Transformer-Based Molecular Generative Model for Antiviral Drug Design

Since the Simplified Molecular Input Line Entry System (SMILES) is oriented to the atomic-level representation of molecules and is not friendly in terms of human readability and editable, however, IUPAC is the closest to natural language and is very friendly in terms of human-oriented readability and performing molecular editing, we can manipulate IUPAC to generate corresponding new molecules and produce programming-friendly molecular forms of SMILES. In addition, antiviral drug design, especially analogue-based drug design, is also more appropriate to edit and design directly from the functional group level of IUPAC than from the atomic level of SMILES, since designing analogues involves altering the R group only, which is closer to the knowledge-based molecular design of a chemist. Herein, we present a novel data-driven self-supervised pretraining generative model called "TransAntivirus" to make select-and-replace edits and convert organic molecules into the desired properties for design of antiviral candidate analogues. The results indicated that TransAntivirus is significantly superior to the control models in terms of novelty, validity, uniqueness, and diversity. TransAntivirus showed excellent performance in the design and optimization of nucleoside and non-nucleoside analogues by chemical space analysis and property prediction analysis. Furthermore, to validate the applicability of TransAntivirus in the design of antiviral drugs, we conducted two case studies on the design of nucleoside analogues and non-nucleoside analogues and screened four candidate lead compounds against anticoronavirus disease (COVID-19). Finally, we recommend this framework for accelerating antiviral drug discovery.

Structure based virtual screening and molecular simulation study of FDA-approved drugs to inhibit human HDAC6 and VISTA as dual cancer immunotherapy

Cancer immunotherapy has significantly contributed to the treatment of various types of cancers mainly by targeting immune checkpoint inhibitors (ICI). Among them, V-domain immunoglobulin suppressor of T cell activation (VISTA) has been explored as a promising therapeutic target. Besides, histone deacetylase 6 (HDAC6) has been demonstrated to be efficacious target for several cancers. The current theoretical work was performed to explore the virtual repurposing of the FDA-approved drugs as inhibitors against these two (VISTA and HDAC6) cancers therapeutic targets. The crystal structure of the two proteins were downloaded from PDB and subjected to virtual screening by DrugRep webserver while using FDA-approved drugs library as ligands database. Our study revealed that Oxymorphone and Bexarotene are the top-ranked inhibitors of VISTA and HDAC6, respectively. The docking score of Bexarotene was predicted as - 10 kcal/mol while the docking score of Oxymorphone was predicted as - 6.2 kcal/mol. Furthermore, a total of 100 ns MD simulation revealed that the two drugs Oxymorphone and Bexarotene formed stable complexes with VISTA and HDAC6 drug targets. As compared to the standard drug the two drugs Oxymorphone and Bexarotene revealed great stability during the whole 100 ns MD simulation. The binding free energy calculation further supported the Root Mean Square Deviation (RMSD) result which stated that as compared to the ref/HDAC6 (- 18.0253 ± 2.6218) the binding free energy score of the Bexarotene/HDAC6 was good (- 51.9698 ± 3.1572 kcal/mol). The binding free energy score of Oxymorphone/VISTA and Ref/VISTA were calculated as - 36.8323 ± 3.4565, and - 21.5611 ± 4.8581 respectively. In conclusion, the two drugs deserve further consideration as cancer treatment option.

Corrigendum: Exploring the molecular mechanism of hepatitis virus inducing hepatocellular carcinoma by microarray data and immune infiltrates analysis

[This corrects the article DOI: 10.3389/fimmu.2022.1032819.].

Development of an innovative data-driven system to generate descriptive prediction equation of dielectric constant on small sample sets

Dielectric constant (DC, ε) is a fundamental parameter in material sciences to measure polarizability of the system. In industrial processes, its value is an imperative indicator, which demonstrates the dielectric property of material and compiles information including separation information, chemical equilibrium, chemical reactivity analysis, and solubility modeling. Since, the available ε-prediction models are fairly primitive and frequently suffer from serious failures especially when deals with strong polar compounds. Therefore, we have developed a novel data-driven system to improve the efficiency and wide-range applicability of ε using in material sciences. This innovative scheme adopts the correlation distance and genetic algorithm to discriminate features’ combination and avoid overfitting. Herein, the prediction output of the single ML model as a coding to estimate the target value by simulating the layer-by-layer extraction in deep learning, and enabling instant search for the optimal combination of features is recruited. Our model established an improved correlation value of 0.956 with target as compared to the previously available best traditional ML result of 0.877. Our framework established a profound improvement, especially for material systems possessing ε value >50. In terms of interpretability, we have derived a conceptual computational equation from a minimum generating tree. Our innovative data-driven system is preferentially superior over other methods due to its application for the prediction of dielectric constants as well as for the prediction of overall micro and macro-properties of any multi-components complex.

De novo molecular design with deep molecular generative models for PPI inhibitors

We construct a protein-protein interaction (PPI) targeted drug-likeness dataset and propose a deep molecular generative framework to generate novel drug-likeness molecules from the features of the seed compounds. This framework gains inspiration from published molecular generative models, uses the key features associated with PPI inhibitors as input and develops deep molecular generative models for de novo molecular design of PPI inhibitors. For the first time, quantitative estimation index for compounds targeting PPI was applied to the evaluation of the molecular generation model for de novo design of PPI-targeted compounds. Our results estimated that the generated molecules had better PPI-targeted drug-likeness and drug-likeness. Additionally, our model also exhibits comparable performance to other several state-of-the-art molecule generation models. The generated molecules share chemical space with iPPI-DB inhibitors as demonstrated by chemical space analysis. The peptide characterization-oriented design of PPI inhibitors and the ligand-based design of PPI inhibitors are explored. Finally, we recommend that this framework will be an important step forward for the de novo design of PPI-targeted therapeutics.

3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors

Spleen tyrosine kinase (SYK) is an essential mediator of immune cell signaling and has been anticipated as a therapeutic target for autoimmune diseases, notably rheumatoid arthritis, allergic rhinitis, asthma, and cancers. Significant attempts have been undertaken in recent years to develop SYK inhibitors; however, limited success has been achieved due to poor pharmacokinetics and adverse effects of inhibitors. The primary goal of this research was to identify potential inhibitors having high affinity, selectivity based on key molecular interactions, and good drug-like properties than the available inhibitor, fostamatinib. In this study, a 3D-QSAR model was built for SYK based on known inhibitor IC₅₀ values. The best pharmacophore model was then used as a 3D query to screen a drug-like database to retrieve hits with novel chemical scaffolds. The obtained compounds were subjected to binding affinity prediction using the molecular docking approach, and the results were subsequently validated using molecular dynamics (MD) simulations. The simulated compounds were ranked according to binding free energy (ΔG), and the binding affinity was compared with fostamatinib. The binding mode analysis of selected compounds revealed that the hit compounds form hydrogen bond interactions with hinge region residue Ala451, glycine-rich loop residue Lys375, Ser379, and DFG motif Asp512. Identified hits were also observed to form a desirable interaction with Pro455 and Asn457, the rare feature observed in SYK inhibitors. Therefore, we argue that identified hit compounds ZINC98363745, ZINC98365358, ZINC98364133, and ZINC08789982 may help in drug design against SYK.

