Pankaj Goyal

Central University of Rajasthan | CURAJ · Department of Biotechnology

The N,C-coupled naphthylisoquinoline alkaloid ancistrocladinium A belongs to a novel class of natural products with potent antiprotozoal activity. Its effects on tumor cells, however, have not yet been explored. We demonstrate the antitumor activity of ancistrocladinium A in multiple myeloma (MM), a yet incurable blood cancer that represents a mode...

Microbial biofilms have been recognized for a vital role in antibiotic resistance and chronic microbial infections for 2-3 decades; still, there are no 'anti-biofilm drugs' available for human applications. There is an urgent need to develop novel 'anti-biofilms' therapeutics to manage biofilm-associated infectious diseases. Several reports have su...

Cofilin-2 is a member of the ADF/cofilin family, expressed extensively in adult muscle cells and involved in muscle maintenance and regeneration. Phosphorylated cofilin-2 is found in pre-fibrillar aggregates formed during idiopathic dilated cardiomyopathy. A recent study shows that phosphorylated cofilin-2, under oxidative distress, forms fibrillar...

Cytokines’ secretion from the decidua and trophoblast cells has been known to regulate trophoblast cell functions, such as Extravillous trophoblasts (EVTs) cell migration and invasion and remodeling of spiral arteries. Defective angiogenesis and spiral arteries transformation are mainly caused by proinflammatory cytokines and excessive thrombin gen...

Cofilin-1, an actin dynamizing protein, forms actin-cofilin rods, which is one of the major events that exacerbates the pathophysiology of amyloidogenic diseases. Cysteine oxidation in cofilin-1 under oxidative stress plays a crucial role in the formation of these rods. Others and we have reported that cofilin-1 possesses a self-oligomerization pro...

Protein kinases of both the parasite and the host are crucial in parasite invasion and survival and might act as drug targets against drug-resistant malaria. STK35L1 was among the top five hits in kinome-wide screening, suggesting its role in malaria’s liver stage. However, the role of host STK35L1 in malaria remains elusive. In this study, we foun...

The pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people and claimed thousands of lives. Starting in China, it is arguably the most precipitous global health calamity of modern times. The entire world has rocked back to fight against the disease an...

Purpose Extracellular matrix remodeling is essential for extravillous trophoblast (EVT) cell migration and invasion during placental development and regulated by matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteases (TIMPs). Sphingosine kinases (SPHK1 and SPHK2) synthesize sphingosine‐1‐phosphate (S1P), which works either intra...

Protein kinases of both the parasite and host are crucial in parasite invasion and survival and might be drug targets against drug-resistant malaria. STK35L1 was among the top five hits in kinome-wide screening, suggesting a role in malaria’s liver stage. The function of STK35L1 in malaria is not known yet. We found that STK35L1 was highly upregula...

Biofilms have a significant role in microbial persistence, antibiotic resistance, and chronic infections; consequently, there is a pressing need for development of novel “anti-biofilm strategies.” One of the fundamental mechanisms involved in biofilm formation is protein–protein interactions of “amyloid-like proteins” (ALPs) in the extracellular ma...

SARS Cov2 RNA-dependent RNA polymerase (RdRp) is an enzyme that catalyzes the synthesis and replication of viral RNA from an RNA template. Our starting model for this study was (SARS-Cov-2) cryo-EM structure published recently (pdb ID 6m71). We have used docking studies to find a better inhibitor for the enzyme that can be used in the treatment of...

Severe acute respiratory syndrome novel coronavirus 2 (SARS-CoV-2) has caused the global pandemic as COVID-19, which is the most notorious global public health crisis in the last 100 years. SARS-CoV-2 is composed of four structural proteins and several non-structured proteins. The multi-facet nucleocapsid (N) protein is the major component of struc...

Biofilms have significant role in microbial persistence, antibiotic resistance and chronic infections. Consequently, there is a pressing need for development of novel anti-biofilm strategies. One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of amyloid like proteins (ALPs) in extracellular matrix. Such...

Experimental data on resistance mechanisms of multiple myeloma (MM) to ixazomib (IXA), a second-generation proteasome inhibitor (PI), are currently lacking. We generated MM cell lines with a 10-fold higher resistance to IXA as their sensitive counterparts, and observed cross-resistance towards the PIs carfilzomib (CFZ) and bortezomib (BTZ). Analyse...

Extravillous trophoblast (EVT) migration and invasion is the crucial step for normal placental development. IL-11 is a cytokine regulating cell migration and invasion in cells and is a critical factor for successful implantation of an embryo. Higher expression of thrombin receptor PAR-1 was reported in early pregnancy. The precise role of thrombin...

