Identifying dual leucine zipper kinase (DLK) inhibitors using e-pharamacophore screening and molecular docking

Alzheimer’s is a neural disorder causing gradual loss in structure and function of nerve cell. To treat such disorders, c-Jun N-terminal Kinase (JNK) Pathway inhibitors were developed by representing chemical compounds that were used to inhibit the JNK signaling pathways. DLK is the stress sensor and implicating as regulatory factor in JNK pathway. Therefore, in the present investigation, pharmacophore screening was tried to identify the chemical compounds that involving inhibition of DLK proteins. To explore the pharmacophore region and mode of binding with DLK protein, N- (I H-pyrazol-3-y l) pyridin-2-aminer inhibitors were docked with DLK. Results reveal the information on the interaction mechanism of protein and ligand with chemical characteristics required to inhibit DLK protein. Such predicted information (AAAARH) was used as query to find out potential novel lead compounds sourced from public database. As an outcome of 65 compounds were listed based on the fitness score (2≥), and were subjected to glide HTVS.SP and XP. Best performing 5 lead compounds were shortlisted for dynamic simulations. This exhibited a constant RMSD over 20?ns of timescale.     

Binding mode exploration of LuxR-thiazolidinedione analogues,e-pharmacophore-based virtual screening in the designing of LuxR inhibitors and its biological evaluation

Master quorum sensing (QS) regulator LuxR of Vibrio harveyi is a unique member of the TetR protein superfamily. Recent studies have demonstrated the contribution of thiazolidinedione analogues in blocking QS by decreasing the DNA-binding ability of LuxR. However, the precise mechanism of thiazolidinedione analogues binding to LuxR is still unclear. In the present study, molecular docking combined with molecular dynamics (MD) simulations was performed to understand the mechanism of ligand binding to the protein. The binding pattern of thiazolidinedione analogues showed strong hydrogen bonding interactions with the amine group (NH) of polar amino acid residue Asn133 and carbonyl (C=O) interaction with negatively charged amino acid residue Gln137 in the binding site of LuxR. The stability of the protein–ligand complexes was confirmed by running 50 ns of MD simulations. Further, the four-featured pharmacophore hypothesis (AHHD) consists of one acceptor (A), two hydrophobic regions (HH) and one donor (D) group was used to screen compounds from ChemBridge database. The identified hit molecules were shown to have excellent pharmacokinetic properties under the acceptable range. Based on the computational studies, ChemBridge_5343641 was selected for in vitro assays. The 1-(4-chlorophenoxy)-3-[(4,6-dimethyl-2-pyrimidinyl)thio]-2-propanol (ChemBridge_5343641) showed significant reduction in bioluminescence in a dose-dependent manner. In addition, ChemBridge_5343641 inhibits biofilm formation and motility in V. harveyi. The result from the study suggests that ChemBridge_5343641 could serve as an anti-QS molecule.     

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.     

Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches

WbpP encoding UDP-GlcNAC C4 epimerase is responsible for the activation of virulence factor in marine pathogen Vibrio vulnificus (V. vulnificus) and it is linked to many aquatic diseases, thus making it a potential therapeutic target. There are few reported compounds that include several natural products and synthetic compounds targeting Vibrio sp, but specific inhibitor targeting WbpP are unavailable. Here, we performed structure-based virtual screening using chemical libraries such as Binding, TOSLab and Maybridge to identify small molecule inhibitors of WbpP with better drug-like properties. Deficient structural information forced to model the structure and the stable protein structure was obtained through 30?ns of MD simulations. Druggability regions are focused for new lead compounds and our screening protocol provides fast docking of entire small molecule library with screening criteria of ADME/Lipinski filter/Docking followed by re-docking of top hits using a method that incorporates both ligand and protein flexibility. Docking conformations of lead molecules interface displays strong H-bond interactions with the key residues Gly101, Ser102, Val195, Tyr165, Arg298, Val209, Ser142, Arg233 and Gln200. Subsequently, the top-ranking compounds were prioritized using the molecular dynamics simulation-based conformation and stability studies. Our study suggests that the proposed compounds may aid as a starting point for the rational design of novel therapeutic agents.     