Exploring the molecular mechanism of hepatitis virus inducing hepatocellular carcinoma by microarray data and immune infiltrates analysis

The number of new cases of hepatocellular carcinoma (HCC) worldwide reached 910,000, ranking the sixth, 80% HCC is associated with viruses, so exploring the molecular mechanism of viral carcinogenicity is imperative. The study showed that both HBV and HCV associated HCC and non-viral HCC have the same molecular phenotype (low gene expression and inhibition of immune pathways), but in the tumor immune micro-environment, there is excessive M2-type macrophage polarization in virus-associated hepatocellular carcinoma. To address this phenomenon, the data sets were analyzed and identified five hub genes (POLR2A, POLR2B, RPL5, RPS6, RPL23A) involved in viral gene expression and associated with PI3K-Akt-mTOR pathway activation by six algorithms. In addition, numerous studies have reported that M2-type macrophages participate in the hepatic fibro-pathological process of the development of HCC and are regulated by the PI3K-Akt-mTOR pathway. On this basis, the study showed that hepatitis virus causes abnormal expression of hub genes, leading to the activation of the pathway, which in turn promote the differentiation of M2-type macrophages and eventually promote the formation of liver fibrosis, leading to the occurrence of HCC. In addition, these hub genes are regulated by transcription factors and m⁶A enzyme, and have good prognosis and diagnostic value. With regard to drug reuse, the results suggest that patients with virus-related HCC for whom Cytidine triphosphate disodium salt and Guanosine-5'-Triphosphate are used as supplementary therapy, and may have a better prognosis. In conclusion, the study has identified novel molecules that are carcinogenic to hepatitis viruses and are expected to serve as molecular markers and targets for diagnosis and treatment.

Traditional knowledge about medicinal plant in the remote areas of Wari Tehsil, Dir Upper, Pakistan

Traditional medicine is cheaper and easily available to local people, to care for most frequent diseases in the Northern parts of Pakistan. Our study aimed at inventorying medicine from local plants, documenting their uses, and assessing their market value in 2015-2018 during spring, summer, and winter seasons. A total of 15 trips were made, 5 in each season. Semi-structured interviews with 165 inhabitant's age range between 20-80 years were conducted, analyzed the data is analyzed using Relative frequency of citation(RFC), Use Value(UV), Fidelity Level(FL), Informants consensus factor(ICF), and Jaccard index(JI) to find the most frequent and well-known used species in the area. A total of 86 species belonging to 39 vascular plant families, 33 genera were documented as medicinally important. Family Asteraceae was observed as the dominant family among all the families with 10 species, the leaf was the most used parts and decoction 36% was the most preferred preparation type. Herb was the predominant life form (67%). The maximum UV (0.92) was demonstrated by J. adhatoda L. species, while A. sativum L. shows maximum RFC (0.58), the highest ICF value represented by diarrhea and dermatitis 0.92, and high FL value is recorded 100%. According to our collections, wild species were 45%, invasive species were 38% and cultivated 17% recorded, dicots species were recorded more 81%. Seven 7 medicinal species is being economically important and export to the local and international market of the world, whereas P. integrima L. species were the most exported species according to the local dealers. The investigated area is rural and the local people depend on the area's plants for their health needs, and other uses like a vegetable, fuelwood, fodder, etc. The current result of RFC, UV, ICF, FL, and JI shows that medicinal flora needs to be pharmacologically and phytochemically investigated to prove their efficacy. The documentation of medicinal knowledge is important to preserve this precious old knowledge before it is lost forever, due to technological and environmental changes in the world.

Postoperative complications and waiting time for surgical intervention after radiologically guided drainage of intra-abdominal abscess in patients with Crohn's disease

BACKGROUND

In patients with active Crohn's disease (CD), treatment of intra-abdominal abscess usually comprises antibiotics and radiologically guided percutaneous drainage (PD) preceding surgery. The aim of this study was to investigate the risk of postoperative complications and identify the optimal time interval for surgical intervention after PD.

METHODS

A multicentre, international, retrospective cohort study was carried out. Details of patients with diagnosis of CD who underwent ultrasonography- or CT-guided PD were retrieved from hospital records using international classification of disease (ICD-10) diagnosis code for CD combined with procedure code for PD. Clinical variables were retrieved and the following outcomes were measured: 30-day postoperative overall complications, intra-abdominal septic complications, unplanned intraoperative adverse events, surgical-site infections, sepsis and pathological postoperative ileus, in addition to abscess recurrence. Patients were categorized into three groups according to the length of the interval from PD to surgery (1-14 days, 15-30 days and more than 30 days) for comparison of outcomes.

RESULTS

The cohort comprised 335 CD patients with PD followed by surgery. Median age was 33 (i.q.r. 24-44) years, 152 (45.4 per cent) were females, and median disease duration was 9 (i.q.r. 3.6-15) years. Overall, the 30-day postoperative complications rate was 32.2 per cent and the mortality rate was 1.5 per cent. After adjustment for co-variables, older age (odds ratio 1.03 (95 per cent c.i. 1.01 to 1.06), P < 0.012), residual abscess after PD (odds ratio 0.374 (95 per cent c.i. 0.19 to 0.74), P < 0.014), smoking (odds ratio 1.89 (95 per cent c.i. 1.01 to 3.53), P = 0.049) and low serum albumin concentration (odds ratio 0.921 (95 per cent c.i. 0.89 to 0.96), P < 0.001) were associated with higher rates of postoperative complications. A short waiting interval, less than 2 weeks after PD, was associated with a high incidence of abscess recurrence (odds ratio 0.59 (95 per cent c.i. 0.36 to 0.96), P = 0.042).

CONCLUSION

Smoking, low serum albumin concentration and older age were significantly associated with postoperative complications. An interval of at least 2 weeks after successful PD correlated with reduced risk of abscess recurrence.