Seminal amyloids are well known for their role in enhancing HIV infection. Among all the amyloidogenic peptides identified in human semen, PAP248‐286 was found to be the most active and was termed as semen‐derived enhancer of viral infection (SEVI). Although amyloidogenic nature of the peptide is mainly linked with enhancement of the viral infectio...

Protegrin‐4 (PG‐4) is a member of the porcine leukocyte protegrins family of cysteine‐rich antimicrobial peptides (AMPs) isolated from Sus scrofa. It consists of 18 amino acid residues and works as a part of innate immune system. In this study, we examined the intrinsic aggregation propensity of this AMP using multiple computational algorithms, nam...

Purpose: Crystallin is a major protein present in eye lens. Peptide fragment αA(66-80) derived from αA-crystallin possesses high aggregation propensity and forms amyloid-like structures. αA(66-80) aggregates are known to interact with soluble crystallins and destabilize native structures that subsequently undergo aggregation. Crystallin aggregation...

Gefitinib, an EGFR tyrosine kinase inhibitor, is used as FDA approved drug in breast cancer and non-small cell lung cancer treatment. However, this drug has certain side effects and complications for which the underlying molecular mechanisms are not well understood. By systems biology based in silico analysis, we identified off-targets of gefitinib...

Both villous and extravillous trophoblast (EVT) cells produce a wide range of cytokines and also respond to them in autocrine and paracrine manner. Deregulation of cytokine secretion may lead to various pathologic conditions including preeclampsia. IL-8, a pro-inflammatory cytokine, regulates various cellular functions such as neutrophil traffickin...

Glycoprotein VI (GPVI) is the essential platelet collagen receptor in atherothrombosis, but its inhibition causes only a mild bleeding tendency. Thus, targeting this receptor has selective antithrombotic potential. This study sought to compare compounds interfering with platelet GPVI-atherosclerotic plaque interaction to improve current antiatherot...

This is the author accepted manuscript. It is currently under an infinite embargo pending publication of the final version.

Angiogenesis and vascular development are essential for foetal development and growth, whereby early pregnancy loss and other pregnancy-related pathologies have been linked to aberrant vascular development. As Wnt signalling has been suggested to play a role in the vascularization of chorionic villi, we investigated the expression of Wnt family mem...

In the luteal phase, human endometrial stromal cells (HESCs) undergo proliferation, migration and differentiation during the decidualization process under the control of the ovarian steroids progesterone and estrogen. Proper decidualization of stromal cells is required for blastocyst implantation and the development of pregnancy. The proliferation,...

Background: ADF/cofilin proteins are key regulators of actin dynamics. Their function is inhibited by LIMK-mediated phosphorylation at Ser-3. Previous in vitro studies have shown that dependent on its concentration, cofilin either depolymerizes F-actin (at low cofilin concentrations) or promotes actin polymerization (at high cofilin concentrations)...

Protein sequence alignment of human non-muscle cofilin (CFL1-Human) and human ADF (ADF-Human). Cysteine residues are highlighted in yellow. The positions of cysteine in human cofilin are indicated. (RTF)

Live cell imaging of human endothelial cells transfected with DsRed2-cofilin. Endothelial cells transfected with cofilin-DsRed2 were stimulated with thrombin (1 U/ml) and then observed under the Nikon TE2000E PFS microscope with 63x magnification at 37°C. Pictures were taken every 30 seconds for 30 minutes using NIS elements software. Movie was edi...

Immunoblotting of cofilin-EGFP and cofilin-S3D-EGFP transfected and cross-linked endothelial cells. Endothelial cells were transfected with EGFP, cofilin-EGFP or cofilin-S3D-EGFP plasmid. After 20 hours of transfection, cells (0.8–1×106 cells/20 µl) were treated with DMSO (1 µl) or BMOE at a final concentration of 1 mM. The cell lysates were subjec...

ADF does not form a distinct 65 kDa oligomer after cross-linking of endothelial cells. Endothelial cells (0.8–1×106 cells/20 µl) were incubated with DMSO (1 µl) or BMOE (1 mM). For formaldehyde cross-linking, endothelial cells (1×106 cells/ml) were treated with formaldehyde at a final concentration (1%). The cell lysates were subjected to SDS-PAGE...

Various cytokines derived from placental cells are essential for normal placenta development and successful pregnancy. Interleukin-6 (IL-6) is a multifunctional cytokine produced by extravillous and cytotrophoblasts regulating the functions of these cells e.g. migration, invasion, trophoblast differentiation, and proliferation. In macrophages, newl...

