 reference and mutant structures had a Ramachandran score of >90% of the amino acids in the favored region. Ten of the drug compounds interacted with amino acid residues in PHISTb and RESA domains, showing potential activity against these proteins. Conclusion: This research identifies inhibitors of exported proteins that can be used in in vitro tests against the Plasmodium parasite.

Chinese tourism enterprises’ host country choice for overseas investment: influencing factors, interactive effects, and national heterogeneity

ABSTRACT Despite being the second-largest overseas investment country and the largest outbound tourist source country in the world, China’s overseas investment in tourism has seldom been discussed. We performed a negative binomial regression on a sample of 73 host countries of China’s overseas tourism investment to systematically identify relevant influencing factors and interactive effects from 2004 to 2018 via national heterogeneity test on countries along the Belt and Road (B&R). Results indicate that, (1) Chinese tourism enterprises’ overseas investment had clear market-seeking and strategy-seeking motivations but no significant tourism resource–seeking motivation. (2) Chinese tourism enterprises’ overseas investment favoured regions with a sound institutional environment, showing significant national heterogeneity in general; specifically, Chinese tourism enterprises’ overseas investment featured an institutional risk preference for countries along the B&R and institutional risk aversion for non-B&R countries.(3) Chinese tourism enterprises’ overseas investment exhibited institutional preferences and path dependence due to multiple investment motivations and bilateral political relations during location selection. Strong and stable bilateral relations were complementary to the host country’s institutional quality, namely mutual high-level government visits. International sister city relations between China and B&R countries could also compensate for the impact of poor bilateral relations on host countries’ institutional quality.

Oscillation of the shock train under synchronous variation of incoming Mach number and backpressure

Experiments were conducted to characterize shock train oscillation under the simultaneous variation of the incoming Mach number and backpressure. Under steady and low-frequency oscillatory backpressure (2 Hz), the incoming Mach number varied from 1.8 to 2.4. According to the intersection of downgoing background wave with bottom front leg, Mach stem, and top front leg of the normal shock train leading edge, the normal shock train/background wave interaction can be divided into three types. Two types of oblique shock train/background wave interaction exist. The downgoing (upgoing) background wave upstream of the oblique shock train can cause the upgoing (downgoing) shock in the shock train leading edge to become the dominated shock. Two modes of shock train oscillation were found: oscillation mode 1, in which the shock train oscillated in the favorable gradient region of the relaxing boundary layer, and oscillation mode 2, where the shock train enters the adverse pressure gradient region caused by the impingement of background wave. Compared with mode 1, mode 2 leads to a larger upstream movement of the shock train and more intense pressure fluctuation. The oscillation of the shock train is caused by instability in the separation region behind the shock train leading edge. The oscillatory backpressure only affected the motion of shock train during each oscillation period. The overall movement trend of shock train is determined by the incoming Mach number and the mean value of backpressure. The increase of incoming Mach number and backpressure can lead to the enhancement of shock train oscillation.

Identification of groundwater potential zones in southern India using geospatial and decision-making approaches

The present study was carried out to identify of the groundwater potential zones (GWPZ) in the northern part of the Anantapur district of Andhra Pradesh State, India using Remote Sensing (RS), Geographical information system (GIS), and Analytical Hierarchy Process (AHP) approaches. In this study, various thematic maps categorized viz. geomorphology (GM), lineament density (LD), drainage density (DD), geology, land use/land cover (LULC), soils, slope, and rainfall for assessment of GWPZs, which is generated using RS and GIS technique. Furthermore, the relative weights were allocated to various thematic maps using the AHP approach and the relative rank assigned to each sub-criterion based on expert advice. The combination of the eight thematic layers in ArcGIS resulted in a groundwater potential map, providing the information about very good 2.45% (87.06 km2), good 12.76 (452.56 km2), moderate 63.47% (2250.75 km2), poor 15.99% (567.16 km2), and very poor 5.32% (188.73 km2) groundwater possible zones. The acquired outcomes were validated with the area under the curve (AUC/ROC) method. The results show that there is a strong positive correlation between the GWPZs with 78% validation high performance and decreases to the low yield potential with poor areas. This study concludes that the AHP model will be a more reliable for the assessment of the GWP. Any groundwater management project carried out in these favourable regions would benefit the stack holders.