Phytochemical analysis and biological activities of ethanolic extract of Curcuma longa rhizome

Curcuma longa is an important dietary plant which possess several pharmacological activities, including antioxidant, antimicrobial, anti-inflamatory, anticancer and anti clotting etc. The aim of the present study was to determine the phenolic profile of Curcuma longa and in vitro antioxidant and antidiabetic activities. In HPLC chromatogram of Curcuma longa rhizome extract 15 phenolic compounds were identified namely Digalloyl-hexoside, Caffeic acid hexoside, Curdione, Coumaric, Caffeic acid, Sinapic acid, Qurecetin-3-D-galactoside, Casuarinin, Bisdemethoxycurcumin, Curcuminol, Demethoxycurcumin, and Isorhamnetin, Valoneic acid bilactone, Curcumin, Curcumin-O-glucuronide respectively. The ethanolic extract displayed an IC50 value of 37.1±0.3 µg/ml against alpha glucosidase. The IC50 value of DPPH radical scavenging activity was 27.2 ± 1.1 μg/mL. It is concluded that ethanolic extract of Curcuma long is rich source of curcumin and contain several important phenolics. The in vitro antioxidant and alpha glucosidase inhibitory effect of the plant justifies its popular use in traditional medicine.

Development, Characterization, and Evaluation of SLN-Loaded Thermoresponsive Hydrogel System of Topotecan as Biological Macromolecule for Colorectal Delivery

BACKGROUND

Chemotherapeutic drugs cause severe toxicities if administered unprotected, without proper targeting, and controlled release. In this study, we developed topotecan- (TPT-) loaded solid lipid nanoparticles (SLNs) for their chemotherapeutic effect against colorectal cancer. The TPT-SLNs were further incorporated into a thermoresponsive hydrogel system (TRHS) (TPT-SLNs-TRHS) to ensure control release and reduce toxicity of the drug. Microemulsion technique and cold method were, respectively, used to develop TPT-SLNs and TPT-SLNs-TRHS. Particle size, polydispersive index (PDI), and incorporation efficiency (IE) of the TPT-SLNs were determined. Similarly, gelation time, gel strength, and bioadhesive force studies of the TPT-SLNs-TRHS were performed. Additionally, in vitro release and pharmacokinetic and antitumour evaluations of the formulation were done.

RESULTS

TPT-SLNs have uniformly distributed particles with mean size in nanorange (174 nm) and IE of ~90%. TPT-SLNs-TRHS demonstrated suitable gelation properties upon administration into the rat's rectum. Moreover, drug release was exhibited in a control manner over an extended period of time for the incorporated TPT. Pharmacokinetic studies showed enhanced bioavailability of the TPT with improved plasma concentration and AUC. Further, it showed significantly enhanced antitumour effect in tumour-bearing mice as compared to the test formulations.

CONCLUSION

It can be concluded that SLNs incorporated in TRHS could be a potential source of the antitumour drug delivery with better control of the drug release and no toxicity.

Synthesis and Biological Evaluation of Amoxicillin Loaded Hybrid Material Composite Spheres Against Methicillin-Resistant Staphylococcus aureus

BACKGROUND

Incoherent use of antibiotics has led toward resistance in MRSA, becoming multidrug-resistant with a high rate of virulence in the community and hospital settings.

OBJECTIVE

Synergistic anti-MRSA activity was investigated in this study for hybrid material composite spheres of amoxicillin, Ag nanoparticles, and chitosan, which were prepared by one-step synthesis method, and various characterizations were performed.

METHODS

Antimicrobial-susceptibility assay on MRSA was achieved by disc diffusion and agar dilution techniques, while agar well diffusion was used for hybrid composite spheres. The in vitro and cytotoxicity studies were conducted on the skin abrasion mouse model and MTT assay on RD cell, respectively.

RESULTS

All isolates showed resistance to the tested antibiotics except vancomycin. MIC against MRSA showed high resistance with amoxicillin from 4 to 128 mg L^-1. The mean diameter of chitosan spheres and Ag nanoparticles was 02 mm and 277 nm, respectively. Morphology of spheres was uneven, varied, porous, and irregular in SEM, and Ag nanoparticles presence and formation was also seen in the micrograph. No substantial interface among drug, nanoparticles, and polymer was found in XRD, and IR showed characteristic peaks of all compounds in the formulation. The in vitro assay showed augmented anti-MRSA activity with amoxicillin loaded hybrid composite spheres (22-29 mm). A significant reduction in microbial burden (~6.5 log₁₀ CFU mL^-1) was seen in vivo with loaded hybrid composite spheres formulation. The MTT assay indicated no potential cytotoxicity with hybrid composite spheres.

CONCLUSION

The synergistic effect of Amoxycillin in the current study predicts a promising hybrid formulation with enhanced anti-MRSA activity.

In-vitro and in-vivo evaluation of the antibacterial potential of Typha elephantina

The present study was aimed to evaluate the in-vitro and in-vivo antibacterial effects of the Typha elephantina aqueous extract (TE.AQ), ethanolic extract (TE.ET) and T. elephantina methanolic extract (TE.ME) against eight selected clinical pathogens. The test samples were tested for in-vitro analysis (by disc diffusion method) at different concentrations of 5, 15, 25, 50 and 100 mg/dL against both gram positive and gram-negative strains. The highest potential was observed in TE.ME at a concentration of 100 mg/dL against Pseudomonas aeruginosa exhibiting 19.67 ± 0.577 mm zone of inhibition (ZOI). The same fraction also showed good activity against Staphylococus aureus with ZOI of 17.50 ± 0.70 mm. The TE.ET was found most active against P. aeruginosa and Streptococcus pyogenes having ZOI of 18.53 ± 0.503 and 16.2 ± 1.55 mm respectively at a concentration of 100 mg/dL. The most sensitive bacteria P. aeruginosa was selected for in-vivo study (using poultry chicks) for induction of infection in chicks. The effects of TE.AQ, TE.ET and TE.ME were determined at concentrations of 300 mg/kg body weight based on hematological parameters, liver enzymes and gross pathological findings of lungs and livers. The findings of the in-vivo study in chick's model showed that treatment of experimental animals with TE.ME significantly restored the hematological parameters, liver enzymes and architecture of lungs and livers. Based on scientific evidence, the current study suggests that TE.ME may serve as a best and new natural antibacterial agent and can be used against infections caused by P. aeruginosa.

Isolation and Characterization of an Acidic, Salt-Tolerant Endoglucanase Cel5A from a Bacterial Strain Martelella endophytica YC6887 Genome

A Martelella endophytica (M. endophytica) strain YC6887 was previously isolated from the roots of a halophyte, Rosa rugosa, which was sequenced and characterized. The genomic and proteomic analysis showed a carbohydrate-degrading enzyme, endoglucanase Cel5A which was further characterized. The protein analysis revealed that this endoglucanase belongs to glycosidic hydrolase family 5 (GH5) with catalytic domain. This gene encodes 349-residue polypeptide and shows closest similarity with cellulases of other Martelella species. The protein was purified to homogeneity and shown that it was a 39 kDa protein. The purified recombinant Cel5A endoglucanase exhibited maximum activity at 50 °C and pH 4.5. The enzyme was salt tolerant and retained more than 50% residual activity up to 15% NaCl. The homology model structure of Cel5A displayed that it is stable and compact protein structure consisting of eleven α-helical structures and eight β-sheets. According to the predicted ligand binding site after superimposition with Pseudomonas stutzeri endoglucanase Cel5A (PDB ID: 4LX4), it consisted of five amino acid Asn157, Tyr116, Glu158, Glu270 and Trp303 that may be the expected active site of Cel5A from YC6887. This presented that our strain M. endophytica YC6887 that produces cellulase partially degrade the insoluble polysaccharides into reducing sugars.

