Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors

Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.

Exploring crucial structural attributes of quinolinyl methoxyphenyl sulphonyl-based hydroxamate derivatives as ADAM17 inhibitors through classification-dependent molecular modelling approaches

A Disintegrin and Metalloproteinase 17 (ADAM17), a Zn2+-dependent metalloenzyme of the adamalysin family of the metzincin superfamily, is associated with various pathophysiological conditions including rheumatoid arthritis and cancer. However, no specific inhibitors have been marketed yet for ADAM17-related disorders. In this study, 94 quinolinyl methoxyphenyl sulphonyl-based hydroxamates as ADAM17 inhibitors were subjected to classification-based molecular modelling and binding pattern analysis to identify the significant structural attributes contributing to ADAM17 inhibition. The statistically validated classification-based models identified the importance of the P1' substituents such as the quinolinyl methoxyphenyl sulphonyl group of these compounds for occupying the S1' - S3' pocket of the enzyme. The quinolinyl function of these compounds was found to explore stable binding of the P1' substituents at the S1' - S3' pocket whereas the importance of the sulphonyl and the orientation of the P1' moiety also revealed stable binding. Based on the outcomes of the current study, four novel compounds of different classes were designed as promising ADAM17 inhibitors. These findings regarding the crucial structural aspects and binding patterns of ADAM17 inhibitors will aid the design and discovery of novel and effective ADAM17 inhibitors for therapeutic advancements of related diseases.

Assessing structural insights into in-house arylsulfonyl L-(+) glutamine MMP-2 inhibitors as promising anticancer agents through structure-based computational modelling approaches

MMP-2 is potentially contributing to several cancer progressions including leukaemias. Therefore, considering MMP-2 as a promising target, novel anticancer compounds may be designed. Here, 32 in-house arylsulfonyl L-(+) glutamines were subjected to various structure-based computational modelling approaches to recognize crucial structural attributes along with the spatial orientation for higher MMP-2 inhibition. Again, the docking-based 2D-QSAR study revealed that the Coulomb energy conferred by Tyr142 and total interaction energy conferred by Ala84 was crucial for MMP-2 inhibition. Importantly, the docking-dependent CoMFA and CoMSIA study revealed the importance of favourable steric, electrostatic, and hydrophobic substituents at the terminal phenyl ring. The MD simulation study revealed a lower fluctuation in the RMSD, RMSF, and Rg values indicating stable binding interactions of MMP-2 and these molecules. Moreover, the residual hydrogen bond and their interaction analysis disclosed crucial amino acid residues responsible for forming potential hydrogen bonding for higher MMP-2 inhibition. The results can effectively aid in the design and discovery of promising small-molecule drug-like MMP-2 inhibitors with greater anticancer potential in the future.

Exploration of structural alerts and fingerprints for novel anticancer therapeutics: a robust classification-QSAR dependent structural analysis of drug-like MMP-9 inhibitors

Among various matrix metalloproteinases (MMPs), overexpression of MMP9 has been established as a key player in a variety of cancers. Therefore, MMP9 has emerged as a promising biomolecule that may be targeted to design potent inhibitors as novel anticancer therapeutics. In this study, a large database containing 1,123 drug-like MMP-9 inhibitors was considered for robust classification-dependent fragment-based QSAR study through SARpy, Bayesian classification, and recursive partitioning analyses and were validated by both internal and external validation techniques. In a nutshell, all these classification-dependent techniques revealed some common structural alerts and sub-structural fingerprints responsible for modulating MMP-9 inhibition. These observations are in agreement with the interactions obtained from the ligand-bound co-crystal structures of MMP-9 justifying the robustness of the current study. Finally, based on these crucial structural fragments, some new lead compounds were designed and further validated by the binding mode of interaction analysis. Therefore, these findings may be beneficial in designing novel and potential MMP-9 inhibitors in the future as a weapon to combat several cancers.

Assessing the impact of varied nitrogen dosages on the vegetative and reproductive parameters of 'Sweet Sensation' and 'Rubygem' strawberry in Morang, Nepal

Between 2020 and 2021, an experimental investigation was conducted in Tropical conditions to assess the effects of varying levels of nitrogen fertilization (0 kgNha^-1, 0.5 kgNha^-1, 1 kgNha^-1, 1.5 kgNha^-1, and 2 kgNha^-1) on the growth and yield parameters of two strawberry cultivars (Sweet Sensation and Rubygem) in a sandy loam soil. The results demonstrated that the application of nitrogen positively influenced both vegetative (such as plant height, leaf number per plant, canopy spread, and crown diameter) and reproductive (such as number of flowers and fruits per plant, fruit yield, and TSS content) traits of both strawberry cultivars. Furthermore, the findings indicated that Sweet Sensation responded more positively to higher nitrogen doses than Rubygem in all aspects. The data showed that the utilization of 2 kgNha^-1 resulted in the highest fruit yield (0.390-0.508 t/ha) and quality traits, including TSS (7.89-9.21%). While there were no significant variations in TSS content among the plants treated with different nitrogen levels, significant differences were observed between the two strawberry cultivars.

