Structure-based virtual screening against multiple Plasmodium falciparum kinases reveals antimalarial compounds.

The continuous emergence of resistance against most frontline antimalarial drugs has led to countless deaths in malaria-endemic countries, counting 619,000 deaths in 2021, with mutation in drug targets being the sole cause. As mutation is correlated frequently with fitness cost, the likelihood of mutation emergence in multiple targets at a time is extremely low. Hence, multitargeting compounds may seem promising to address drug resistance issues with additional benefits like increased efficacy, improved safety profile, and the requirement of fewer pills compared to traditional single and combinational drugs. In this study, we attempted to use the High Throughput Virtual Screening approach to predict multitarget inhibitors against six chemically validated Plasmodium falciparum (Pf) kinases (PfPKG, PfMAP2, PfCDPK4, PfTMK, PfPK5, PfPI4K), resulting in 21 multitargeting hits. The molecular dynamic simulation of the top six complexes (Myricetin-MAP2, Quercetin-CDPK4, Myricetin-TMK, Quercetin-PKG, Salidroside-PK5, and Salidroside-PI4K) showed stable interactions. Moreover, hierarchical clustering reveals the structural divergence of the compounds from the existing antimalarials, indicating less chance of cross-resistance. Additionally, the top three hits were validated through parasite growth inhibition assays, with quercetin and myricetin exhibiting an IC50 value of 1.84 and 3.93 µM, respectively.

A meta-analysis of differentially expressed circulatory micro-RNAs in chronic traumatic encephalopathy and other tauopathies: A significant role of miR-181c-5p.

BACKGROUND: Micro-RNA (miRs) targeting kinases and phosphatases regulate the hyper-phosphorylation of tau protein, which is a characteristic feature of Chronic Traumatic Encephalopathy (CTE). PRIMARY OBJECTIVE: Identification of lead dysregulated miR expressed in CTE, and other similar tauopathies. METHODS: A search strategy was devised using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to mine into multiple indexing databases such as Web of Science, Google Scholar, and PubMed spanning from 2005 to June 2022. Seven articles were screened out of 34,221 publications based on inclusion criteria and were categorized into two groups i.e., (1) CTE and its risk factors and (2) Age-related neurodegenerative disorders. RESULTS: Statistical analysis [RevMan 5.4.1] results showed that the overall risk ratio (RR) of the first group is significant (RR = 0.62, 95% CI = [0.38, 1.00], z = 1.95, p = 0.05) whereas, the second group favours the control population (RR = 1.64, 95% CI = [0.85, 3.16], z = 1.14, p = 0.14). CONCLUSION: We observed that among all other dysregulated miRs, miR-181c-5p is significantly overexpressed in Alzhimers disease (AD) and CTE. Further, we found that miR-210-3p is also upregulated notably in all groups. In sum, we conclude that these miRs can be considered as potential target and biomarker in the diagnosis and treatment of various tauopathies.

Caffeic acid, a dietary polyphenol, pre-sensitizes pancreatic ductal adenocarcinoma to chemotherapeutic drug.

Resistance to chemotherapeutics is an eminent cause that leads to search for options that help in diminution of pancreatic ductal adenocarcinoma (PDAC) by overcoming resistance issues. Caffeic acid (CFA), a polyphenol occurring in many dietary foods, is known to show antidiabetic and anticancer properties potential. To unveil the effect of CFA on PDAC, we carried out this research in PDAC cells, following which we checked the combination effect of CFA and chemotherapeutics and pre-sensitization effects of CFA. Multitudinous web-based approaches were applied for identifying CFA targets in PDAC and then getting their interconnections. Subsequently, we manifested CFA effects by in-vitro analysis showing IC50 concentrations of 37.37 and 15.06 µM on Panc-1 and Mia-PaCa-2, respectively. The combination index of CFA with different drugs was explored which showed the antagonistic effects of combination treatment leading to further investigation of the pre-sensitizing effects. CFA pre-sensitization reduced IC50 concentration of doxorubicin in both PDAC cell lines which also triggered ROS generation determined by 2',7'-dichlorofluorescin diacetate assay. The differential gene expression analysis after CFA treatment showed discrete genes affected in both cells, i.e. N-Cad and Cas9 in Panc-1 and Pi3K/AkT/mTOR along with p53 in Mia-PaCa-2. Collectively, this study investigated the role of CFA as PDAC therapeutics and explored the mechanism in mitigating resistance of PDAC by sensitizing to chemotherapeutics.Communicated by Ramaswamy H. Sarma.

Pharmacoinformatic screening of phytoconstituent and evaluation of its anti-PDAC effect using in vitro studies.