In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics

Drug resistance is a core issue in cancer chemotherapy. A known folate antagonist, methotrexate (MTX) inhibits human dihydrofolate reductase (hDHFR), the enzyme responsible for the catalysis of 7,8-dihydrofolate reduction to 5,6,7,8-tetrahydrofolate, in biosynthesis and cell proliferation. Structural change in the DHFR enzyme is a significant cause of resistance and the subsequent loss of MTX. In the current study, wild type hDHFR and double mutant (engineered variant) F31R/Q35E (PDB ID: 3EIG) were subject to computational study. Structure-based pharmacophore modeling was carried out for wild type (WT) and mutant (MT) (variant F31R/Q35E) hDHFR structures by generating ten models for each. Two pharmacophore models, WT-pharma and MT-pharma, were selected for further computations, and showed excellent ROC curve quality. Additionally, the selected pharmacophore models were validated by the Guner-Henry decoy test method, which yielded high goodness of fit for WT-hDHFR and MT-hDHFR. Using a SMILES string of MTX in ZINC¹⁵ with the selections of 'clean', in vitro and in vivo options, 32 MTX-analogs were obtained. Eight analogs were filtered out due to their drug-like properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment tests and Lipinski's Rule of five. WT-pharma and MT-pharma were further employed as a 3D query in virtual screening with drug-like MTX analogs. Subsequently, seven screening hits along with a reference compound (MTX) were subjected to molecular docking in the active site of WT- and MT-hDHFR. Through a clustering analysis and examination of protein-ligand interactions, one compound was found with a ChemPLP fitness score greater than that of MTX (reference compound). Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM/PBSA binding free energy. In conclusion, we report on an MTX analog which is capable of inhibiting hDHFR in wild type form, as well as in cases where the enzyme acquires resistance to drugs during chemotherapy treatment.

Effectiveness of occupational therapy in improving activities of daily living performance in complete cervical tetraplegic patients; A quasi experimental study

OBJECTIVE

To determine the effectiveness of Occupational therapy (OT) in improving activities of daily living performance in complete cervical tetraplegic patients.

METHODS

A quasi experimental study was conducted at Paraplegic Center Peshawar from May 2018 to March 2019. Seventy two spinal cord injury patients with complete cervical tetraplegia having age 18-60 years were included in the study using non probability convenience sampling technique. A trained Occupational therapist conducted two occupational therapy sessions per day, three times a week on alternative days for a period of six weeks. Self-care portion of Spinal cord injury independence measure (SCIM) was used to collect pre and post data. Data was analyzed using SPSS version 20.

RESULTS

Mean age of the participants was 30.21±13.52.Majority of the participants were (n= 61, 84.7%) male while remaining 11 (15.3%) participants were female. Pre self-care total score was 0.39±0.987 and post self-care total score was 7.17±5.536. There was significant differences (P value <0.05) between pre and post scores of feeding, upper & lower body bathing, upper & lower body dressing, grooming and total self-care scores.

CONCLUSION

Occupational therapy significantly improves activities of daily living performance in complete cervical tetraplegic spinal cord injury patients.

Employment status of person with disability in Government Departments in Khyber Pakhtunkhwa Pakistan

Objective:

The objective of the study was to determine whether anticipated number of person with disabilities was employed in different government departments of Khyber Pakhtunkhwa (KPK), Pakistan.

Methods:

Using across sectional survey, data from 16 different departments of provincial government of KPK was collected by volunteers of ‘Friends of Paraplegics.

Results:

Out of total 1, 71,137 Govt. employees, only 1151 (0.67%) were person with disabilities. None of the included departments fulfilled 2% allocated job quota for person with disabilities. Majority of the employees included in study were from Elementary & Secondary Education Department (n=140345) and Agriculture, Livestock & Cooperation Department (n=14315). The number of person with disabilities in these departments were 960 (0.68%) and 68 (0.48%) respectively. The highest percentage of person with disabilities were working in Higher Education Archives & Libraries Department (1.65%)followed by Law, Parliamentary Affairs & Human Rights Department (1.42%), Planning & Development Department (1.39%) and Administration & Establishment Department (1.16%).

Conclusion:

It is concluded that a small number of person with disabilities are employed in different Govt. Departments. Moreover, these departments has not ensured providing 2% job quota for person with disabilities.

Identification of Novel Scaffolds with Dual Role as Antiepileptic and Anti-Breast Cancer

Aromatase inhibitors with an $\mathrm{IC}_{50}$ IC 50 value ranging from 1.4 to 49.7 µM are known to act as antiepileptic drugs besides being potential breast cancer inhibitors. The aim of the present study is to identify novel antiepileptic aromatase inhibitors with higher activity exploiting the ligand-based pharmacophore approach utilizing the experimentally known inhibitors. The resultant Hypo1 consists of four features and was further validated by using three different strategies. Hypo1 was allowed to screen different databases to identify lead molecules and were further subjected to Lipinski's Rule of Five and ADMET to establish their drug-like properties. Consequently, the obtained 68-screened molecules were subjected to molecular docking by GOLD v5.2.2. Furthermore, the compounds with the highest dock scores were assessed for molecular interactions. Later, the MD simulation was applied to evaluate the protein backbone stabilities and binding energies adapting GROMACS v5.0.6 and MM/PBSA which was followed by the density functional theory (DFT), to analyze their orbital energies, and further the energy gap between them. Eventually, the number of Hit molecules was culled to three projecting Hit1, Hit2, and Hit3 as the potential lead compounds based on their highest dock scores, hydrogen bond interaction, lowest energy gap, and the least binding energies and stable MD results.

Spinal cord injury due to fall from electricity poles after electrocution

Objective:

The objective of this study was to report epidemiology, complications and rehabilitation outcomes of patients who sustained spinal cord injury (SCI) due to fall from electricity poles after electrocution.

Methods:

A prospective observational study was conducted in which patients admitted to Paraplegic Centre Peshawar from July 2016 to July 2018 who sustained SCI due to fall from electricity poles after electrocution were included. Of total 852 patients, 39 (4.58%) sustained SCI due to fall from electricity poles after electrocution. Two patients were excluded and data of 37 patients was analyzed.

