Structural and functional analysis of Chitinase-IV of Brassica juncea: molecular modeling and dynamic simulation study.

Brassica juncea is an important oil seed crop. The productivity of this plant, however, is known to be low due to the attack of plant pathogens. The plant chitinase-IV is known to hydrolyse the chitin present in the cell walls of the plant pathogens and thus enhance the plant defense systems. In this connection, studies were carried out by us on the prediction and characterization of the 3D structure of chitinase-IV, the structural changes that take place when the protein is in complex with Allosamidin and the chitin fragments (Tri-oligosaccharide and N-acetyl glucosamine) that act as elicitors to induce plant innate immunity against the invading pathogens, and molecular dynamic simulation studies on the stability of these complexes. These studies are expected to give us an insight into the chitin-binding domain and information on the dynamics and energetics of the protein, which is not possible to obtain by experimental methods. The predicted 3D structure of the protein should give us a better understanding of the molecular function of the chitinase gene in Brassica juncea for devising better methods of biocontrol against fungal phytopathogens and harmful insects so as to increase the crop yield.

Identification of Therapeutic Drug Target of Stenotrophomonas maltophilia Through Subtractive Genomic Approach and in-silico Screening Based on 2D Similarity Filtration and Molecular Dynamic Simulation.

BACKGROUND: Stenotrophomonas maltophilia is a multi-drug resistant, gram-negative bacterium that causes opportunistic infections and is associated with high morbidity and mortality in severely immunocompromised individuals. AIM: The study aimed to find out the drug target and a novel inhibitor for Stenotrophomonas maltophilia. OBJECTIVES: The current study focused on identifying specific drug targets by subtractive genomes analysis to determine the novel inhibitor for the specified target protein by virtual screening, molecular docking, and molecular simulation approach. MATERIALS AND METHODS: In this study, we performed a subtractive genomics approach to identify the novel drug target for S.maltophilia. After obtaining the specific target, the next step was to identify inhibitors that include calculating 2D similarity search, molecular docking, and molecular simulation for drug development for S.maltophilia. RESULTS: With an efficient subtractive genomic approach, out of 4386 proteins, five unique targets were found, in which UDP-D-acetylmuramic (murF) was the most remarkable target. Further virtual screening, docking, and dynamics analyses resulted in the identification of seven novel inhibitors. CONCLUSION: Further, in vitro and in vivo bioassay of the identified novel inhibitors could facilitate effective drug use against S.maltophilia.

Molecular docking analysis of α-Topoisomerase II with δ-Carboline derivatives as potential anticancer agents.

The enzyme, α-topoisomerase II (α-Topo II), is known to regulate efficiently the topology of DNA. It is highly expressed in rapidly proliferating cells and plays an important role in replication, transcription and chromosome organisation. This has prompted several investigators to pursue α-Topo II inhibitors as anticancer agents. δ-Carboline, a natural product, and its synthetic derivatives are known to exert potent anticancer activity by selectively targeting α-Topo II. Therefore, it is of interest to design carboline derivatives fused with pyrrolidine-2,5-dione in this context. δ-Carbolines fused with pyrrolidine-2,5-dione are of interest because the succinimide part of fused heteroaromatic molecule can interact with the ATP binding pocket via the hydrogen bond network with selectivity towards α-Topo II. The 300 derivatives designed were subjected to the Lipinski rule of 5, ADMET and toxicity prediction. The designed compounds were further analysed using molecular docking analysis on the active sites of the α-Topo II crystal structure (PDB ID:1ZXM). Molecular dynamic simulations were also performed to compare the binding mode and stability of the protein-ligand complexes. Compounds with ID numbers AS89, AS104, AS119, AS209, AS239, AS269, and AS299 show good binding activity compared to the co-crystal ligand. Molecular Dynamics simulation studies show that the ligand binding to α-Topo II in the ATP domain is stableand the protein-ligand conformation remains unchanged. Binding free energy calculations suggest that seven molecules designed are potential inhibitors for α-Topo II for further consideration as anticancer agents.

Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PLPRO and 3CLPRO proteases.