OVO-like proteins (OVOL) are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies...

Alignment of OVOL proteins from different vertebrates, B. floridae and N. vectensis. We created this alignment using MUSCLE [43], [44] and further edited for visualization using GENEDOC [45]. Secondary structures of human OVOL1 were predicted using PSIPRED [46] and these secondary structures are marked above the alignment. Four C2H2 zinc finger mot...

Similarities and differences among Drosophila OVOA-D and mouse OVOL1-OVOL3 using protein sequence alignment. Zinc finger motif is a highly conserved region (red shading). The presence of multiple stretches of the same amino acids are visible in this alignment in the N-terminal regions. (PDF)

Protein sequence alignment of selected regions of OVOL. We generated this alignment using MUSCLE [43], [44] at default parameters. This alignment was used for the reconstruction of the Bayesian phylogenetic tree (Figure 7B). (TXT)

A highly conserved motif is found immediately after the fourth C2H2 motif present in the majority of OVOL proteins from metazoan origin. We generated this sequence logo using WebLogo 3.0 [81]. (PNG)

Background Mesothelial cells are critical in the pathogenesis of post-surgical intraabdominal adhesions as well as in the deterioration of the peritoneal membrane associated with long-term peritoneal dialysis. Mesothelial denudation is a pathophysiolocigally important finding in these processes. Matrix metalloproteinase (MMP) biology underlies aspe...

TIMP-1-GPI treatment moderates the steady state TNF-α, PAI-1 and t-PA gene expression. Primary human mesothelial cells were left untreated, or were treated with 7 ng/ml TIMP-1-GPI, 14 ng/ml TIMP-1-GPI, 14 ng/ml of heat treated TIMP-1-GPI or 14 ng/ml of rhTIMP-1. After 48 hrs RNA was isolated and subjected to analysis using TaqMan RT-PCR. The genes...

TIMP-1-GPI 14 ng/ml. (AVI)

RT-PCR analyses. (DOC)

Control rTIMP-1 14 ng/ml. (AVI)

Medium control. (AVI)

Vehicle control. (AVI)

TIMP-1-GPI 7 ng/ml. (AVI)

Micro-synteny analysis of MC3 receptors. A. Ortholog of MC3R is conserved in tetrapods. B. MC3R like gene is found in only zebrafish whereas other ray-finned fishes have another thyrotropin-releasing hormone receptor 3 (TRHR3) gene at this locus instead of MC3R. Takifugu has two copies of TRHR3, which are named as TRHR3a-b. (TIFF)

Chromosomal mapping of MC1 receptors. This figure illustrates that MC1R ortholog is found conserved from teleost fishes to mammals. (TIFF)

Intron insertions in MC5 receptor during diversification of ray-finned fishes. There are three intron inserted at positions 41a, 77c and 140c (numbering human MC5R with suffix a–c for intron phasing; blue background) in MC5Rs of four fishes - Takifugu, Tetraodon, stickleback and medaka, but not in MC5R like genes from zebrafish, elephant shark and...

Intron insertions in P2Y6 receptor during diversification of ray-finned fishes. One novel intron is inserted at positions 120c (human MC5R amino acid numbering with suffix a–c for intron phasing) in the P2Y6 receptor of four fishes - Takifugu, Tetraodon, stickleback and medaka (blue background), but not in P2Y2 genes from zebrafish, and tetrapods....

List of CHRM3 genes from fishes. Codon usage in DRY motif is shown and codons of the R residue is marked by red color. The absence of intron is marked by grey background in R residue. (DOC)

List of selected GPCRs used in this study, other than MC receptors. Codon usage in the DRY motif is shown and codon usage of the R residue is marked by red color. Proto-splice site forming codons are indicated by bold letters. The presence and the absence of intron is marked by blue background and grey background for R residue respectively. (DOC)

Comprehensive protein alignment of MC receptors from evolutionary important organisms. There are three MC receptors such MC1R, MC3R and MC3R were detected from elephant shark (C. milii) genome. Lampreys L. fluviatilis and P. marinus have two copies of MC receptors named as MCAR and MCBR. There are total 69 protein sequences of MC receptors used in...

Intron insertions in P2Y2 receptor during diversification of ray-finned fishes. There are three introns inserted at positions 124a, 181c and 267a (human MC5R amino acid numbering with suffix a–c for intron phasing) in P2Y2 receptor of four fishes - Takifugu, Tetraodon, stickleback and medaka (blue background), but not in P2Y2 genes from zebrafish,...