Results:

The mean age of the participants was 35.03±13.47 years. Twenty-two (59.4%) patients had associated burns on different parts of body. Twenty-seven (72.9%) had pressure ulcers, 31 (83.8%) had spasticity, 18 (48.6%) had neuropathic pain and 2 (5.4%) had limb amputations due to injury. Mean Spinal cord injury independence measure score at the time of discharge was 53.4±5.7.

Conclusion:

SCI due to fall from electricity poles after electrocution is rare however combined effect of injury by electricity along with fall from electricity poles are associated with severe complications. Rehabilitation outcomes in these patients are also minimal

Computational Simulations Identify Pyrrolidine-2,3-Dione Derivatives as Novel Inhibitors of Cdk5/p25 Complex to Attenuate Alzheimer's Pathology

: Mechanistically, neurotoxic insults provoke Ca2+-mediated calpain activation, which cleaves the cytoplasmic region of membrane-embedded p35 and produces its truncated form p25. Upon physical interaction, cyclin-dependent kinase 5 (Cdk5) and p25 forms hyperactivated Cdk5/p25 complex and causes severe neuropathological aberrations including hyperphosphorylated tau-mediated neurofibrillary tangles formation, Alzheimer's symptoms, and neuronal death. Therefore, the inhibition of Cdk5/p25 complex may relieve p-tau-mediated Alzheimer's pathology. Herein, computational simulations have identified pyrrolidine-2,3-dione derivatives as novel inhibitors of Cdk5/p25 complex. A ligand-based pharmacophore was designed and employed as 3D query to retrieve drug-like molecules from chemical databases. By molecular docking, drug-like molecules obtaining dock score > 67.67 (Goldcore of the reference compound) were identified. Molecular dynamics simulation and binding free energy calculation retrieved four pyrrolidine-2,3-dione derivatives as novel candidate inhibitors of Cdk5/p25. The root means square deviation of Cdk5/p25 in complex with candidate inhibitors obtained an average value of ~2.15 Å during the 30 ns simulation period. Molecular interactions analysis suggested that each inhibitor occupied the ATP-binding site of Cdk5/p25 and formed stable interactions. Finally, the binding free energy estimation suggested that each inhibitor had lowest binding energy than the reference compound (-113.10 kJ/mol) to recapitulate their strong binding with Cdk5/p25. Overall, these inhibitors could mitigate tau-mediated Alzheimer's phenotype.

Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders

Deregulation of Cdk5 is a hallmark in neurodegenerative diseases and its complex with p25 forms Cdk5/p25, thereby causes severe neuropathological insults. Cdk5/p25 abnormally phosphorylates tau protein, and induces tau-associated neurofibrillary tangles in neurological disorders. Therefore, the pharmacological inhibition of Cdk5/p25 alleviates tau-associated neurological disorders. Herein, computational simulations probed two candidate inhibitors of Cdk5/p25. Structure-based pharmacophore investigated the essential complementary chemical features of ATP-binding site of Cdk5 in complex with roscovitine. Resultant pharmacophore harbored polar interactions with Cys83 and Asp86 residues and non-polar interactions with Ile10, Phe80, and Lys133 residues of Cdk5. The chemical space of selected pharmacophore was comprised of two hydrogen bond donors, one hydrogen bond acceptor, and three hydrophobic features. Decoy test validation of pharmacophore obtained highest Guner-Henry score (0.88) and enrichment factor score (7.23). The screening of natural product drug-like databases by validated pharmacophore retrieved 1126 compounds as candidate inhibitors of Cdk5/p25. The docking of candidate inhibitors filtered 10 molecules with docking score >80.00 and established polar and non-polar interactions with the ATP-binding site residues of Cdk5/p25. Finally, molecular dynamics simulation and binding free energy analyses identified two candidate inhibitors of Cdk5/p25. During 30 ns simulation, the candidate inhibitors established <3.0 Å root mean square deviation and stable hydrogen bond interactions with the ATP-binding site residues of Cdk5/p25. The final candidate inhibitors obtained lowest binding free energies of -122.18 kJ/mol and - 117.26 kJ/mol with Cdk5/p25. Overall, we recommend two natural product candidate inhibitors to target the pharmacological inhibition of Cdk5/p25 in tau-associated neurological disorders.

Structure-Based Drug Designing Recommends HDAC6 Inhibitors To Attenuate Microtubule-Associated Tau-Pathogenesis

Protein acetylation and deacetylation play vital roles in the structural and physiological behavior of target proteins. Histone deacetylase 6 (HDAC6) remains a key therapeutic target in several chronic diseases such as cancer, neurodegenerative, and hematological diseases. In tau-pathogenesis, HDAC6 tightly regulates microtubule-associated tau physiology, and its inhibition suppresses Alzheimer's phenotype. To this end, the current study has identified novel HDAC6 inhibitors by structure-based drug designing method. A pharmacophore was generated from HDAC6 in complex with trichostatin A. The selected pharmacophore had five features including two hydrogen bond donors, one hydrogen bond acceptor, and two hydrophobic features. Pharmacophore validation obtained the highest GH score of 0.80. By applying Lipinski's rule of five and ADMET Descriptors, a drug-like database of 29 183 molecules was generated from the Zinc Natural Product Database. The validated pharmacophore screened 841 drug-like molecules and was subsequently subjected to molecular docking in the active site of HDAC6. Molecular docking identified 11 hits, where they showed the highest ChemPLP score (>90.00), stable conformation, and hydrogen-bond interactions with catalytic residues of HDAC6. Finally, molecular dynamics simulation identified three molecules as potent HDAC6 inhibitors with stable root-mean-square deviation and the highest number of hydrogen bonds with the catalytic residues of HDAC6. Overall, we recommend three novel inhibitors of HDAC6, capable of suppressing the microtubule-associated tau-pathogenesis.