A comparative quantitative structural assessment of benzothiazine-derived HDAC8 inhibitors by predictive ligand-based drug designing approaches

Histone deacetylase 8 (HDAC8) is a verified biomolecular target associated with diverse diseases including cancer. Though several HDAC inhibitors emerged effective against such diseases, no selective HDAC8 inhibitor is approved to date. Therefore, the development of potent HDAC8-selective inhibitors is inevitable to combat such diseases. Here, some benzothiazine-derived HDAC8 inhibitors were considered for a comparative QSAR analysis which may elucidate the prime structural components responsible for modulating their efficacy. Several outcomes from these diverse modelling techniques justified one another and thus validated each other. The ligand-based pharmacophore modelling study identified ring aromatic, positive ionizable, and hydrophobic features as essential structural attributes for HDAC8 inhibition. Besides, MLR, HQSAR and field-based 3D-QSAR studies signified the utility of the positive ionizable and hydrophobic features for potent HDAC8 inhibition. Again, the field-based 3D-QSAR study provided useful insight regarding the substitution in the fused phenyl ring. Moreover, the current observations also validated the previously reported molecular docking observations. Based on the outcomes, some new molecules were designed and predicted. Therefore, this comparative structural analysis of these HDAC8 inhibitors will surely assist in the development of potent HDAC8 inhibitors as promising anticancer therapeutics in the future.

A quantitative structural analysis of AR-42 derivatives as HDAC1 inhibitors for the identification of promising structural contributors

Alteration and abnormal epigenetic mechanisms can lead to the aberration of normal biological functions and the occurrence of several diseases. The histone deacetylase (HDAC) family of enzymes is one of the prime regulators of epigenetic functions modifying the histone proteins, and thus, regulating epigenetics directly. HDAC1 is one of those HDACs which have important contributions to cellular epigenetics. The abnormality of HDAC is correlated to the occurrence, progression, and poor prognosis in several disease conditions namely neurodegenerative disorders, cancer cell proliferation, metastasis, chemotherapy resistance, and survival in various cancers. Therefore, the progress of potent and effective HDAC1 inhibitors is one of the prime approaches to combat such diseases. In this study, both regression and classification-based molecular modelling studies were conducted on some AR-42 derivatives as HDAC1 inhibitors to elucidate the crucial structural aspects that are responsible for regulating their biological responses. This study revealed that the molecular polarizability, van der Waals volume, the presence of aromatic rings as well as the higher number of hydrogen bond acceptors might affect prominently their inhibitory activity and might be responsible for proper fitting and interactions at the HDAC1 active site to pertain effective inhibition.

Search for Subsolar-Mass Binaries in the First Half of Advanced LIGO's and Advanced Virgo's Third Observing Run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2  M_{⊙} and 1.0  M_{⊙} in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend our previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q≥0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14  yr^{-1}. This implies an upper limit on the merger rate of subsolar binaries in the range [220-24200]  Gpc^{-3} yr^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes in the mass range 0.2  M_{⊙}<m_{PBH}<1.0  M_{⊙} is f_{PBH}≡Ω_{PBH}/Ω_{DM}≲6%. This improves existing constraints on primordial black hole abundance by a factor of ∼3. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_{min}=1  M_{⊙}, where f_{DBH}≡Ω_{DBH}/Ω_{DM}≲0.003%. These are the first constraints placed on dissipative dark models by subsolar-mass analyses.

Prevalence and Factors Associated with Postpartum Depression among Mothers Visiting Immunization Clinic at Birendranagar Municipality, Surkhet, Nepal

Background Postpartum depression (PPD) is a disabling but treatable mental disorder that represents one of the most common complications of childbearing which can exert a wide range of effect on social, physical and mental health conditions of the mother and baby. Objective To identify the prevalence and factors associated with postpartum depression among mothers visiting immunization clinic at Birendranagar Municipality, Surkhet in year 2020. Method This study was a cross-sectional study. A total of 347 postpartum mothers were interviewed for data collection. Validated Nepali version of Edinburg Postnatal Depression Scale (EPDS) was used to identify postpartum depression. These mothers were permanent resident of Birendranagar who had delivered their babies in municipal hospital. Analysis was done using SPSS version 21.0. Chi square test was applied to identify association of postpartum depression with major interest of variables namely parity of mother, sex of a baby and recent planned or unplanned pregnancy. Odds ratio (OR) was calculated with 95% Confidence Interval (CI). Result The prevalence of postpartum depression was found to be 32.9% (27.9%, 37.8%). Several factors which were significantly associated with postpartum depression were; sex of the baby, history of abortion and recent pregnancy planned or unplanned. Conclusion Nearly one-third of postpartum mothers had depression. Hence screening of mothers for depression is of prime importance throughout the continuum of care. Likewise, the factors identified for postpartum depression needs to be taken care of well in advance for healthy mother and a baby.

Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition

Histone deacetylase 2 (HDAC2) has been implicated in a variety of cardiovascular and neurodegenerative disorders as well as in cancers. Thus, HDAC2 has become an exclusive target for anticancer drug development. Therefore, the development of newer HDAC2 inhibitors in disease conditions is a prime goal to restrain such a scenario. Although a handful of HDAC inhibitors was accepted for the treatment of HDAC-related disease conditions, the non-selective nature of these entities is one of the major setbacks in the treatment of specific HDAC isoform-related pathophysiology. In this framework, the analyses of pre-existing molecules are essential to identify the important structural features that can fulfil the requirements for the cap and linker moieties to obtain potent and effective HDAC2 inhibition. Thus, in this study, the implementation of a combined comparative 2D and 3D molecular modelling techniques was done on a group of 92 diverse hydroxamate derivatives having a wide range of HDAC2 inhibitory potency. Besides other crucial features, this study upheld the importance of groups like triazole and benzyl moieties along with the molecular fields that are crucial for regulating HDAC2 inhibition. The outcomes of this study may be employed for the designing of HDAC2 inhibitors in future.