The pandemic, COVID-19, has spread worldwide and affected millions of people. There is an urgent need, therefore, to find a proper treatment for the novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent. This paper focuses on identifying inhibitors that target SARS-CoV-2 proteases, PLPRO and 3CLPRO, which control the duplication and manages the life cycle of SARS-CoV-2. We have carried out detailed in silico Virtual high-throughput screening using Food and Drug Administration (FDA) approved drugs from the Zinc database, COVID-19 clinical trial compounds from Pubchem database, Natural compounds from Natural Product Activity and Species Source (NPASS) database and Maybridge database against PLPRO and 3CLPRO proteases. After thoroughly analyzing the screening results, we found five compounds, Bemcentinib, Pacritinib, Ergotamine, MFCD00832476, and MFCD02180753 inhibit PLPRO and six compounds, Bemcentinib, Clofazimine, Abivertinib, Dasabuvir, MFCD00832476, Leuconicine F inhibit the 3CLPRO. These compounds are stable within the protease proteins' active sites at 20ns MD simulation. The stability is revealed by hydrogen bond formations, hydrophobic interactions, and salt bridge interactions. Our study results also reveal that the selected five compounds against PLPRO and the six compounds against 3CLPRO bind to their active sites with good binding free energy. These compounds that inhibit the activity of PLPRO and 3CLPRO may, therefore, be used for treating COVID-19 infection.

In-silico virtual screening for identification of potent inhibitor for L2-ß-lactamase from Stenotrophomonas maltophilia through molecular docking, molecular dynamics analysis study.

Stenotrophomonas maltophilia, a Multiple-Drug-Resistant proteobacterium found in healthy normal flora and fauna with an aerobic and non-fermentative respiratory process, is majorly involved in Healthcare-Associated Infections (HAI). The Multiple-Drug-Resistance takes place by secretion of the ß-Lactamase enzyme, which hydrolyzes the ß-Lactam antibiotics and currently serving as a significant clinical challenge by substantially effecting the mortality rate. In this study, involved 2D Similarity, Molecular docking, and Molecular Simulation for the commercially available ZINC database compounds to overcome this resistance mechanism and find out a proper potent inhibitor for the target L2-ß-Lactamase, which would not get cleaved by the hydrolytic activity of the L2-ß-Lactamase natural enzyme. The ZINC35053014 compound had the highest binding energy: -8.51Kcal/mol with hydrophobic interaction at THR235 and formation of hydrogen bonds at SER70, SER130, ASN170, LYS234, THR235, SER237, and ARG244. In total, 08 hit compounds subjected for the stability check of the protein-ligand complex (MD simulation) analysis which, concluded in the same RMSD, RMSF, and Rg values at the comparison between known compounds and the selected virtual hit compounds. These selected virtual hit compounds can be experimentally verified and used as lead compounds for the future search of ß-Lactamase potent inhibitors for S. maltophilia. Communicated by Ramaswamy H. Sarma.

Anti-proliferative activity and characterization data on oxadiazole derivatives.

This data in brief article explains the anti-cancer activity and characterization of oxadiazoles [1]. The main objective of this article was to provide general synthetic procedures, spectral discussion and physical data on the new oxadiazole tethered indazole (OTDs). This article discusses the 1H NMR, 13C NMR, mass spectroscopy, HPLC and melting point of the synthetic compounds. MTT assay was used to determine the anti-proliferative activity in hepatocellular cell lines.

Exploring the newer oxadiazoles as real inhibitors of human SIRT2 in hepatocellular cancer cells.

A novel series of indazole tethered oxadiazoles (OTDs) derivatives were synthesized, characterized and screened for their anti-proliferative activity against hepatocellular carcinoma (HCC) cells. OTDs structure was further confirmed by Single-crystal X-ray diffraction studies. Among the tested OTDs, compound 2-(4-methoxyphenyl)-5-(1-methyl-1H-indazol-3-yl)-1,3,4-oxadiazole was found to inhibit the catalytical activity of SIRT2 and brings about apoptosis as shown by western blot analysis and flow cytometry data. Also, the tested OTDs were found to interact with the active site of human SIRT2 in silico but not with the cavity of co-crystal ligand 5-(3- hydroxypropyl)-3-(4-chlorophenyl)-1,2,4-oxadiazole, which indicate that these OTDs has potential in the development of SIRT2 inhibitors in liver cancer models.