Discovery of Novel Acetylcholinesterase Inhibitors as Potential Candidates for the Treatment of Alzheimer's Disease

Acetylcholinesterase (AChE) catalyzes the hydrolysis of neurotransmitter acetylcholine to acetate and choline in a synaptic cleft. Deficits in cholinergic neurotransmitters are linked closely with the progression of Alzheimer’s disease (AD), which is a neurodegenerative disorder characterized by memory impairment, and a disordered cognitive function. Since the previously approved AChE inhibitors, donepezil (Aricept), galantamine (Reminyl), and rivastigmine (Exelon), have side effects and several studies are being carried out out to develop novel AD drugs, we have applied a three-dimensional quantitative structure−activity relationship (3D QSAR) and structure-based pharmacophore modeling methodologies to identify potential candidate inhibitors against AChE. Herein, 3D QSAR and structure-based pharmacophore models were built from known inhibitors and crystal structures of human AChE in complex with donepezil, galantamine, huperzine A, and huprine W, respectively. The generated models were used as 3D queries to screen new scaffolds from various chemical databases. The hit compounds obtained from the virtual screening were subjected to an assessment of drug-like properties, followed by molecular docking. The final hit compounds were selected based on binding modes and molecular interactions in the active site of the enzyme. Furthermore, molecular dynamics simulations for AChE in complex with the final hits were performed to evaluate that they maintained stable interactions with the active site residues. The binding free energies of the final hits were also calculated using molecular mechanics/Poisson-Boltzmann surface area method. Taken together, we proposed that these hits can be promising candidates for anti-AD drugs.

In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics

Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes thereduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of humanDHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cellproliferation. In the current study, ligand-based pharmacophore modeling identified and evaluatedthe critical chemical features of hDHFR inhibitors. A pharmacophore model (Hypo1) was generatedfrom known inhibitors of DHFR with a correlation coefficient (0.94), root mean square (RMS)deviation (0.99), and total cost value (125.28). Hypo1 was comprised of four chemical features,including two hydrogen bond donors (HDB), one hydrogen bond acceptor (HBA), and onehydrophobic (HYP). Hypo1 was validated using Fischer's randomization, test set, and decoy setvalidations, employed as a 3D query in a virtual screening at Maybridge, Chembridge, Asinex,National Cancer Institute (NCI), and Zinc databases. Hypo1-retrieved compounds were filtered byan absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment test andLipinski's rule of five, where the drug-like hit compounds were identified. The hit compounds weredocked in the active site of hDHFR and compounds with Goldfitness score was greater than 44.67(docking score for the reference compound), clustering analysis, and hydrogen bond interactionswere identified. Furthermore, molecular dynamics (MD) simulation identified three compounds asthe best inhibitors of hDHFR with the lowest root mean square deviation (1.2 Å to 1.8 Å), hydrogenbond interactions with hDHFR, and low binding free energy (-127 kJ/mol to -178 kJ/mol). Finally,the toxicity prediction by computer (TOPKAT) affirmed the safety of the novel inhibitors of hDHFRin human body. Overall, we recommend novel hit compounds of hDHFR for cancer and rheumatoidarthritis chemotherapeutics.

Discovery of Potential Plant-Derived Peptide Deformylase (PDF) Inhibitors for Multidrug-Resistant Bacteria Using Computational Studies

Bacterial peptide deformylase (PDF) is an attractive target for developing novel inhibitors against several types of multidrug-resistant bacteria. The objective of the current study is to retrieve potential phytochemicals as prospective drugs against Staphylococcus aureus peptide deformylase (SaPDF). The current study focuses on applying ligand-based pharmacophore model (PharmL) and receptor-based pharmacophore (PharmR) approaches. Utilizing 20 known active compounds, pharmL was built and validated using Fischer's randomization, test set method and the decoy set method. PharmR was generated from the knowledge imparted by the Interaction Generation protocol implemented on the Discovery Studio (DS) v4.5 and was validated using the decoy set that was employed for pharmL. The selection of pharmR was performed based upon the selectivity score and further utilizing the Pharmacophore Comparison module available on the DS. Subsequently, the validated pharmacophore models were escalated for Taiwan Indigenous Plants (TIP) database screening and furthermore, a drug-like evaluation was performed. Molecular docking was initiated for the resultant compounds, employing CDOCKER (available on the DS) and GOLD. Eventually, the stability of the final PDF⁻hit complexes was affirmed using molecular dynamics (MD) simulation conducted by GROMACS v5.0.6. The redeemed hits demonstrated a similar binding mode and stable intermolecular interactions with the key residues, as determined by no aberrant behaviour for 50 ns. Taken together, it can be stated that the hits can act as putative scaffolds against SaPDF, with a higher therapeutic value. Furthermore, they can act as fundamental structures for designing new drug candidates.

Identification of Proteins Differentially Expressed in the Striatum by Melatonin in a Middle Cerebral Artery Occlusion Rat Model-a Proteomic and in silico Approach

Ischemic stroke is characterized by permanent or transient obstruction of blood flow, which initiates a cascading pathological process, starting from acute ATP loss to subsequent membrane depolarization, glutamate excitotoxicity, and calcium overload. Melatonin is a potent antioxidant that exerts protective effects in different experimental stroke models. In this study, melatonin effects were demonstrated by a proteomic and in silico approach. The proteomic study identified differentially expressed proteins by 2D gel electrophoresis in the striatum 24 h after middle cerebral artery occlusion. Proteomic analysis revealed several proteins with aberrant expression and was validated by western blot and immunofluorescence analysis. Homology modeling was performed to build 3D structures for γ-enolase, thioredoxin (TRX), and heat shock 60 (HSP60) by the template crystal structures using a protein data bank as a sequence database. The structure refinement of each model was achieved by energy minimization via molecular dynamic simulation, and the generated models were further assessed for stability by Procheck and ProSA. The models were processed for docking analysis using AutoDock Vina, and post-docking analysis was determined by discovery studio. The proteomic study showed decreased expression of γ-enolase, TRX, and protein phosphatase 2A subunit B and increased expression of collapsin response mediator protein 2 and HSP60 in the striatum after ischemic injury. Treatment with melatonin modulated the expression profiles of these proteins. This study demonstrated the neuroprotective role of melatonin in the ischemic striatum using a proteomic and in silico approach. Collectively, melatonin may act in a multimechanistic way by modulating the expression of several proteins in the ischemic striatum.

Epidemiology, Clinical Features and Consequences of Spinal Cord Injury in Children

OBJECTIVE

To describe epidemiology, clinical features and clinical consequences of Spinal Cord Injury (SCI) in children.

STUDY DESIGN

Case series.

PLACE AND DURATION OF STUDY

Paraplegic Centre, Hayatabad, Peshawar, from July 2011 to March 2017.

METHODOLOGY

SCI patients having age up to 15 years, admitted to Paraplegic Centre, were inducted in 2017. Exclusion criteria was foreign-national SCI patients, and/or SCI patients re-admitted to paraplegic centre. List of all SCI patients admitted to the centre was retrieved and 102 patients were identified. Data of these patients was evaluated for demographic information, physiological intactness (complete SCI/incomplete SCI), neurological level and complications.