A robust classification-dependent multi-molecular modelling study on some biphenyl sulphonamide based MMP-8 inhibitors

Matrix metalloproteinases (MMPs) are a group of zinc and calcium-dependent endopeptidases, which contribute to different physiological and biological activities via extracellular matrix (ECM) degradation. Matrix metalloproteinase-8 (MMP-8) belongs to type-II collagenases of the MMP family that has contribution in several physiological disorders such as cardiovascular diseases, joint, renal, digestive and respiratory disorders as well as in cancer. In clinical study, MMP-8 is found to be associated with periodontal disease condition. Therefore, MMP-8 specific inhibitors should be developed to target these disorders. The biphenyl sulphonamide (BPS) moiety is one of the crucial structural characteristics found in several MMP-8 inhibitors. Here, different classification-based molecular modelling methods were used to explore the structural features that lead to the activity variation of a series of MMP-8 inhibitors possessing a BPS moiety. Our current classification-based structural analysis of these BPS-derived MMP-8 inhibitors was able to identify the importance of several structural features such as the tetrahydroisoquinoline and N-Boc pyridyl groups, which have positive influences on MMP-8 inhibition. This study was also reflected the importance of the zinc-binding groups (ZBGs) like the hydroxamate and phosphonate for potent and sub-nanomolar range MMP-8 inhibition, which may benefit the development of highly potent MMP-8 inhibitors.

Robust classification-based molecular modelling of diverse chemical entities as potential SARS-CoV-2 3CLpro inhibitors: theoretical justification in light of experimental evidences

COVID-19 is the most unanticipated incidence of 2020 affecting the human population worldwide. Currently, it is utmost important to produce novel small molecule anti-SARS-CoV-2 drugs urgently that can save human lives globally. Based on the earlier SARS-CoV and MERS-CoV infection along with the general characters of coronaviral replication, a number of drug molecules have been proposed. However, one of the major limitations is the lack of experimental observations with different drug molecules. In this article, 70 diverse chemicals having experimental SARS-CoV-2 3CL^proinhibitory activity were accounted for robust classification-based QSAR analysis statistically validated with 4 different methodologies to recognize the crucial structural features responsible for imparting the activity. Results obtained from all these methodologies supported and validated each other. Important observations obtained from these analyses were also justified with the ligand-bound crystal structure of SARS-CoV-2 3CL^pro enzyme. Our results suggest that molecules should contain a 2-oxopyrrolidine scaffold as well as a methylene (hydroxy) sulphonic acid warhead in proper orientation to achieve higher inhibitory potency against SARS-CoV-2 3CL^pro. Outcomes of our study may be able to design and discover highly effective SARS-CoV-2 3CL^pro inhibitors as potential anticoronaviral therapy to crusade against COVID-19.

Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal

Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARSCoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 - B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.

Exploring the structural aspects of ureido-amino acid-based APN inhibitors: a validated comparative multi-QSAR modelling study

The zinc-dependent enzyme aminopeptidase N (APN) is a member of the M1 metalloenzyme family. The multi-functionality of APN as a peptidase, a receptor and a signalling molecule has provided it the access to influence a number of disease conditions namely viral diseases, angiogenesis, cellular metastasis and invasion including different cancer conditions. Hence, the development of potent APN inhibitors is a possible route for the treatment of diseases related to the activity of APN. In this study, different QSAR approaches have been adopted to identify the structural features of a group of hydroxamate-based ureido-amino acid derivative APN inhibitors. This study was able to identify different constitutional aspects of these APN inhibitors which are important for their inhibitory potency. Additionally, some of these observations were also aligned with the observations of previously performed QSAR studies conducted on different APN inhibitors. Therefore, the results of this study may help to design potent and effective APN inhibitors in the future.

Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), N-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.

Inkjet-Printed Organohalide 2D Layered Perovskites for High-Speed Photodetectors on Flexible Polyimide Substrates

The synthesis of solution-processed two-dimensional (2D) layered organohalide (CH₃(CH₂)₃NH₃)₂(CH₃NH₃)_n-1Pb_nI_3n+1 (n = 2, 3, and 4) perovskites is presented, where inkjet printing was used to fabricate heterostructure flexible photodetector (PD) devices on polyimide (PI) substrates. Inks for the n = 4 formulation were developed to inkjet-print PD devices that were photoresponsive to broadband incoming radiation in the visible regime, where the peak photoresponsivity R was calculated to be ∼0.17 A/W, which is higher compared to prior reports, while the detectivity D was measured to be ∼3.7 × 10¹² Jones at a low light intensity F ≈ 0.6 mW/cm². The ON/OFF ratio was also high (∼2.3 × 10³), while the response time τ on the rising and falling edges was measured to be τ_rise ≈ 24 ms and τ_fall ≈ 65 ms, respectively. Our strain-dependent measurements, conducted here for the first time for inkjet-printed perovskite PDs, revealed that the I_p decreased by only ∼27% with bending (radius of curvature of ∼0.262 cm^-1). This work demonstrates the tremendous potential of the inkjet-printed, composition-tunable, organohalide 2D perovskite heterostructures for high-performance PDs, where the techniques are readily translatable toward flexible solar cell platforms as well.