Preclinical Evidence of Nanomedicine Formulation to Target Mycobacterium tuberculosis at Its Bone Marrow Niche.

One-third of the world's population is estimated to be latently infected with Mycobacterium tuberculosis (Mtb). Recently, we found that dormant Mtb hides in bone marrow mesenchymal stem cells (BM-MSCs) post-chemotherapy in mice model and in clinical subjects. It is known that residual Mtb post-chemotherapy may be responsible for increased relapse rates. However, strategies for Mtb clearance post-chemotherapy are lacking. In this study, we engineered and formulated novel bone-homing PEGylated liposome nanoparticles (BTL-NPs) which actively targeted the bone microenvironment leading to Mtb clearance. Targeting of BM-resident Mtb was carried out through bone-homing liposomes tagged with alendronate (Ald). BTL characterization using TEM and DLS showed that the size of bone-homing isoniazid (INH) and rifampicin (RIF) BTLs were 100 ± 16.3 nm and 84 ± 18.4 nm, respectively, with the encapsulation efficiency of 69.5% ± 4.2% and 70.6% ± 4.7%. Further characterization of BTLs, displayed by sustained in vitro release patterns, increased in vivo tissue uptake and enhanced internalization of BTLs in RAW cells and CD271+BM-MSCs. The efficacy of isoniazid (INH)- and rifampicin (RIF)-loaded BTLs were shown using a mice model where the relapse rate of the tuberculosis was decreased significantly in targeted versus non-targeted groups. Our findings suggest that BTLs may play an important role in developing a clinical strategy for the clearance of dormant Mtb post-chemotherapy in BM cells.

Simultaneous Immunization with Omp25 and L7/L12 Provides Protection against Brucellosis in Mice.

Currently used Brucella vaccines, Brucella abortus strain 19 and RB51, comprises of live attenuated Brucella strains and prevent infection in animals. However, these vaccines pose potential risks to recipient animals such as attenuation reversal and virulence in susceptible hosts on administration. In this context, recombinant subunit vaccines emerge as a safe and competent alternative in combating the disease. In this study, we formulated a divalent recombinant vaccine consisting of Omp25 and L7/L12 of B. abortus and evaluated vaccine potential individually as well as in combination. Sera obtained from divalent vaccine (Omp25+L7/L12) immunized mice group exhibited enhanced IgG titers against both components and indicated specificity upon immunoblotting reiterating its authenticity. Further, the IgG1/IgG2a ratio obtained against each antigen predicted a predominant Th2 immune response in the Omp25+L7/L12 immunized mice group. Upon infection with virulent B. abortus 544, Omp25+L7/L12 infected mice exhibited superior Log10 protection compared to individual vaccines. Consequently, this study recommends that simultaneous immunization of Omp25 and L7/L12 as a divalent vaccine complements and triggers a Th2 mediated immune response in mice competent of providing protection against brucellosis.

Triazole-Pyridine Dicarbonitrile Targets Phosphodiesterase 4 to Induce Cytotoxicity in Lung Carcinoma Cells.

Phosphodiesterase 4 (PDE4) is a key enzyme involved in the hydrolysis of cyclic adenosine monophosphate (cAMP) and widely expressed in several types of cancers. The inhibition of PDE4 results in an increased concentration of intracellular cAMP levels that imparts the anti-inflammatory response in the target cells. In the present report, two series of triazolo-pyridine dicarbonitriles and substituted dihydropyridine dicarbonitriles were synthesized using green protocol (TBAB in refluxed water). We next evaluated the title compounds for their cytotoxicity towards lung cancer (A549) cells and identified 7'-[4-(methylsulfonyl)phenyl]-5'-oxo-1',5'-dihydrospiro[cyclohexane-1,2'-[1,2,4]triazolo[1,5-a]pyridine]-6',8'-dicarbonitrile (5h) and 7'-(1-methyl-1H-imidazol-2-yl)-5'-oxo-1',5'-dihydrospiro[cyclohexane-1,2'-[1,2,4]triazolo[1,5-a]pyridine]-6',8'-dicarbonitrile (5j) as lead analogs with the IC50 values of 15.2 and 24.1 µm, respectively. Furthermore, all the new compounds were tested for PDE4 inhibitory activity and 5j showed relatively good inhibitory activity towards PDE4 with inhibition of 50.9 % at 10 µm. In silico analysis demonstrated the favorable interaction of the title compounds with the target enzyme. Taken together, the present study introduces a new scaffold for the development of novel PDE4 inhibitors to fight against inflammatory diseases.