EVALUATION OF STRUCTURAL, MOLECULAR INTERACTION AND SIMULATION STUDY OF L-ASPARAGINASE OF Streptomyces koyangensis

A vital step in drug discovery is structural and interaction assessment. L-asparaginase is a highly used compound in various treatment regimens which includes combinational therapies. The application is not only limited to treating Acute lymphoblastic leukemia, where it is also found effective for myeloid leukemia and canine lymphoma. The study details about L-asparaginase of Streptomyces koyangensis (WP_203215894). Structural insights are obtained by evaluation with GalaxyTBM. The constructed 3D-model is based on L-asparaginase models belonging to Escherichia coli, Wolinella succinogenes and Helicobacter pylori. The Ramachandran assessment corresponds to 91.4% of residues in the favourable region while ProSA infers to -8.9 Z-score. Further, QMEAN4 score of -0.46, 92.903 ERRAT score as well as 100% of residues in agreement with Verify3D theory describe the quality of the protein to be good and acceptable. The protein is identified to be secreted in the cytoplasm as per subsequent CELLO version2.5. Docking studies involving L-asparaginase (WP_203215894) molecule with L-asparagine resulted in the lowest energy of -4.5 kcal/mol along with prominent active sites recognized by PyRx. Similar prediction in addition to -4.6 and -4.8 kcal/mol is also resulted by CB-Dock. Further, the binding conformation referring to affinity of -4.5 kcal/mol is also supported by the interpretation of GalaxySite with identification of the same residues involved in ligand interaction. High values of affinity correspond to the analysis by SwissDock referring to -9.42 kcal/mol. The RMSF plot generated as part of protein flexibility analysis by CABS flex 2.0 depicted varied fluctuations however, the crucial residues interacting with the ligand are computed to have RMSF value &lt; 2 represents rigidity. The therapeutic effectiveness of the enzyme has created interest in terms of tracing prospective sources and conducting computational analysis. The anticipated structure of WP_203215894 and derived assumptions are helpful and contribute valuable information for future in-vitro findings on L-asparaginase.

BEST impact on sterile neutrino hypothesis

Recently the Baksan Experiment on Sterile Transitions (BEST) has presented results confirming the gallium anomaly -- a lack of electron neutrinos $\nu_e$ at calibrations of SAGE and GALLEX -- at the statistical significance exceeding 5$\,\sigma$. This result is consistent with explanation of the gallium anomaly as electron neutrino oscillations into sterile neutrino, $\nu_s$. Within this explanation the BEST experiment itself provides the strongest evidence for the sterile neutrino among all the previous anomalous results in the neutrino sector. We combine the results of gallium experiments with searches for sterile neutrinos in reactor antineutrino experiments (assuming CPT-conservation in the $3+1$ neutrino sector). While the "gallium" best fit point in the model parameter space (sterile neutrino mass squared $m_{\nu_s}^2\approx 1.25\,$eV$^2$, sterile-electron neutrino mixing $\sin^22\theta\approx 0.34$) is excluded by these searches, a part of the BEST-favored 2$\,\sigma$ region with $m^2_{\nu_s}>5\,$eV$^2$ is consistent with all of them. Remarkably, the regions advertised by anomalous results of the NEUTRINO-4 experiment overlap with those of the BEST experiment: the best fit point of the joint analysis is $\sin^22\theta\approx 0.38$, $m_{\nu_s}^2\approx7.3\,$eV$^2$, the favored region will be explored by the KATRIN experiment. The sterile neutrino explanation of the BEST results would suggest not only the extension of the Standard Model of particle physics, but also either serious modifications of the Standard Cosmological Model and Solar Model, or a specific modification of the sterile sector needed to suppress the sterile neutrino production in the early Universe and in the Sun.

Phylogenetic assessment and in silico characterization of cytochrome b protein of three alpheid shrimps

Cytochrome b (cyt b) is one of the cytochrome proteins involved in electron transport in the respiratory chain of mitochondria. Cyt b is the only gene among the cytochrome complex coded by mitochondrial DNA. It is the most widely used gene for phylogenetic assessment and inter species variation studies. Here, the amino acid sequence of cyt b in three snapping shrimps such as, Alpheus lobidens, A. randali, A. bellulus was analysed and the results showed higher similarity in A. lobidens and A. randali as reflected in the phylogenetic tree. This study describes the applications of bioinformatics tools to predict the physico-chemical characters of cyt b protein. This protein was composed of least percentage of Cys (0.8%) and highest percentage of Leu (13.8%). The maximum molecular weight (MW) was predicted as 42.62 KDa in A. randali. The theoretical pI value was ranged from 8.35 to 8.36 and confirmed that cyt b was alkali in nature. The instability index value was in the range of 42.29 to 46.94 which showed the protein was more stable. The secondary structure of this protein was primarily composed of α-helixes and random coil, revealing the stable structure. The comparative modelling was performed by Swiss model where the 3-D crystal structure of bovine cyt bc1 (6haw1.c) was used as template. Ramachandran plot analysis showed that most of the amino acids (&gt;92%) falling on the favoured region. Seven conserved motifs were identified by MEME analysis. The modelled 3-D structure of this protein was validated by PROCHECK and QMEAN. The transmembrane protein topology and helix probability curve was predicted by TMHMM server. Protein-protein interactions was analysed by STRING tool and found the network of cyt b with related proteins. The results of this study may provide valuable insights into fundamental characteristics of cyt b in Alpheid shrimps.