Identification of potent anti-immunogenic agents through virtual screening, 3D-QSAR studies, and in vitro experiments.

A wealth of literature has highlighted the discovery of various immune modulators, frequently used in clinical practice, yet associated with numerous drawbacks. In light of this pharmacological deficiency, medical scientists are motivated to develop new immune modulators with minimized adverse effects yet retaining the improved therapeutic potential. T-cell differentiation and growth are central to human defense and are regulated by interleukin-2 (IL-2), an immune-modulatory cytokine. However, scientific investigation is hindered due to its flat binding site and widespread hotspot residues. In this regard, a prompt and logical investigation guided by integrated computational techniques was undertaken to unravel new and potential leads against IL-2. In particular, the combination of score-based and pharmacophore-based virtual screening approaches were employed, reducing the data from millions of small molecules to a manageable number. Subsequent docking and 3D-QSAR prediction via CoMFA further helped remove false positives from the data. The reliability of the model was assessed via standard metrics, which explain the model's fitness and the robustness of the model in predicting the activity of new compounds. The extensive virtual screening herein led to the identification of a total of 24 leads with potential anti-IL-2 activity. Furthermore, the theoretical findings were corroborated with in vitro testing, further endorsing the anti-inflammatory potential of the identified leads.

Computation-based experimentation: Identification of piperazine containing antidepressants.

Depression, a common mental disorder, is one of the major contributors to the overall global burden with more than 264 million individuals affected worldwide. Monoamine oxidase inhibitors (MAOIs) have well-known efficacy for treating depression and other related disorders. Herein we report the implementation of extensive in-silico calculations to predict the mono-amine inhibitory potential of an in-house library of piperazine-based compounds. In this connection, a multistep virtual screening protocol based on pharmacophore modeling, molecular docking and Quantitative Structure-Activity Relationship (QSAR) was carried out by MOE. Further, to assess its ability to cross the blood brain barrier, ADME properties of the compounds were predicted. Compounds predicted the highest enzyme inhibition by QSAR was synthesized for experimental validation. Both the synthesized compounds (I15 and I21) presented good strength against Monoamine Oxidase in in vitro enzyme inhibitory activity.

Molecular docking, synthesis and biological evaluation of phenacyl derivatives of 9-aminoacridine as anti-Alzheimer's agent.

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder mainly characterized by progressive deterioration of memory and impaired cognitive function. The most promising approach for symptomatic relief of AD is to inhibit acetylcholinesterase (AChE). On the basis of this approach in-house library of 9-aminoacridine derivatives were constructed and allowed to docked against human acetylcholinesterase (hAChE) (PDB ID: 4EY7), using MOE 2018.01 and PyRx 0.9.2 (AutoDock Vina). Top ranked and best fitted molecules were synthesized by targeting the 9-amino group of aminoacridine with substituted phenacyl halides. Anti-Alzheimer's potential was checked by in vitro AChE inhibition, antioxidant activity (DPPH scavenging ability) and fibril disaggregation. Subjected ligands suggested as promising multitargeted candidate with pronounced results in term of IC50 values (AChE inhibition 2.400-26.138µM), however, none of them showed potential towards fibril inhibition.

Awareness, knowledge and attitude towards breast cancer, breast screening and early detection techniques among women in Pakistan.

OBJECTIVE: To document the knowledge and attitudes of women towards breast cancer, breast screening and early detection techniques. METHODS: This cross-sectional survey was conducted from December 2015 to May 2016 in Karachi and Islamabad, Pakistan, and comprised women aged above 18 years. The survey used breast cancer inventory as a research instrument after piloting and validation. SPSS 20 was used for data analysis. RESULTS: Of the 1,304 respondents, 948(72.7%) were single, 1,082(83%) belonged to the 18-30 age group, 800(61.3%) had Urdu-speaking ethnicity and 794(60.9%) were educated. The prevalence of breast cancer in family was 226(17.33%). Besides, 446(34.2%) had low knowledge regarding the subject, 646(49.5%) appeared welcoming to the idea of breast screening, 1,008(77.3%) indicated their discomfort in discussing the topic, whereas 1,080(82.8%)preferred a female physician. CONCLUSIONS: There was a dearth of knowledge regarding breast cancer among the participants..

Crude to leads: a triple-pronged direct NMR approach in coordination with docking simulation.