With no prominent treatment for pancreatic ductal adenocarcinoma (PDAC) in conventional chemotherapy, recent studies have focused on uniting conventional and traditional medicines including plant phytoconstituents. Herein, we used pharmacoinformatic studies to identify potent phytoconstituent as ligand having inhibition activities against canonical anticancer targets, and evaluated its effect on PDAC cell lines. SwissTargetPrediction and SuperPred tools were utilized to segregate protein targets of ligand in humans, following which FunRich was applied to garner its targets in PDAC. STRING analysis predicted protein-protein interactions and dynamic simulation studies confirmed stability of ligand-protein complex. For in vitro cytotoxic potential, ligand treatment at different concentrations was given to PDAC cell lines both alone and combined with gemcitabine, followed by evaluation of effects on migration. Differential gene expression was checked using PCR for evaluating mechanism of cytotoxicity. Results showed pentagalloylglucose (PGG) with highest docking and MMGBSA scores for Cyclooxygenase 2 (Cox2) inhibition site. SwissTargetPrediction and SuperPred analysis detected 40 targets of PGG in PDAC. Simulation data showed stability of protein-ligand complex. In in vitro experiments Mia-PaCa-2 was more sensitive to PGG than Panc-1. PGG successfully inhibited migration both alone and in combination with gemcitabine. Additionally, PGG treatment induced apoptosis in both the cell lines; but showed antagonism when combined with gemcitabine. In conclusion, our report demonstrates PGG has good binding with Cox2 and showed anti-PDAC activity by inhibiting migration and inducing apoptosis, thus it can be used as a therapy option. But further studies are required to confirm its behaviour as a combination therapy drug.Communicated by Ramaswamy H. Sarma.

Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach.

Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03258-4.

Novel inhibitors of Rho-kinase mediated neuroinflammatory pathways and their potential application in recovery of injured spinal cord.

Spinal cord injury (SCI) involves damage to any part of the spinal cord which results in temporary or permanent changes in its function. Spinal cord secondary injury activates Rho-associated protein kinase 2 (ROCK2), which is involved in neuroinflammation and cell death by mediating secretion of inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1 beta (IL-1ß), interleukin-2 (IL-2), and CXC chemokines. Here we evaluated potential inhibitors of ROCK2, Caspase-1, and TNF-α from Cissus quadrangularis derived natural compounds and compared them with structural analogues of quadrangularin by molecular docking, followed by correlation using molecular dynamic simulations studies. The results clearly demonstrate that the naturally derived compounds, quadrangularin and luteolin potentially inhibit ROCK2 and Caspase-1 with high binding affinity, and showed stable conformation throughout simulation trajectory period. Interestingly, quadrangularin and its structural analogues demonstrate effective binding affinity against ROCK2, caspase-1, and TNF-α when compared to their respective known inhibitors. From our studies, we can infer that natural compounds derived from C. quadrangularis are potentially capable of inhibitory activity against ROCK2, Caspase-1, and TNF-α. These findings could help in identifying novel therapeutic drugs targeting SCI.Communicated by Ramaswamy H. Sarma.

Femtosecond laser pulse assisted photoporation for drug delivery in Chronic myelogenous leukemia cells.

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder occurs in the pluripotent hematopoietic stem cell. Currently, first-generation tyrosine kinase inhibitor (TKI) imatinib is the mainstay for the treatment of CML. Second generation TKI's like ponatinib, dasatinib, nilotinib, and bafetinib were treated against resistant CML. However, several CML patients develop resistance towards all existing inhibitors. Curcumin (Curcuma longa) a plant-derived natural compound is an effective bioactive component against various cancers including CML. Many studies have shown that curcumin induces time- and dose-dependent apoptosis in CML cells by regulating various downstream molecular regulators. Despite curcumin's selective cytotoxicity towards cancer cells, it has very poor bioavailability both in in-vitro and in-vivo conditions. In this present study, we have used femtosecond laser (fs-laser) pulses to ablate the cell membrane and standardized the conditions required for creating a cell membrane pores with less lethality. Following fs-laser pulse irradiation, K562 cells were incubated along with curcumin 30 µM for 0 h, 6 h,12 h and 24 h. Interestingly irradiated cells have shown higher sensitivity towards curcumin than non-irradiated cells. Immunoblotting studies showed higher induction levels of cleaved caspase 3 and 9 in irradiated population than non-irradiated. In summary, the results prove that irradiation by fs-laser pulses enhanced the bioavailability of curcumin and shows caspase-mediated cell death in irradiated CML cells than other populations.

Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study.

BCR-ABL tyrosine kinase plays a major role in the pathogenesis of chronic myeloid leukemia (CML) and is a proven target for drug development. Currently available drugs in the market are effective against CML; however, side-effects and drug-resistant mutations in BCR-ABL limit their full potential. Using high throughput virtual screening approach, we have screened several small molecule databases and docked against wild-type and drug resistant T315I mutant BCR-ABL. Drugs that are currently available, such as imatinib and ponatinib, were also docked against BCR-ABL protein to set a cutoff value for our screening. Selected lead compounds were further evaluated for chemical reactivity employing density functional theory approach, all selected ligands shows HLG value > 0.09900 and the binding free energy between protein-ligand complex interactions obtained was rescored using MM-GBSA. The selected compounds showed least ΔG score -71.53 KJ/mol to maximum -126.71 KJ/mol in both wild type and drug resistant T315I mutant BCR-ABL. Following which, the stability of the docking complexes were evaluated by molecular dynamics simulation (MD) using GROMACS4.5.5. Results uncovered seven lead molecules, designated with Drug-Bank and PubChem ids as DB07107, DB06977, ST013616, DB04200, ST007180 ST019342, and DB01172, which shows docking scores higher than imatinib and ponatinib.