Identification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human α-GAL a and α-NAGA enzymes.

Fabry disease (FD) is caused by a defective α-galactosidase A (α-GAL A) enzyme responsible for breaking down globotriaosylceramide (Gb3). To develop affordable therapeutics, more effort is needed to obtain insights into the underlying mechanism of FD and understanding human α-GAL A structure and function in related animal models. We adopted C. elegans as a model to elucidate the sequence and 3D structure of its GANA-1 enzyme and compared it to human α-GAL A. We constructed GANA-1 3D structure by homology modelling and validated the quality of the predicted GANA-1 structure, followed by computational docking of human ligands. The GANA-1 protein shared sequence similarities up to 42.1% with the human α-GAL A in silico and had dual active sites. GANA-1 homology modelling showed that 11 out of 13 amino acids in the first active site of GANA-1 protein overlapped with the human α-GAL A active site, indicating the prospect for substrate cross-reaction. Computational molecular docking using human ligands like Gb3 (first pocket), 4-nitrophenyl-α-D-galactopyranoside (second pocket), α-galactose (second pocket), and N-acetyl-D-galactosamine (second pocket) showed negative binding energy. This revealed that the ligands were able to bind within both GANA-1 active sites, mimicking the human α-GAL A and α-NAGA enzymes. We identified human compounds with adequate docking scores, predicting robust interactions with the GANA-1 active site. Our data suggested that the C. elegans GANA-1 enzyme may possess structural and functional similarities to human α-GAL A, including an intrinsic capability to metabolize Gb3 deposits.Communicated by Ramaswamy H. Sarma.

Anti-Methanogenic Traits of Safflower Oil Compounds Against Methyl-Coenzyme M Reductase Receptor in Equines: An In Silico Docking Analysis.

Greenhouse gases emission from livestock is the major concern for the ecosystem. Despite the lower contribution of non-ruminants towards greenhouse gas emission as compared to the ruminants, the emission of methane (CH4) gas from equines is expected to be increased in future due to its increasing population. Thus, it is essential to find or screen potential anti-methanogenic agent in a cost-effective and quicker manner. Considering this, the present investigation was aimed to analyze anti-methanogenic characteristic of bioactive compounds of safflower oil by targeting methanogenesis catalyzing enzyme (Methyl-coenzyme M reductase; MCR) via in silico tool. Initially, a total of 25 compounds associated with safflower oil were selected and their drug-likeness traits were predicted through Lipinski's rule of 5. Of 25 compounds, 9 compounds passed all the parameters of Lipinski's rule of five. These 9 ligands were further submitted for ADME traits analysis using Swiss ADME tool. Results revealed the absence of Lipinski's violation and approval of drug-likeness attributes of methyl tetradecanoate, 3-isopropyl-6-methylenecyclohex-1-ene, trans-2,4-decadienal, cis-6-nonenal, limonene, syringic acids, matairesinol, acacetin, and 2,5-octanedione. Molecular docking analysis was performed for analyzing the affinity between the selected 9 ligands and MCR receptor using FRED v3.2.0 from OpenEye Scientific Software and Discovery Studio client v16.1.0. Results showed maximum binding interaction of acacetin with MCR with the chemguass4 score of -13.35. Other ligands showed comparatively lower binding affinity in the order of matairesinol (-12.43) > methyl tetradecanoate (-9.25) > cis-6-nonenal (-7.88) > syringic acids (-7.73) > limonene (-7.18) > trans-2,4-decadienal (-7.07) > 3-isopropyl-6-methylenecyclohex-1-ene (-7.01) > 2,5-octanedione (-7.0.). In a nutshell, these identified compounds were observed as potential agents to reduce CH4 production from equines by targeting MCR. This in silico study emphasized the role of safflower-associated compounds in developing anti-methanogenic drug for equines in future.

Natural bioactive compounds as a new source of promising G protein-coupled estrogen receptor (GPER) modulators: comprehensive in silico approach.

Cancer ranks in second place among the cause of death worldwide. Cancer progress in multiple stages of carcinogenesis and metastasis programs through complex pathways. Sex hormones and their receptors are the major factors in promoting cancer progression. Among them, G protein-coupled estrogen receptor-1 (GPER) has shown to mediate cellular signaling pathways and cancer cell proliferation. However, the lack of GPER protein structure limited the search for new modulators. In this study, we curated an extensive database of natural products to discover new potential GPER modulators. We used a combination of virtual screening techniques to generate a homology model of GPER and subsequently used that for the screening of 30,926 natural products from a public database to identify potential active modulators of GPER. The best hits were further screened through the ADMET filter and confirmed by docking analysis. Moreover, molecular dynamics simulations of best hits were also carried out to assess the stability of the ligand-GPER complex. This study predicted several potential GPER modulators with novel scaffolds that could be further investigated and used as the core for the development of novel GPER modulators.Communicated by Ramaswamy H. Sarma.

Prospect of Anterior Gradient 2 homodimer inhibition via repurposing FDA-approved drugs using structure-based virtual screening.