The screening of compounds that bind to the target of interest (specific proteins) plays a vital role in drug discovery. Usually, the identification of biologically active compounds is done from a library of structurally known compounds. However, we successfully illustrate here, that NMR techniques including saturation transfer difference (STD), transfer nuclear Overhauser spectroscopy (TrNOESY) and STD-TOCSY (total correlation spectroscopy) in combination with separation methods not only enable the rapid and comprehensive screening of active components, but also their unequivocal structural characterization. Furthermore, a time saving for the recognition of leads is also possible with this application. To probe the binding studies, a hydroethanolic fraction of crude extract (1 mg) from natural product (Rauia resinous) was used for the initial assessment with BSA protein. The docking simulation was performed with BSA in the region of Thr190, Arg198, Arg217, Trp213, Arg256, Ala290 and Tyr451 to further refine the active compound towards the leads. Docking results mimic binding as identified by STD, Tr-NOESY and STD-TOCSY. Isovetexine-2-rhamnosoide (2) was found to be most active through group epitope mapping results as well as the docking simulation with relative free energy of -7.2770. This experiment provided excellent results through the direct NMR screening method. Using Bovine Serum Albumin as a reference, we illustrate that this approach offers an excellent way for the first hand detection of the active constituents/inhibitors from natural remedies used in folk medicinal treatments.

Site-directed Fragnomics and MD Simulations Approaches to Identify Interleukin-2 Inhibitors.

INTRODUCTION: The aberrant expression of Interleukin-2 (IL2), the chief regulator of immunity, is associated with many auto-immune diseases. At present, there is no FDA approved drug targeting IL2, which puts forth the need for small molecular inhibitors to block IL2 and its receptor interaction. METHODOLOGY: Herein, we used the contemporary fragnomics approach to design novel drug-like inhibitors targeting IL2. Briefly, the RECAP (Retrosynthetic Combinatorial Analysis Procedure) package implemented in MOE (Molecular Operating Environment check) software suite was utilised to obtain fragments fulfilling the 'rule of three' criteria for fragments. The binding site of IL2 was divided into three smaller grooves, and the fragments were docked to screen their affinity for a particular site, followed by site-directed RECAP synthesis. RESULTS: A focused library of 10,000 compounds was prepared by re-combining the fragments according to their affinity for a particular site as observed in docking. Docking and subsequent analysis of newly synthesised compounds identified 40 privileged leads, presenting hydrogen bonding with basic residues of the pocket. A QSAR model was implied to predict the IC50 of the compounds and to analyse the electrostatic and hydrophobic contour maps. The resulting hits were found to be modest IL2 inhibitors with predicted inhibitory activity in the range of 5.17-4.40 nM. Further Dynamic simulation studies were carried out to determine the stability of the inhibitor-IL2 complex. CONCLUSION: Our findings underline the potential of the novel compounds as valuable pharmacological agents in diseases characterised by IL2 overexpression.

Estimation of the Direct Cost of Poliomyelitis Rehabilitation Treatment to Pakistani Patients: A 53-Year Retrospective Study.

BACKGROUND: Pakistan is one of the last few countries in which poliomyelitis is endemic. Evidence indicates that out-of-pocket expenditures are a barrier to polio rehabilitation treatment, yet there are no reported figures related to the financial burden of this disease on patients in a recently polio-endemic country. OBJECTIVE: This study investigated direct costs attributed to rehabilitation treatment of poliomyelitis among Pakistani patients and reported its duration along with the socioeconomic status of poliomyelitis survivors. CONCLUSION: The cost of poliomyelitis rehabilitation in Pakistan is high; it has an economic effect on the lives of patients and their families. Despite good education, polio survivors in Pakistan appear to have low socioeconomic status, lower chances of employment and marriage, as well as fewer children. Further research is recommended to explore the burden of disease on society, i.e., indirect costs and suffering.

In silico based investigation of dynamic variations in neprilysin (NEP and NEP2) proteins for extracting the point of specificity.

Neprilysin-2 (NEP2) in the central nervous system controls Alzheimer's protein (amyloid-ß) deposition, and prevents its occurrence. However, in the peripheral system, its closest homolog, neutral endopeptidase (NEP), regulates hypertension and heart related diseases. Inhibitors of NEP with a lesser degree of specificity can treat hypertension with an increased risk of cerebral deposition of amyloid-ß. In order to rationalize the point of selectivity, the dynamic behavior of human NEP and NEP2 proteins was monitored by conducting molecular dynamics (MD) simulations. A computationally reliable model of NEP2 was achieved with 79.9%, 19.1% and 0.2% residues in the allowed, additionally allowed and disallowed regions respectively, using as a reference protein. Additionally, molecular docking studies were carried out for a set of five already known inhibitors of NEP and modeled NEP2 to obtain the comparative behaviors of the complexes. MD results highlighted their different responses along with important residues having a part in ligand-protein binding. For substrate and inhibitor binding, Arg664/661 and Zn697/694 were identified as the most conserved residues. High degree flexible transitions during the MD simulations were also observed in loop areas along with active site residues. Energy calculations, hydrogen bonds and their occupancy rates helped to conclude each ligand's potency towards a particular target. In most complexes of hNEP2, the ligands showed weak interactions which might be due to its larger pocket size or huge conformational variations in active site residues upon complexation. In the case of inhibitors of a small size like thiorphan, Arg49 and Arg664 are found to be acting to support the ligand binding in NEP while only Arg661 is acting in NEP2.