Dramatic Enhancement of Optoelectronic Properties of Electrophoretically Deposited C60-Graphene Hybrids

Fullerene (C₆₀) and multilayer graphene hybrid devices were fabricated using electrophoretic deposition, where the C₆₀ clusters are electrically charged upon the application of an external bias in a polar solvent, acetonitrile, mixed with toluene, which facilitates their deposition on the graphene membranes. Raman spectroscopy unveiled the unique vibrational fingerprints associated with the A_2g mode of the C₆₀ molecules at ∼1453 cm^-1, while blue shifts of ∼6 and ∼17 cm^-1 were also attributed to the G- and 2D-bands of the hybrids relative to bare graphene, suggestive of p-doped graphene. The intensity ratio of the G- and the 2D-bands I_2D/I_G (hybrid) dropped to ∼0.18 from ∼0.3 (bare graphene), and this reduction in I_2D/I_G is also a signature of hole-doped graphene, consistent with the relatively strong electron accepting nature of C₆₀. The electronic conductance of the two-terminal hybrid devices increased relative to bare graphene at room temperature which was attributed to the increased carrier density, and temperature-dependent electronic transport measurements were also conducted from ambient down to ∼5.8 K. Additionally, a low energy shift in the Fermi level, E_F ≈ 140 meV, was calculated for the hybrids. When the hybrid devices were irradiated with a broadband white light source and a tunable laser source (with a wavelength λ ranging from ∼400-1100 nm), a strong photoresponse was evident, in contrast to the bare graphene devices which appeared unresponsive. The responsivity R of the hybrids was measured to be ∼10⁹ A/W at λ ≈ 400 nm and ∼298 K, while the detectivity and external quantum efficiency were also exceptional, ∼10¹⁵ jones and ∼10⁹%, respectively, at ∼1 V and a light power density of ∼3 mW/cm². The R values are ∼10 times higher compared to other hybrid devices derived from graphene reported previously, such as quantum dot-graphene and few-layer MoS₂-graphene heterostructures. The strong photoresponse of the C₆₀-graphene hybrids reported here is attributed to the doping enhancement arising in graphene upon the adsorption of C₆₀. This work demonstrates the exceptional potential of such hybrid nanocarbon-based structures for optoelectronics.

Insight into structural features of phenyltetrazole derivatives as ABCG2 inhibitors for the treatment of multidrug resistance in cancer

ABCG2 is the principal ABC transporter involved in the multidrug resistance of breast cancer. Looking at the current demand in the development of ABCG2 inhibitors for the treatment of multidrug-resistant cancer, we have explored structural requirements of phenyltetrazole derivatives for ABCG2 inhibition by combining classical QSAR, Bayesian classification modelling and molecular docking studies. For classical QSAR, structural descriptors were calculated from the free software tool PaDEL-descriptor. Stepwise multiple linear regression (SMLR) was used for model generation. A statistically significant model was generated and validated with different parameters (For training set: r = 0.825; Q² = 0.570 and for test set: r = 0.894, r²_pred = 0.783). The predicted model was found to satisfy the Golbraikh and Trospha criteria for model acceptability. Bayesian classification modelling was also performed (ROC scores were 0.722 and 0.767 for the training and test sets, respectively). Finally, the binding interactions of phenyltetrazole type inhibitor with the ABCG2 receptor were mapped with the help of molecular docking study. The result of the docking analysis is aligned with the classical QSAR and Bayesian classification studies. The combined modelling study will guide the medicinal chemists to act faster in the drug discovery of ABCG2 inhibitors for the management of resistant breast cancer.

QSAR modelling on a series of arylsulfonamide-based hydroxamates as potent MMP-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a lucrative therapeutic target as far as anticancer drug discovery is concerned. Overexpression of MMP-2 is found to facilitate tumour propagation through the involvement of vascular endothelial growth factor (VEGF). However, even after different techniques, finding a target-specific MMP-2 inhibitor with respectable pharmacodynamic properties is still a challenging task. Regression-dependent quantitative structure-activity relationship (QSAR) strategies might be among the possible drug design methods to explore the essential structural features that would be valuable to find a suitable MMP-2 inhibitor. In this paper, 72 molecules were explored using the PaDEL descriptors and stepwise multiple linear regression (S-MLR). The partial least squares (PLS) method was also used to create a viable statistical model with an acceptable metric related to these models. The final statistical models were formed with statistical parameters within acceptable range (r² = 0.797, Q² = 0.725 and r²_pred = 0.643 for the MLR model, and r² = 0.780, Q² = 0.685 and r²_pred = 0.666 for the PLS model). The models were analysed and compared with those already published on the same endpoint.

Chemical exfoliation efficacy of semiconducting WS2 and its use in an additively manufactured heterostructure graphene–WS2–graphene photodiode

In the present work, various chemical exfoliation routes for semiconducting two-dimensional (2D) layered material WS₂ are explored, which include magnetic stirring (MS), shear mixing (SM), and horn-tip (HT) sonication. Current–voltage measurements, Raman spectroscopy, and photoluminescence (PL) spectroscopy were used to characterize the drop-casted WS₂ nanosheets produced by these three techniques and our analysis revealed that HT sonication produced the most optimal dispersions. Heterostructure photodetector devices were then fabricated using inkjet printing of the HT sonicated dispersions of WS₂ and graphene. The photodetector device performance was measured using a stream of ON/OFF light pulses generated using a red laser with wavelength λ ∼ 660 nm, and an arbitrary waveform generator. From this analysis, the photoresponsivity and detectivity of the graphene–WS₂–graphene heterostructure devices were calculated to be ∼0.86 A W⁻¹ and ∼10¹³ Jones, respectively. Capacitance–voltage (C–V) and C–frequency (f) measurements were also conducted, where the V was swept from –6 V to +6 V, while the change in C was measured from f ∼ 20 kHz up to 3 MHz to gain insights into the nature of the graphene–WS₂ interface. From the C–V measurements, the C plateaued at ∼324.3 pF from ∼−4 V to +4 V for the lowest f of 20 kHz and it reduced to ∼200 pF from −6 V to ∼−4 V, and similarly from ∼4 V to 6 V, C was ∼190 pF. The decrease in C for V > +4 V and V < −4 V was attributed to the reduction of the interfacial barrier at the electrodes which is suggestive of a Schottky-based photodiode at the graphene–WS₂ interface. A sharp decrease in C from ∼315.75 pF at 25.76 kHz to ∼23.79 pF at 480 kHz (at 0 V bias) from the C–f measurements suggests a strong effect of interface trap density on C built-up at the graphene–WS₂ interface and the ensuing Schottky barrier height. Our work confirms the excellent potential of solution-cast, trilayer graphene–WS₂–graphene heterostructures as a promising photodetector platform using additively manufactured inkjet printing.