Anterior Gradient 2 (AGR2) has recently been reported as a tumor biomarker in various cancers, i.e., breast, prostate and lung cancer. Predominantly, AGR2 exists as a homodimer via a dimerization domain (E60-K64); after it is self-dimerized, it helps FGF2 and VEGF to homo-dimerize and promotes the angiogenesis and the invasion of vascular endothelial cells and fibroblasts. Up till now, no small molecule has been discovered to inhibit the AGR2-AGR2 homodimer. Therefore, the present study was performed to prepare a validated 3D structure of AGR2 by homology modeling and discover a small molecule by screening the FDA-approved drugs library on AGR2 homodimer as a target protein. Thirteen different homology models of AGR2 were generated based on different templates which were narrowed down to 5 quality models sorted by their overall Z-scores. The top homology model based on PDB ID = 3PH9 was selected having the best Z-score and was further assessed by Verify-3D, ERRAT and RAMPAGE analysis. Structure-based virtual screening narrowed down the large library of FDA-approved drugs to ten potential AGR2-AGR2 homodimer inhibitors having FRED score lower than - 7.8 kcal/mol in which the top 5 drugs' binding stability was counter-validated by molecular dynamic simulation. To sum up, the present study prepared a validated 3D structure of AGR2 and, for the first time reported the discovery of 5 FDA-approved drugs to inhibit AGR2-AGR2 homodimer by using structure-based virtual screening. Moreover, the binding of the top 5 hits with AGR2 was also validated by molecular dynamic simulation. A validated 3D structure of Anterior Gradient 2 (AGR2) was prepared by homology modeling, which was used in virtual screening of FDA-approved drugs library for the discovery of prospective inhibitors of AGR2-AGR2 homodimer.

G protein-coupled estrogen receptor-1: homology modeling approaches and application in screening new GPER-1 modulators.

G protein-coupled receptors (GPCRs) belong to the largest family of protein targets comprising over 800 members in which at least 500 members are the therapeutic targets. Among the GPCRs, G protein-coupled estrogen receptor-1 (GPER-1) has shown to have the ability in estrogen signaling. As GPER-1 plays a critical role in several physiological responses, GPER-1 has been considered as a potential therapeutic target to treat estrogen-based cancers and other non-communicable diseases. However, the progress in the understanding of GPER-1 structure and function is relatively slow due to the availability of a only a few selective GPER-1 modulators. As with many GPCRs, the X-ray crystal structure of GPER-1 is yet to be resolved and thus has led the researchers to search for new GPER-1 modulators using homology models of GPER-1. In this review, we aim to summarize various approaches used in the generation of GPER-1 homology model and their applications that have resulted in new GPER-1 ligands.

Polyphenolic profiling of Ipomoea carnea Jacq. by HPLC-DAD and its implications in oxidative stress and cancer.

Ipomoea carnea Jacq. is an important folklore medicinal plant, assessed for its underexplored biological potential. Antioxidant, cytotoxic, antiproliferative and polyphenolic profile of whole plant was evaluated using various techniques. Maximum extract recovery (29% w/w), phenolic [13.54 ± 0.27 µg GAE/mg dry weight (DW)] and flavonoid (2.11 ± 0.10 µg QE /mg DW) content were recorded in methanol-distilled water (1:1) flower extract. HPLC-DAD analysis quantified substantial amount of six different polyphenols ranging from 0.081 to 37.95 µg/mg extract. Maximum total antioxidant and reducing potential were documented in methanol-distilled water and acetone-distilled water flower extracts (42.62 ± 0.47 and 24.38 ± 0.39 µg AAE/mg DW) respectively. Ethanol-chloroform root extract manifested highest free radical scavenging (IC50 of 61.22 µg/mL) while 94.64% of the extracts showed cytotoxicity against brine shrimps. Ethanol leaf extract exhibited remarkable activity against THP-1 cell line (IC50 = 8 ± 0.05 µg/mL) and protein kinases (31 mm phenotype bald zone).

Sequential ligand- and structure-based virtual screening approach for the identification of potential G protein-coupled estrogen receptor-1 (GPER-1) modulators.

G protein-coupled estrogen receptor-1 (GPER-1) is a seven transmembrane receptor, responsible for mediating rapid estrogen signaling in many physiological responses in reproductive, nervous, endocrine, immune and cardiovascular systems. Due to unavailability of the crystal structure of GPER-1, we have performed sequential ligand-based virtual screening (LBVS) and structure-based screening (SBVS) to identify potential GPER-1 modulators. LBVS and SBVS approaches were validated retrospectively using the Receiver Operating Curve (ROC) plot and the early Enrichment Factor (EF). LBVS was performed based on a GPER-1 agonist, G1, as a query model for screening of the eMolecules library using the Rapid Overlay of Chemical Structure (ROCS) and the electrostatic potential screening (EON) approaches. Top-scored hits from LBVS were further screened by SBVS. SBVS was based on generating homology models of GPER-1 and subsequent molecular docking studies. Using Chemguass4 score, we filtered the final hits with the higher score in comparison to G1 (Chemguass4 score = -11.575). The top-ranked hits were clustered based on similarity in their scaffolds. Prospective validation was performed by evaluating the antiproliferative activity of synthesized compounds (SK0 and SK0P) which were representative of top hits obtained from our virtual screening approach.