Sulfated Ceria Catalyzed Synthesis of Imidazopyridines and Their Implementation as DNA Minor Groove Binders.

The small molecules that bind to DNA minor groove are considered as potential therapeutic agents to fight against many human diseases. They induce cell death by interfering with transcription, replication and progression of cell cycle. Herein, we report the synthesis of imidazopyridine-3-amines using sulfated ceria catalyst by employing Groebkee-Blackburne-Bienayme reaction. We evaluated the possible antiproliferative and antimycobacterial activity against A549 cells and Mycobacterium tuberculosis, respectively. Among the tested compounds, N-tert-butyl-2-(2-butyl-4-chloro-1H-imidazol-5-yl)-5,7-dimethylimidazo[1,2-a]pyridin-3-amine (4g) was identified as cytotoxic heterocycle and antimycobacterial agent. Molecular docking studies of the imidazopyridine derivatives revealed the consistent positioning in the minor groove with a tight shape fit between receptor and ligands. Therefore, we speculate that new imidazopyridines induce their pharmacological effect by targeting the minor groove of DNA.

Diagnostic Office Vaginohysteroscopy in Evaluation of Infertility Prior to IVF: A Retrospective Analysis of 1000 Cases.

AIM: The aim of this study was to analyze the utility of routine use of diagnostic office vaginohysteroscopy in the evaluation of uterine cavity in infertility patients prior to IVF-ET. MATERIALS AND METHODS: We conducted a retrospective analysis of 1000 women who had undergone routine diagnostic office vaginohysteroscopy as an institutional protocol in the evaluation of infertility prior to IVF-ET cycle at a tertiary care hospital. They were divided into two groups: primary infertility (group I) and secondary infertility (group II). The primary outcome was the finding of an abnormal uterine cavity (congenital abnormality vs acquired abnormality). RESULTS: One thousand women underwent routine diagnostic office vaginohysteroscopy in the evaluation of infertility prior to IVF-ET. There were no intraoperative or postoperative complications. Vaginohysteroscopy revealed an abnormal uterine cavity in 13.8% (1000 patients) of women. Primary infertility group (I) had 13.19% (811 patients), and secondary infertility group (II) had 16.4% (189 patients) abnormal uterine cavities. CONCLUSION: Diagnostic office vaginohysteroscopy has a definite role in the uterine cavity evaluation in infertility patients prior to IVF, but routine use should not be recommended considering the low incidence of abnormal uterine cavity findings. Moreover, the majority of these uterine cavity abnormalities can be detected by less invasive tests such as HSG, TVS, SSG and 3D ultrasound.

Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway.

Overactivation of PI3K/Akt/mTOR is linked with carcinogenesis and serves a potential molecular therapeutic target in treatment of various cancers. Herein, we report the synthesis of trisubstituted-imidazoles and identified 2-chloro-3-(4, 5-diphenyl-1H-imidazol-2-yl) pyridine (CIP) as lead cytotoxic agent. Naïve Base classifier model of in silico target prediction revealed that CIP targets RAC-beta serine/threonine-protein kinase which comprises the Akt. Furthermore, CIP downregulated the phosphorylation of Akt, PDK and mTOR proteins and decreased expression of cyclin D1, Bcl-2, survivin, VEGF, procaspase-3 and increased cleavage of PARP. In addition, CIP significantly downregulated the CXCL12 induced motility of breast cancer cells and molecular docking calculations revealed that all compounds bind to Akt2 kinase with high docking scores compared to the library of previously reported Akt2 inhibitors. In summary, we report the synthesis and biological evaluation of imidazoles that induce apoptosis in breast cancer cells by negatively regulating PI3K/Akt/mTOR signaling pathway.