Among magnetic stirring (MS), shear mixing (SM), and horn-tip (HT) sonication for the chemical exfoliation of semiconducting WS₂, HT sonication resulted in stable dispersions which were used to demonstrate ink-jet printed graphene–WS₂–graphene photodiodes.

Structural exploration of hydroxyethylamines as HIV-1 protease inhibitors: new features identified

The current study deals with chemometric modelling strategies (Naïve Bayes classification, hologram-based quantitative structure-activity relationship (HQSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)) to explore the important features of hydroxylamine derivatives for exerting potent human immunodeficiency virus-1 (HIV-1) protease inhibition. Depending on the statistically validated reliable and robust quantitative structure-activity relationship (QSAR) models, important and crucial structural features have been identified that may be responsible for enhancing the activity profile of these hydroxylamine compounds. Arylsulfonamide function along with methoxy or fluoro substitution is important for enhancing activity. Bulky steric substitution at the sulfonamide nitrogen disfavours activity whereas smaller hydrophobic substitution at the same position is found to be favourable. Apart from the crucial oxazolidinone moiety, pyrrolidine, cyclic urea and methyl ester functions are also responsible for increasing the HIV-1 protease inhibitory profile. Observations derived from these modelling studies may be utilized further in designing promising HIV-1 protease inhibitors of this class.

Extended Spectrum β-lactamase (ESBL) Producing Multi Drug Resistant (MDR) Urinary Pathogens in a Children Hospital from Nepal

Background Multidrug resistant in clinical bacterial isolates has increasingly been reported through out the world and is associated with high morbidity, mortality and increased health care costs. It is important to determine the status of multidrug resistance pattern to understand the current resistance trend so that appropriate antibiotics can be used in practice. Objective To determine the antibiotic resistant profile and prevalence of extended spectrum β-lactamase producing multidrug resistant strains in pediatric patients of Kanti Children's Hospital, Kathmandu, Nepal. Method Urine sample was cultured by standard microbiological techniques and bacterial isolates were identified using different biochemical tests. Antibiotic susceptibility testing was performed by Kirby Bauer disc diffusion method and extended spectrum β-lactamase detection was carried out using combined disc method as recommended by Clinical Laboratory Standard Institute guidelines. Result All together 65 different bacteria were isolated and subsequently identified. E. coli was the most common isolate with 46 (71%) isolates 63% of these isolates were multidrug resistant. Gram negative isolates were most resistant to nalidixic acid (81.97%) followed by ampicillin (69.35%) and co-trimoxazole (69.35%). The extended spectrum β-lactamase producing isolates were 43% among total isolates. Conclusion Higher rate of Extended Spectrum β-lactamase production among multidrug resistant isolates suggested routine extended spectrum β-lactamase testing in clinical isolates.

Multiple molecular modelling studies on some derivatives and analogues of glutamic acid as matrix metalloproteinase-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a potential target in anticancer drug discovery due to its association with angiogenesis, metastasis and tumour progression. In this study, 67 glutamic acid derivatives, synthesized and evaluated as MMP-2 inhibitors, were taken into account for multi-QSAR modelling study (regression-based 2D-QSAR, classification-based LDA-QSAR, Bayesian classification QSAR, HQSAR, 3D-QSAR CoMFA and CoMSIA as well as Open3DQSAR). All these QSAR studies were statistically validated individually. Regarding the 3D-QSAR analysis, the Open3DQSAR results were better than CoMFA and CoMSIA, although all these 3D-QSAR models supported each other. The importance of biphenylsulphonyl moiety over phenylacetyl/naphthylacetyl moieties was established due to its association with favourable steric and hydrophobic characters. HQSAR, LDA-QSAR and Bayesian classification QSAR studies also suggested that the biphenylsulphonamido group was better than the phenylacetylcarboxamido function. Additionally, glutamines were proven to be far better inhibitors than isoglutamines. Observations obtained from the current study were revalidated and supported by the earlier reported molecular modelling studies. Depending on these observations, newer glutamic acid-based compounds may be designed further in future for potent MMP-2 inhibitory activity.

Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization

Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors. The best models from different splits were selected on the basis of statistically validated characteristics of the test set and have the following statistical parameters: r² = 0.806, Q² = 0.788 (split 1); r² = 0.842, Q² = 0.826 (split 2); r² = 0.774, Q² = 0.755 (split 3). The structural attributes obtained from the best models were analysed to understand the structural requirements of the selected series for HIV-1 protease inhibitory activity. On the basis of obtained structural attributes, 11 new compounds were designed, out of which five compounds were found to have better activity than the best active compound in the series.