RESULTS

A total of 102 patients (66 males and 36 females) with mean age 10.9 ±3.7 years were included in this study. Firearm injury was the most common cause (n=39, 38.2%) of SCI in these patients, followed by fall from height (n=23, 22.5%), road traffic accidents (n=14, 13.7%), and weight fallen over (n=14, 13.7%). Bomb blast injury (n=7, 6.9%), diving accident (n=3, 2.9%), and sports related injuries (n=2, 2.0%). Majority of the patients (n=82, 80.4%) had complete SCI (ASIA A); the commonest SCI level was thoracic region (n=59, 57.8%) and the least reported region was (n=14, 13.7%) cervical. Out of the total, 50 (49.0%) patients had pressure ulcer in which 15 (30.0%) patients were having grade IV pressure ulcer, 9 (18.0%), 15 (30.0%) and 11 (22.0%) patients were had grade I, grade II and grade III pressure ulcer, respectively.

CONCLUSION

Majority of causes of SCI in children are similar to those reported in adult population. However, the commonest causes of SCI in children in Pakistan were firearm injury and bomb blast, which are rarely reported in other countries. Like adult population, these children with SCI are prone to developing pressure ulcer.

Effectiveness of transcutaneous electrical nerve stimulation in management of neuropathic pain in patients with post traumatic incomplete spinal cord injuries

Objective:

To determine the effectiveness of Transcutaneous Electrical Nerve Stimulation (TENS) in management of neuropathic pain in post-traumatic incomplete spinal cord injury patients.

Methods:

A quasi-experimental study was conducted at from January 2017 to June 2017 at Paraplegic Center Hayatabad, Peshawar. Total 60 incomplete spinal cord injured patients with diagnosis of neuropathic pain were subjected to high frequency TENS of 80 HZ. One session was of 45 minutes while there were two sessions per day. TENS was applied for four days in a week and all patients were followed for eight week duration. Pain intensity was measured by using VAS (Visual analogue scale).

Results:

Mean pain intensity on VAS at baseline was 6.45 which was decreased to 4.77 post intervention at day-1 while it was decreased to 3.48 at day-4 of week one. After application of TENS for 8 weeks, mean pain intensity was decreased to 2.80 ± 1.74. During the consecutive sessions of the TENS application, the pain intensity decreases in a linear fashion and there were significant difference (p<0.05) between pre and post treatment sessions.

Conclusion:

TENS is useful and safe adjuvant in spinal cord injury patients for the management of neuropathic pain.

Molecular and in silico analyses validates pathogenicity of homozygous mutations in the NPR2 gene underlying variable phenotypes of Acromesomelic dysplasia, type Maroteaux

Homozygous and/or heterozygous loss of function mutations in the natriuretic peptide receptor B (NPR2) have been reported in causing acromesomelic dysplasia, type Maroteaux with variable clinical features and idiopathic short stature with nonspecific skeletal deformities. On the other hand, gain of function mutations in the same gene result in overgrowth disorder suggesting that NPR2 and its ligand, natriuretic peptide precursor C (CNP), are the key players of endochondral bone growth. However, the precise mechanism behind phenotypic variability of the NPR2 mutations is not fully understood so far. In the present study, three consanguineous families of Pakistani origin (A, B, C) with variable phenotypes of acromesomelic dysplasia, type Maroteaux were evaluated at clinical and molecular levels. Linkage analysis followed by Sanger sequencing of the NPR2 gene revealed three homozygous mutations including p.(Leu314 Arg), p.(Arg371*), and p.(Arg1032*) in family A, B and C, respectively. In silico structural and functional analyses substantiated that a novel missense mutation [p.(Leu314 Arg)] in family A allosterically affects binding of NPR2 homodimer to its ligand (CNP) which ultimately results in defective guanylate cyclase activity. A nonsense mutation [p.(Arg371*)] in family B entirely removed the transmembrane domain, protein kinase domain and guanylate cyclase domains of the NPR2 resulting in abolishing its guanylate cyclase activity. Another novel mutation [p.(Arg1032*)], found in family C, deteriorated the guanylate cyclase domain of the protein and probably plundered its guanylate cyclase activity. These results suggest that guanylate cyclase activity is the most critical function of the NPR2 and phenotypic severity of the NPR2 mutations is proportional to the reduction in its guanylate cyclase activity.

Investigation of non-hydroxamate scaffolds against HDAC6 inhibition: A pharmacophore modeling, molecular docking, and molecular dynamics simulation approach

Proteins deacetylation by Histone deacetylase 6 (HDAC6) has been shown in various human chronic diseases like neurodegenerative diseases and cancer, and hence is an important therapeutic target. Since, the existing inhibitors have hydroxamate group, and are not HDAC6-selective, therefore, this study has designed to investigate non-hydroxamate HDAC6 inhibitors. Ligand-based pharmacophore was generated from 26 training set compounds of HDAC6 inhibitors. The statistical parameters of pharmacophore (Hypo1) included lowest total cost of 115.63, highest cost difference of 135.00, lowest RMSD of 0.70 and the highest correlation of 0.98. The pharmacophore was validated by Fischer's Randomization and Test Set validation, and used as screening tool for chemical databases. The screened compounds were filtered by fit value ([Formula: see text]), estimated Inhibitory Concentration (IC[Formula: see text]) ([Formula: see text]), Lipinski's Rule of Five and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Descriptors to identify drug-like compounds. Furthermore, the drug-like compounds were docked into the active site of HDAC6. The best docked compounds were selected having goldfitness score [Formula: see text] and [Formula: see text], and hydrogen bond interaction with catalytic active residues. Finally, three inhibitors having sulfamoyl group were selected by Molecular Dynamic (MD) simulation, which showed stable root mean square deviation (RMSD) (1.6-1.9[Formula: see text]Å), lowest potential energy ([Formula: see text][Formula: see text]kJ/mol), and hydrogen bonding with catalytic active residues of HDAC6.

Targeting natural compounds against HER2 kinase domain as potential anticancer drugs applying pharmacophore based molecular modelling approaches

Human epidermal growth factor receptors are implicated in several types of cancers characterized by aberrant signal transduction. This family comprises of EGFR (ErbB1), HER2 (ErbB2, HER2/neu), HER3 (ErbB3), and HER4 (ErbB4). Amongst them, HER2 is associated with breast cancer and is one of the most valuable targets in addressing the breast cancer incidences. For the current investigation, we have performed 3D-QSAR based pharmacophore search for the identification of potential inhibitors against the kinase domain of HER2 protein. Correspondingly, a pharmacophore model, Hypo1, with four features was generated and was validated employing Fischer's randomization, test set method and the decoy test method. The validated pharmacophore was allowed to screen the colossal natural compounds database (UNPD). Subsequently, the identified 33 compounds were docked into the proteins active site along with the reference after subjecting them to ADMET and Lipinski's Rule of Five (RoF) employing the CDOCKER implemented on the Discovery Studio. The compounds that have displayed higher dock scores than the reference compound were scrutinized for interactions with the key residues and were escalated to MD simulations. Additionally, molecular dynamics simulations performed by GROMACS have rendered stable root mean square deviation values, radius of gyration and potential energy values. Eventually, based upon the molecular dock score, interactions between the ligands and the active site residues and the stable MD results, the number of Hits was culled to two identifying Hit1 and Hit2 has potential leads against HER2 breast cancers.