A Nano-MgO and Ionic Liquid-Catalyzed 'Green' Synthesis Protocol for the Development of Adamantyl-Imidazolo-Thiadiazoles as Anti-Tuberculosis Agents Targeting Sterol 14α-Demethylase (CYP51).

In this work, we describe the 'green' synthesis of novel 6-(adamantan-1-yl)-2-substituted-imidazo[2,1-b][1,3,4]thiadiazoles (AITs) by ring formation reactions using 1-(adamantan-1-yl)-2-bromoethanone and 5-alkyl/aryl-2-amino1,3,4-thiadiazoles on a nano material base in ionic liquid media. Given the established activity of imidazothiadiazoles against M. tuberculosis, we next examined the anti-TB activity of AITs against the H37Rv strain using Alamar blue assay. Among the tested compounds 6-(adamantan-1-yl)-2-(4-methoxyphenyl)imidazo[2,1-b][1,3,4]thiadiazole (3f) showed potent inhibitory activity towards M. tuberculosis with an MIC value of 8.5 µM. The inhibitory effect of this molecule against M. tuberculosis was comparable to the standard drugs such as Pyrazinamide, Streptomycin, and Ciprofloxacin drugs. Mechanistically, an in silico analysis predicted sterol 14α-demethylase (CYP51) as the likely target and experimental activity of 3f in this system corroborated the in silico target prediction. In summary, we herein report the synthesis and biological evaluation of novel AITs against M. tuberculosis that likely target CYP51 to induce their antimycobacterial activity.

Managing adnexal masses: a medical quandary.

INTRODUCTION: Management of Adnexal masses poses a double edged problem. There is a dilemma of performing extensive surgery in the form of staging laparotomy for a benign disease on one hand and the lurking fear of missing the diagnosis of malignancy on the other. Thus, it seems that it is important to establish risk profiles of all patients with adnexal masses so that they can reap the benefit of minimally invasive surgery wherever possible and be rightly subjected to staging laparotomy where indicated. MATERIAL AND METHODS: This prospective study was carried out at a Tertiary care Hospital. 136 women with an adnexal mass on ultrasound which met the said criteria were enrolled into the study from January 2008 to July 2011. They were then taken up for laparoscopic management. RESULTS: All but 2 cases were found to be benign (134/136) after the final histopathology report using the said criteria. CONCLUSION: Hence, by using simple readily available investigations like ultrasound (pattern recognition approach, Tumour morphology and ascites) and CA-125, the nature of adnexal mass can be reliably predicted and these patients can be safely offered the benefits of laparoscopic surgery.

Expression of medium and heavy chain neurofilaments in the developing human auditory cortex.

Neurofilament medium (NF-M) and heavy (NF-H) chain proteins have been used as markers for maturity in the developing brain since their accumulation in axons leads to an increase in conduction velocity. Earlier studies have demonstrated immunoreactivity of neurofilaments in Layer I of the human auditory cortex at 22 gestation weeks (GW), whereas that in other layers developed between 1 and 12 postnatal years, suggesting a gradual increase in the processing of sounds. However, third trimester fetuses and infants are fairly sophisticated in their ability to discern different aspects of complex sounds. Given these contradictory findings, we decided to study the expression of neurofilaments in human auditory cortex between 15 GW and adulthood. We found that mRNA and protein for both NF-M and NF-H were present in the presumptive human auditory cortex in the second trimester and during the postnatal period (1 year--adulthood). Axons in all layers of the auditory cortex were immunoreactive for neurofilaments by 25 GW and the density of the neurofilament-rich plexus in the cortical wall became adult-like during the first postnatal year in humans (9 postnatal months). Our results suggest that in terms of neurofilament expression, axons within the preterm human auditory cortex may be more mature than previously thought.