Environmentally Friendly Plasma-Treated PEDOT:PSS as Electrodes for ITO-Free Perovskite Solar Cells

Solution processed poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) transparent electrodes (TEs) offer great potential as a low cost alternative to expensive indium tin oxide (ITO). However, strong acids are typically used for enhancing the conductivity of PEDOT:PSS TEs, which produce processing complexity and environmental issues. This work presents an environmentally friendly acid free approach to enhance the conductivity of PEDOT:PSS using a light oxygen plasma treatment, in addition to solvent blend additives and post treatments. The plasma treatment was found to significantly reduce the sheet resistance of PEDOT:PSS TEs from 85 to as low as 15 Ω sq^-1, which translates to the highest reported conductivity of 5012 S/cm for PEDOT:PSS TEs. The plasma treated PEDOT:PSS TE resulted in an ITO-free perovskite solar cell efficiency of 10.5%, which is the highest reported efficiency for ITO-free perovskite solar cells with a PEDOT:PSS electrode that excludes the use of acid treatments. This research presents the first demonstration of this technology. Moreover, the PEDOT:PSS TEs enabled better charge extraction from the perovskite solar cells and reduced hysteresis in the current density-voltage (J-V) curves.

Nasal Carriage Rate of Methicillin Resistant Staphylococcus aureus among Health Care Workers at a Tertiary Care Hospital in Kathmandu, Nepal

BACKGROUND

Methicillin-resistant Staphylococcus aureus is one of the most common causes of nosocomial infections. Due to its multidrug resistant nature; infections due to Methicillin-resistant Staphylococcus aureus are often very difficult to treat. Colonized health care workers are the important sources of Methicillin-resistant Staphylococcus aureus. The objectives of this study were to determine the nasal carriage rate of Methicillin-resistant Staphylococcus aureus among health care workers at Kathmandu Medical College and Teaching Hospital, Nepal and to assess their antimicrobial susceptibility patterns.

METHODS

A cross sectional study was conducted among 252 health care workers from July to November 2013. Mannitol salt agar was used to culture the nasal swabs. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion technique following Clinical and Laboratory Standards Institute guidelines. Methicillin-resistant Staphylococcus aureus strains were confirmed by using cefoxitin disc and by determining the minimum inhibitory concentration of oxacillin by agar dilution method.

RESULTS

Of 252 healthcare workers, 46(18.3%) were positive for Staphylococcus aureus among which 19(41.3%) were Methicillin-resistant Staphylococcus aureus carriers. Overall rate of nasal carriage of Methicillin-resistant Staphylococcus aureus was 7.5% (19/252).The higher percentages of lab personnel were nasal carriers of S. aureus (31.6%) and Methicillin-resistant Staphylococcus aureus (10.5%).The percentages of nasal carriage of S. aureus (35.7%) and Methicillin-resistant Staphylococcus aureus (14.3%) were highest in the health care workers from post operative department. Higher percentage of Methicillin-resistant Staphylococcus aureus were susceptible toward amikacin (100%) and vancomycin (100%) followed by cotrimoxazole (84.2%).

CONCLUSIONS

High rates of nasal carriage of S. aureus and Methicillin-resistant Staphylococcus aureus were observed among the healthcare workers, which indicate the need of strict infection control measures to be followed to control the nosocomial infections.

Shelf life stability comparison in air for solution processed pristine PDPP3T polymer and doped spiro-OMeTAD as hole transport layer for perovskite solar cell

This data in brief includes forward and reverse scanned current density-voltage (J-V) characteristics of perovskite solar cells with PDPP3T and spiro-OMeTAD as HTL, stability testing conditions of perovskite solar cell shelf life in air for both PDPP3T and spiro-OMeTAD as HTL as per the description in Ref. [1], and individual J-V performance parameters acquired with increasing time exposed in ambient air are shown for both type of devices using PDPP3T and spiro-OMeTAD as HTL. The data collected in this study compares the device stability with time for both PDPP3T and spiro-OMeTAD based perovskite solar cells and is directly related to our research article "solution processed pristine PDPP3T polymer as hole transport layer for efficient perovskite solar cells with slower degradation" [2].

Crystallization of a perovskite film for higher performance solar cells by controlling water concentration in methyl ammonium iodide precursor solution

An optimal small amount of water added into methyl ammonium iodide (MAI) solution in isopropyl alcohol (IPA) helps perovskite crystallization and leads to larger grain size from sequential deposition of perovskite films. The concentration of water was varied from 1% to 7% (vol% of IPA) in MAI solution and optical absorption, crystallization, morphology of perovskite films and their photovoltaic performance were studied in perovskite solar cells. 5% by volume was found to lead to preferential crystallization in the (110) plane with grain size about three times that of perovskite films prepared without adding water into the MAI solution. The optimal water concentration of 5% by volume in the MAI solution led to average perovskite grain size of ∼600 nm and solar cell efficiency of 12.42% at forward scan with a rate of 0.5 V s(-1). Device performance decreases after increasing water concentration beyond 5% in the MAI solution due to formation of the PbI2 phase. Transient photocurrent and photovoltage measurements show the shortest charge transport time at 0.99 μs and the longest charge carrier life time at 13.6 μs for perovskite films prepared from 5% water in MAI solution, which improved perovskite solar cell efficiency from 9.04% to 12.42%.