Binding site identification and role of permanent water molecule of PIM-3 kinase: A molecular dynamics study.

The kinome is a protein kinase complement of the human genome, categorized as serine/threonine and tyrosine kinases. These kinases catalyze phosphorylation reaction by using ATP as phosphoryl donor. Proviral Integration Site for Moloney Murine Leukemia Virus (PIM) kinase encodes serine/threonine protein kinases that recognized as proto-oncogene, responsible for rapid growth of cancerous cells. It is implicated in cell survival and function via cell cycle progression and its metabolism. PIM-3, sub-member of PIM kinases is a proto-oncogene, its overexpression inhibits apoptosis, and results in progression of hepatocellular carcinoma. PIM-3 is considered as a promising drug target but attempts to develop its specific inhibitors is slowed down due to the lack of 3D structure by any experimental technique. In silico techniques generally facilitate scientist to explore hidden structural features in order to improve drug discovery. In the present study, homology modeling, molecular docking and MD simulation techniques were utilized to explore the structure and dynamics of PIM-3 kinase. Induction of water molecules during molecular docking simulation explored differences in the hinge region between PIM-1 and PIM-3 kinases that may be responsible for specificity. Furthermore, role of water molecules in the active site was also explored via radial distribution function (RDF) after a 10 ns molecular dynamics (MD) simulations. Generated RDF plots exhibited the importance of water for inhibitor binding through their bridging capability that links the ligand with binding site residues.

A combined 3D-QSAR and docking studies for the In-silico prediction of HIV-protease inhibitors.

BACKGROUND: Tremendous research from last twenty years has been pursued to cure human life against HIV virus. A large number of HIV protease inhibitors are in clinical trials but still it is an interesting target for researchers due to the viral ability to get mutated. Mutated viral strains led the drug ineffective but still used to increase the life span of HIV patients. RESULTS: In the present work, 3D-QSAR and docking studies were performed on a series of Danuravir derivatives, the most potent HIV- protease inhibitor known so far. Combined study of 3D-QSAR was applied for Danuravir derivatives using ligand-based and receptor-based protocols and generated models were compared. The results were in good agreement with the experimental results. Additionally, docking analysis of most active 32 and least active 46 compounds into wild type and mutated protein structures further verified our results. The 3D-QSAR and docking results revealed that compound 32 bind efficiently to the wild and mutated protein whereas, sufficient interactions were lost in compound 46. CONCLUSION: The combination of two computational techniques would helped to make a clear decision that compound 32 with well inhibitory activity bind more efficiently within the binding pocket even in case of mutant virus whereas compound 46 lost its interactions on mutation and marked as least active compound of the series. This is all due to the presence or absence of substituents on core structure, evaluated by 3D-QSAR studies. This set of information could be used to design highly potent drug candidates for both wild and mutated form of viruses.

In-silico analysis of chromone containing sulfonamide derivatives as human carbonic anhydrase inhibitors.

Computational tools of analysis were used on a set of synthetic chromone containing sulfonamide derivatives for evaluation of their enzyme inhibitory activity against Carbonic Anhydrase (CA) isozymes. GOLD docking software was utilized to dock the compounds against two human Carbonic Anhydrase (hCA) proteins; hCAII and hCA-IX. Differences in conformation and orientation of molecules within hCA-II and hCA-IX binding pockets were studied in detail which revealed that compounds with fluorine at R1 position and phenyl sulfonamide substituent at para position served as potent inhibitors against both proteins due to anomalous chemistry of fluorine atom. It was also noticed that the activity was decreased when sulfonamide moiety was shifted from para to meta position since it dragged the interacting specie of compounds away from Zn metal. Similarly, when substituents were replaced by F > Br > C2H5 > H, the activity declined due to the electronegativity effect. Binding interaction results against CA-IX seemed to be better than CA-II due to large binding cavity, predicting the more potent inhibitory activity against hCA-IX.