Computational investigations of the binding mechanism of novel benzophenone imine inhibitors for the treatment of breast cancer.

4-Hydroxytamoxifen (4-OHT), the most common hormone used for the treatment of breast cancer, is a selective estrogen receptor modulator (SERM) inhibitor that acts as an antagonist in breast tissue and a partial agonist in the endometrium. However, the detailed molecular mechanism of 4-OHT structure modification has not been well investigated to date. Herein, molecular docking, molecular dynamics simulations and free energy calculations were performed to explore the mechanisms of the molecular interactions between newly designed benzophenone imines (BIs) and the three forms apo, antagonist and agonist of the human estrogen receptor hERα. The proposed inhibitors were designed by replacing the triarylethylene estrogenic scaffold found in 4-OHT with Schiff base triarylimine derivatives. The antiestrogen scaffold i.e. the O-alkyl side chain in 4-OHT was developed by incorporating an alanine amino acid side chain functionality into the triarylimine scaffold. Docking results reveal that the newly designed BIs bind to the hydrophobic open pocket of the apo and antagonist hERα conformations with higher affinity as compared to the natural and synthetic estrogen estradiol (E2) and 4-OHT. The analysis of the molecular dynamics simulation results based on six different systems of the best docked BI (5c) with hERα receptors demonstrates stable interactions, and the complex undergoes fewer conformational fluctuations in the open apo/antagonist hERα receptors as compared to the case of the closed agonist. In addition, the calculated binding free energies indicate that the main factor that contributes to the stabilization of the receptor-inhibitor complexes is hydrophobic interactions. This study suggests that the development of these Schiff base derivatives may be worth exploring for the preparation of new 4-OHT analogues.

Substituted (E)-2-(2-benzylidenehydrazinyl)-4-methylthiazole-5-carboxylates as dual inhibitors of 15-lipoxygenase & carbonic anhydrase II: synthesis, biochemical evaluation and docking studies.

15-Lipoxygenase (15-LOX) plays a major role in many inflammatory lung diseases including chronic obstructive pulmonary disease (COPD), asthma and chronic bronchitis. Over-expression of 15-LOX is related with some specific carcinomas including pancreatic, gastric and brain tumor. Similarly among different isozymes of carbonic anhydrase (CA), CA II is expressed in pancreatic, gastric carcinomas as well as in brain tumors. Therefore, novel potent inhibitors of both 15-LOX and CA II are required to explore the role of these enzymes further and to enable the drug discovery efforts. For this purpose, a series of benzyledinyl-hydrazinyl substituted thiazole derivatives were designed, synthesized and characterized by FTIR, 1H, &13C NMR spectroscopy. The derivatives were then evaluated for their potential to inhibit 15-LOX and bovine carbonic anhydrase II (bCA II). Most of these compounds showed excellent inhibitory potential for 15-LOX with an IC50 of 0.12 ± 0.002 to 0.69 ± 0.5 µM and showed moderate inhibition potency for bCA II with compound 5h (IC50 = 1.26 ± 0.24 µM) being the most active. The most potent compound 5a that emerged as a dual inhibitor of both enzymes, exhibiting 24 times greater selectivity for 15-LOX over bCA II. Compound 5a exhibited dual potent inhibitory activity against both 15-LOX and bCA II enzymes having IC50 values of 0.12 ± 0.002 and 2.93 ± 0.22 µM, respectively. Molecular docking studies of potent as well as dual inhibitors were also carried out to provide an insight into the binding site interactions.

Etiology and pattern of maxillofacial injuries in the Armed Forces of Pakistan.

OBJECTIVE: To determine the etiology and pattern of maxillofacial injuries in the Armed Forces of Pakistan in terms of anatomical distribution of injuries. DESIGN: A descriptive study. PLACE AND DURATION OF STUDY: January 2001 to Jan 2004 at the Oral and Maxillofacial Surgery Department, AFID, Rawalpindi. PATIENTS AND METHODS: Three hundred consecutive patients of Armed Forces of Pakistan with maxillofacial injuries reporting to AFID and admitted to the hospital or treated as out-patients in the oral surgery clinic, were included in this study. Isolated nasal bone and frontal sinus fractures were excluded from the study. Anatomical distribution, frequency and etiology of fractures, rank at job and occupational as well as personal hobbies were recorded. Descriptive analyses were used to determine mean, standard deviation, percentage and range values. RESULTS: The most frequent bone fractured was the mandible, which accounted for 159 cases (53%). The zygomatic complex was fractured in 51 cases (17%), the maxilla in 12 cases (4 %), and the alveolar process in 21 cases (7%). The most common cause was road traffic accident (168 cases; 56%), followed by accidental fall (69 cases; 23%), gunshot injuries (27 cases; 9%), sports related injuries (15 cases; 5%), and injury associated with a fight (12 cases; 4%); there were only 9 cases of animals related injuries (3%). CONCLUSION: In this series, mandible was the most commonly fractured facial bone, while road traffic accident was the most common etiological factor. Results could be influenced by the personal and working environment.