Interfacial Study To Suppress Charge Carrier Recombination for High Efficiency Perovskite Solar Cells

We report effects of an interface between TiO2-perovskite and grain-grain boundaries of perovskite films prepared by single step and sequential deposited technique using different annealing times at optimum temperature. Nanoscale kelvin probe force microscopy (KPFM) measurement shows that charge transport in a perovskite solar cell critically depends upon the annealing conditions. The KPFM results of single step and sequential deposited films show that the increase in potential barrier suppresses the back-recombination between electrons in TiO2 and holes in perovskite. Spatial mapping of the surface potential within perovskite film exhibits higher positive potential at grain boundaries compared to the surface of the grains. The average grain boundary potential of 300-400 mV is obtained upon annealing for sequentially deposited films. X-ray diffraction (XRD) spectra indicate the formation of a PbI2 phase upon annealing which suppresses the recombination. Transient analysis exhibits that the optimum device has higher carrier lifetime and short carrier transport time among all devices. An optimum grain boundary potential and proper band alignment between the TiO2 electron transport layer (ETL) and the perovskite absorber layer help to increase the overall device performance.

Social Consequences of Alcohol Use among Urban Poor: A Cross-sectional Study in Kathmandu Valley

BACKGROUND

Nepal is not an exception to alcohol use; urban poor are more prone than the general population. The question of social consequences of alcohol use among urban poor remains largely unanswered in Nepal. Study explored the alcohol linked social consequences among the urban poor of Kathmandu Valley.

METHODS

Taking 422 urban poor from four squatter settlements of Kathmandu Valley, a cross-sectional study was carried out. A series of univariate and bivariate analysis were performed in R version 3.1.2.

RESULTS

Four out of 10 current drinkers (42.86%, 95% CI: 31.4-54.3) encountered various social consequences. The number one consequence hitting 23.19% drinkers was money loss. Male drinkers were 4.43 times (95% CI: 1.810.8) more likely to face social consequences than their female counterparts. Being male frequent drinker increased the odds of social consequence 3.80 times (95% CI:1.3-11.0) than that of female frequent drinker.

CONCLUSIONS

A behaviour change communication campaign needs initiation; male populace and frequent drinkers being the target.

Origin of photogenerated carrier recombination at the metal–active layer interface in polymer solar cells

This article sheds some light on the origin of photogenerated carrier recombination at the metal–active layer interface in bulk heterojunction solar cells.

In vitro Temocillin efficacy against extended spectrum β-lactamase producing multidrug resistant gram negative bacterial isolates from Nepal

Temocillin is relatively more stable against most β-lactamases and requires re-evaluation to include it in common clinical practice as a therapeutic alternative. At the National Reference Laboratory of Nepal, we evaluated multidrug resistance (MDR) and extended spectrum β-lactamase (ESBL) phenotypes among 292 gram-negative clinical bacterial isolates of 18 different genera during 2009/2010 by Kirby-Bauer disc diffusion method following CLSI guidelines. ESBL screen positive isolates were tested for Temocillin efficacy by disc diffusion method following British Society of Antimicrobial Chemotherapy (BSAC) guidelines and other antibiotics following Clinical and Laboratory Standards Institute (CLSI) guidelines. Of the 292 isolates, 75.0% isolates were MDR, among which 61.6% were primarily screened positive for ESBL production but only 38.8% were confirmed as ESBL producers. We report relatively lower Temocillin resistance of 28.9% and 15.6% among MDR and ESBL positive populations, respectively. Among ESBL positive isolates, no Proteus mirabilis, 19.7% Escherichia coli and 33.3% Klebsiella oxytoca showed resistance to Temocillin, although such resistance was higher among Acinetobacter spp. (66.7%) and K. pneumoniae 50.0%. Among ESBL negative isolates, none of the K. oxytoca and few (13.3%) Acinetobacter spp. were resistant to Temocillin, while all Citrobacter freundii, Pseudomonas aeruginosa (85.7%) and K. pneumoniae (66.7%) showed Temocillin resistance. Only 14.8% and 3.0% of total MDR isolates were resistant to Imipenem and Meropenem, respectively. However, Imipenem resistance was remarkably high (86.7%) among ESBL negative Acinetobacter spp. than Meropenem (13.3%). Temocillin showed comparable efficacy against MDR and ESBL producing bacterial isolates and could be a next therapeutic option.

Bacteriological profile and associated risk factors of neonatal sepsis in Paropakar Maternity and Women's Hospital Thapathali, Kathmandu

Neonatal Sepsis is one of the most common reasons for admission to neonatal units in developing countries. It is also a major cause of mortality in both developed and developing countries. Identification of the common bacteria and risk factors causing such infections and their susceptibility patterns will provide necessary information for timely intervention. This study was carried out to determine the bacteriological profile and associated risk factors of neonatal sepsis in Paropakar Maternity and Women's hospital. A cross-sectional prospective study was conducted among neonates suspected of neonatal sepsis. Blood culture was performed and organisms were identified and antibiotic susceptibility was carried out with standard microbiological methods. Data were analysed by using SPSS. Ver. 16 software. The positive yield of blood culture was 21%. The most common isolates were Staphylococcus epidermidis, E. coli, Staphylococcus aureus, Klebsiella pneumoniae and Pseudomonas spp. In Antibiotic susceptibility pattern Gentamycin showed the highest sensitivity to all types of isolated organisms. Vancomycin sensitivity was highest for Gram positive organism and Ciprofloxacin was most effective for Gram negative organisms isolated. Ampicillin and Amoxycillin were the least effective drug. Multiple drug resistance was observed in 77.15% of isolates. Prematurity, low birth weight and maternal pyrexia before delivery were found to be strongly associated with neonatal sepsis. Gram positive organisms were more prevalent than gram negative organisms.