Ginger (Zingiber officinale) phytochemicals-gingerenone-A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches

BACKGROUND

Antibiotic resistance is a defense mechanism, harbored by pathogens to survive under unfavorable conditions. Among several antibiotic resistant microbial consortium, Staphylococcus aureus is one of the most havoc microorganisms. Staphylococcus aureus encodes a unique enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK), against which, none of existing antibiotics have been reported.

METHODS

Computational approaches have been instrumental in designing and discovering new drugs for several diseases. The present study highlights the impact of ginger phytochemicals on Staphylococcus aureus SaHPPK. Herein, we have retrieved eight ginger phytochemicals from published literature and investigated their inhibitory interactions with SaHPPK. To authenticate our work, the investigation proceeds considering the known antibiotics alongside the phytochemicals. Molecular docking was performed employing GOLD and CDOCKER. The compounds with the highest dock score from both the docking programmes were tested for their inhibitory capability in vitro. The binding conformations that were seated within the binding pocket showing strong interactions with the active sites residues rendered by highest dock score were forwarded towards the molecular dynamic (MD) simulation analysis.

RESULTS

Based on molecular dock scores, molecular interaction with catalytic active residues and MD simulations studies, two ginger phytochemicals, gingerenone-A and shogaol have been proposed as candidate inhibitors against Staphylococcus aureus. They have demonstrated higher dock scores than the known antibiotics and have represented interactions with the key residues within the active site. Furthermore, these compounds have rendered considerable inhibitory activity when tested in vitro. Additionally, their superiority was corroborated by stable MD results conducted for 100 ns employing GROMACS package.

CONCLUSIONS

Finally, we suggest that gingerenone-A and shogaol may either be potential SaHPPK inhibitors or can be used as fundamental platforms for novel SaHPPK inhibitor development.

Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Background

Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression.

Methods

In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2.

Results

The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW.

Conclusion

The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.

Chemistry and liquid chromatography methods for the analyses of primary oxidation products of triacylglycerols

Triacylglycerols (TAGs) are one of the major components of the cells in higher biological systems, which can act as an energy reservoir in the living cells. The unsaturated fatty acid moiety is the key site of oxidation and formation of oxidation compounds. The TAG free radical generates several primary oxidation compounds. These include hydroperoxides, hydroxides, epidioxides, hydroperoxy epidioxides, hydroxyl epidioxides, and epoxides. The presence of these oxidized TAGs in the cell increases the chances of several detrimental processes. For this purpose, several liquid chromatography (LC) methods were reported in their analyses. This review is therefore focused on the chemistry, oxidation, extraction, and the LC methods reported in the analyses of oxidized TAGs. The studies on thin-layer chromatography were mostly focused on the total oxidized TAGs separation and employ hexane as major solvent. High-performance LC (HPLC) methods were discussed in details along with their merits and demerits. It was found that most of the HPLC methods employed isocratic elution with methanol and acetonitrile as major solvents with an ultraviolet detector. The coupling of HPLC with mass spectrometry (MS) highly increases the efficiency of analysis as well as enables reliable structural elucidation. The use of MS was found to be helpful in studying the oxidation chemistry of TAGs and needs to be extended to the complex biological systems.

Prediction of pre-eclampsia during early pregnancy in primiparas with soluble fms-like tyrosine kinase-1 and placental growth factor

BACKGROUND

We hypothesized that pre-eclampsia (PE) can be predicted early in primiparas by measuring serum levels of soluble fms-like tyrosine kinase-1 (sFlt-1) and placental growth factor (PlGF).

METHODS

All normotensive primiparas attending the antenatal clinics of Aga Khan University Hospital and Aga Khan Hospital for Women, Karachi, Pakistan without any known risk factor for PE were invited to participate in the study. They were divided into two groups based on the development of PE. Their blood samples were collected at 8-15, 16-22, 23-28, 29v34 weeks of pregnancy and once within 1 week of delivery. All samples were analysed for sFlt-1 and PlGF.

RESULTS

Six hundred and eleven (46.7%) of 1307 recruited primiparas completed the study according to the protocol. Of these, 39 (6.4%) women developed PE. The difference in serum sFlt-1 was evident as early as 15 weeks of gestation. Higher levels of serum sFlt-1 were present in women who later developed PE. Relatively higher levels of PlGF were observed in non-PE women compared to PE women up to 22 weeks of gestation. However, after 23 weeks of pregnancy, PlGF levels increased in both the groups, but less so in the PE group. Receiver operator characteristics (ROC) curve analysis showed that even in early pregnancy (<15 weeks of gestation), serum sFlt-1 alone has the potential to predict PE with area under the curve (AUC), sensitivity and specificity of 0.81, 75.9 and 72.4, respectively.

CONCLUSION

PE can be predicted in primiparas in the early part of second trimester with serum levels of sFlt-1 and in the later part of second trimester with serum levels of PlGF.

(E)-1-(3-Nitro-phen-yl)ethanone (2-methyl-phen-yl)hydrazone

In the title Schiff base compound, C₁₅H₁₅N₃O₂, the azomethine double bond adopts an E configuration. The dihedral angle between the two aromatic rings is 13.4 (12)°. In the crystal, mol­ecules are arranged in wave-like layers parallel to (100) without any classical hydrogen bonding.

Effect of surfactants and dispersed components on the activity and reactivity of sorbic acid

In common with many other carboxylic acids, sorbic acid shows significant solubility in aqueous and non-aqueous solvents. The presence of a non-aqueous phase (e.g. fat) can markedly affect the concentration of the preservative in the aqueous phase. Solute distribution between the two phases is pH- and concentration-dependent. The presence of dissolved surfactants in the aqueous phase will also affect the activity of sorbic acid. This effect is due to the partitioning of the solute into surfactant micelles. The presence of dispersed components and surfactant micelles also has a marked effect on the reactivity of sorbic acid. Whereas thiols react slowly with sorbic acid, the rate of reaction is increased many-fold by the addition of low molecular weight surfactants. The mechanism of this catalysis will be explained. It has been suggested that sorbic acid inhibits enzymes by reacting with sulphydryl groups of the proteins. Kinetic data from model system studies suggest that the sorbic acid-thiol reaction may be too slow for it to be an obvious means of enzyme inhibition. However, this does not take account of possible catalysis of the reaction in the microenvironment of the protein, perhaps in a manner similar to that identified with low molecular weight surfactants.