The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase

Archaeal A-ATP synthases catalyze the formation of the energy currency ATP. The chemical mechanisms of ATP synthesis in A-ATP synthases are unknown. We have determined the crystal structure of a transition-like state of the vanadate-bound form of catalytic subunit A (A_Vi) of the A-ATP synthase from Pyrococcus horikoshii OT3. Two orthovanadate molecules were observed in the A_Vi structure, one of which interacts with the phosphate binding loop through residue S238. The second vanadate is positioned in the transient binding site, implicating for the first time the pathway for phosphate entry to the catalytic site. Moreover, since residues K240 and T241 are proposed to be essential for catalysis, the mutant structures of K240A and T241A were also determined. The results demonstrate the importance of these two residues for transition-state stabilization. The structures presented shed light on the diversity of catalytic mechanisms used by the biological motors A- and F-ATP synthases and eukaryotic V-ATPases.     

Mechanistic insights into the dual inhibition strategy for checking Leishmaniasis

Leishmaniasis ^{1 1}These authors contributed equally.Communicated by Ramaswamy H. SarmaCommunicated by Ramaswamy H. Sarma is an endemic disease mainly caused by the protozoan Leishmania donovani (Ld). Polyamines have been identified as essential organic compounds for the growth and survival of Ld. These are synthesized in Ld by polyamine synthesis pathway comprising of many enzymes such as ornithine decarboxylase (ODC), spermidine synthase (SS), and S-adenosylmethionine decarboxylase. Inhibition of these enzymes in Ld offers a viable prospect to check its growth and development. In the present work, we used computational approaches to search natural inhibitors against ODC and SS enzymes. We predicted three-dimensional structures of ODC and SS using comparative modeling and molecular dynamics (MD) simulations. Thousands of natural compounds were virtually screened against target proteins using high throughput approach. MD simulations were then performed to examine molecular interactions between the screened compounds and functional residues of the active sites of the enzymes. Herein, we report two natural compounds of dual inhibitory nature active against the two crucial enzymes of polyamine pathway of Ld. These dual inhibitors have the potential to evolve as lead molecules in the development of antileishmanial drugs.     

Current evidence on mesenchymal stem cell therapy for traumatic spinal cord injury: systematic review and meta-analysis

Background aimsThe authors aim to analyze the evidence in the literature regarding the efficacy and safety of mesenchymal stem cell (MSC) therapy in human subjects with traumatic spinal cord injury (SCI) and identify its potential role in the management of SCI.MethodsThe authors conducted independent and duplicate searches of electronic databases, including PubMed, Embase and the Cochrane Library, until May 2020 for studies analyzing the efficacy and safety of stem cell therapy for SCI. American Spine Injury Association (ASIA) impairment scale (AIS) grade improvement, ASIA sensorimotor score, activities of daily living score, residual urine volume, bladder function improvement, somatosensory evoked potential (SSEP) improvement and adverse reactions were the outcomes analyzed. Analysis was performed in R platform using OpenMeta[Analyst] software.ResultsNineteen studies involving 670 patients were included for analysis. On analysis, the intervention group showed statistically significant improvement in AIS grade (P < 0.001), ASIA sensory score (P < 0.017), light touch (P < 0.001), pinprick (P = 0.046), bladder function (P = 0.012), residual urine volume (P = 0.023) and SSEP (P = 0.002). However, no significant difference was noted in motor score (P = 0.193) or activities of daily living score (P = 0.161). Although the intervention group had a significant increase in complications (P < 0.001), no serious or permanent adverse events were reported. On subgroup analysis, low concentration of MSCs (<5 × 10⁷ cells) and initial AIS grade A presentation showed significantly better outcomes than their counterparts.ConclusionsThe authors’ analysis establishes the efficacy and safety of MSC transplantation in terms of improvement in AIS grade, ASIA sensory score, bladder function and electrophysiological parameters like SSEP compared with controls, without major adverse events. However, further research is needed to standardize dose, timing, route and source of MSCs used for transplantation.