Growing Resistance to Vancomycin among Methicillin Resistant Staphylococcus Aureus Isolates from Different Clinical Samples

INTRODUCTION

Methicillin resistant Staphylococcus aureus (MRSA), majorly associated with nosocomial and community infections worldwide, are emerging as resistant strains to many antibiotics narrowing down the efficacy of antimicrobial therapy. In order to investigate the changing resistant pattern of MRSA to empirical drugs, the study was carried out at KIST Medical College and Hospital, Nepal. It also aims to determine the minimum inhibitory concentration (MIC) of vancomycin among MRSA.

METHODS

Altogether 3500 clinical samples including 1303 blood, 1489 urine and 708 body fluids were collected and processed. Isolated S. aureus were further screened for methicillin resistance by Kirby-Bauer disk diffusion technique using cefoxitin (30µg) disk. All MRSA were subjected to in vitro determination of MIC of vancomycin by agar dilution method as recommended by CLSI guidelines.

RESULTS

Total 287 S. aureus were isolated from the different clinical samples. Altogether 248 (86.41%) were found to be multidrug resistance (MDR) while 42 (14.63%) of the isolates were methicillin resistance with the highest prevalence in the age group of 16-30. All 42 (100%) MRSA isolates were resistant to ampicillin and penicillin followed by 41 (97.62%), 32 (76.19%), 31(73.81%), 29 (69.05%), 9 (21.43%) and seven (16.67%) to cefotaxime, gentamycin, cotrimoxazole, erythromycin, tetracycline and ciprofloxacin respectively. Although all MRSA strains were sensitive to vancomycin on disc diffusion, four isolates were intermediates in vitro determination of MIC of vancomycin. The break point for vancomycin was found to be 15mm.

CONCLUSIONS

The increment in vancomycin MIC among MRSA is alarming. Strict control measures to prevent MRSA spread and a routine surveillance for VRSA must be incorporated in hospitals.

Post-operative drop in hemoglobin and need of blood transfusion in cesarean section at Dhulikhel Hospital, Kathmandu University Hospital

BACKGROUND

Cesarean section has been identified as one of the commonest indication for blood transfusion in obstetric practice because it involves risk of major intra-operative blood loss. Different figures varying from less than 500 ml to more than 1000 ml have been quoted as estimated blood loss associated with caesarean section. There is also a wide variation in blood ordering practices for this surgery.

OBJECTIVE

The objective of this study is to evaluate the blood ordering practice and transfusion for cesarean sections at our institute, to see post-operative drop in hemoglobin and hematocrit and to correlate those parameters with the duration between uterine incision and repair.

METHODS

In this prospective observational study, non-randomised purposive sample was taken from 121 ladies who underwent elective and emergency cesarean section at the department of obstetrics of Dhulikhel Hospital-Kathmandu University Hospital. Post-cesarean drop in hemoglobin and hematocrit and their relation with duration of uterine manipulation was calculated. Cross-match to transfusion (C/T ratio) ratio, transfusion probability (%T) and transfusion index (Ti) were also calculated.

RESULTS

Most frequent blood group was found to be O positive (38%) among those ladies. Average post-cesarean drop in hemoglobin was 1.52±1.27 gm/dl and drop in haematocrit was 5.49±4.1%. Post-operative drop in hemoglobin and haematocrit had weak and positive linear relation with duration between uterine incision and repair. Cross-match to transfusion ratio was 1, transfusion probability 100% and transfusion index was 2.

CONCLUSION

There is no need of routine cross-matching of blood for cesarean section. Only grouping with confirmation of availability should be done for emergency situation.

Benzothiadiazole-based polymer for single and double junction solar cells with high open circuit voltage

Single and double junction solar cells with high open circuit voltage were fabricated using poly{thiophene-2,5-diyl-alt-[5,6-bis(dodecyloxy)benzo[c][1,2,5]thiadiazole]-4,7-diyl} (PBT-T1) blended with fullerene derivatives in different weight ratios. The role of fullerene loading on structural and morphological changes was investigated using atomic force microscopy (AFM) and X-ray diffraction (XRD). The XRD and AFM measurements showed that a higher fullerene mixing ratio led to breaking of inter-chain packing and hence resulted in smaller disordered polymer domains. When the PBT-T1:PC60BM weight ratio was 1 : 1, the polymer retained its structural order; however, large aggregated domains formed, leading to poor device performance due to low fill factor and short circuit current density. When the ratio was increased to 1 : 2 and then 1 : 3, smaller amorphous domains were observed, which improved photovoltaic performance. The 1 : 2 blending ratio was optimal due to adequate charge transport pathways giving rise to moderate short circuit current density and fill factor. Adding 1,8-diiodooctane (DIO) additive into the 1 : 2 blend films further improved both the short circuit current density and fill factor, leading to an increased efficiency to 4.5% with PC60BM and 5.65% with PC70BM. These single junction solar cells exhibited a high open circuit voltage at ∼ 0.9 V. Photo-charge extraction by linearly increasing voltage (Photo-CELIV) measurements showed the highest charge carrier mobility in the 1 : 2 film among the three ratios, which was further enhanced by introducing the DIO. The Photo-CELIV measurements with varying delay times showed significantly higher extracted charge carrier density for cells processed with DIO. Tandem devices using P3HT:IC60BA as bottom cell and PBT-T1:PC60BM as top cell exhibited a high open circuit voltage of 1.62 V with 5.2% power conversion efficiency.