List of MC receptors from selected genomes, identified from Ensembl database release 59 (August 2010). At times data is gathered from additional databases as indicated. (XLS)

List of GPCRs sharing a common DRY intron from different vertebrates. Vertebrates with compacted genomes are marked in yellow background. Codon usage of DRY motif is shown with | as point of intron insertion. Only mammalian PRLHR gene has no intron, shown in orange background. # Only partial sequence available that renders detection of DRY motif. *...

Sequences of novel introns inserted into MC receptors of selected ray-finned fishes. Only introns mapping to core MCR domain (TM1–7) are considered. The numbering of intron positions refers to the full length amino acid numbering of human MC5R. (PDF)

Micro-synteny analysis of MC4R genes depicting presence of orthologs of MC4R gene from fish to mammals. (TIFF)

Analysis of intron insertions in MC2R from selected ray-finned fishes. There is one intron inserted at position 140c (numbering human MC5R with suffix a–c for intron phasing; blue background) in MC2Rs of four fishes - Takifugu, Tetraodon, stickleback and medaka, but not in zebrafish and tetrapods. This intron is also conserved in MC5Rs of these sel...

Intron insertions in P2Y3-like (P2Y3L) receptor during diversification of ray-finned fishes. One novel intron is inserted at position 187c (human MC5R amino acid numbering with suffix a–c for intron phasing) in the P2Y3L receptor of four fishes - Takifugu, Tetraodon, stickleback and medaka (blue background), but not in P2Y3L genes from zebrafish, e...

Intron insertions in CHRM3 receptor during diversification of ray-finned fishes. There are two introns inserted at positions 67a, 166c (DRY intron or 140c by human MC5R numbering) in CHRM3 receptor of four fishes - Takifugu, Tetraodon, stickleback and medaka (blue background), but not in P2Y2 genes from zebrafish, elephant shark and tetrapods. Vari...

List of genomes used in this study. (DOC)

Insertions of spliceosomal introns are very rare events during evolution of vertebrates and the mechanisms governing creation of novel intron(s) remain obscure. Largely, gene structures of melanocortin (MC) receptors are characterized by intron-less architecture. However, recently a few exceptions have been reported in some fishes. This warrants a...

Protein sequence alignment of mammalian STK35L1. N-terminal region and kinase domain of STK35L1 are shaded in gray and yellow color respectively. The conserved bipartite NLS (boxed) is marked in red color. Stretches of arginine and lysine are colored in gold. (PDF)

List of genes and their position on the RT-PCR array 96 well plate. (PDF)

Migration assay using the IBIDI insert. Endothelial cells transfected with STK35L1 siRNA (left side) or control siRNA (right side) were seeded into different reservoirs of an IBIDI insert. After 8 hours the insert was removed and the closure of the gap was observed on Nikon TE2000E-PFS fluorescence microscope equipped with incubation camber (37°C)...

Prediction of protein-binding motifs within STK35L1 using the ELM web server. Predicted binding motifs within STK35L1 are shown. The consensus binding sequence for the given binding domains is labeled in red. LIG, binding for. (PDF)

Live cell imaging of human endothelial cells transfected with EGFP-PDM. EGFP-PDM containing the PDZ-binding motif (see text for details), distributes thought the cytoplasm and the nucleus. In migrating cells, it concentrates in membrane ruffles at the leading edge as indicated by white arrows. Pictures were taken every four minutes for 90 minutes....

Endothelial cell prolifiration using AlamarBlue®. HUVECs were seeded (25000 cells/well) in 24 well plates and were grown for 24 hours, 48 hours and 72 hours. Before four hours of every time points, cells were incubated with AlamarBlue reagent as described in Materials and methods. The absorbance of control siRNA treated cells was considered as 100%...

Migration and proliferation of vascular endothelial cells are essential for repair of injured endothelium and angiogenesis. Cyclins, cyclin-dependent kinases (CDKs), and cyclin-dependent kinase inhibitors play an important role in vascular tissue injury and wound healing. Previous studies suggest a link between the cell cycle and cell migration: ce...

The human kinome containing 478 eukaryotic protein kinases has over 100 uncharacterized kinases with unknown substrates and biological functions. The Ser/Thr kinase 35 (STK35, Clik1) is a member of the NKF 4 (New Kinase Family 4) in the kinome with unknown substrates and biological functions. Various high throughput studies indicate that STK35 coul...

List of the Markers flanking different STK35L1, PDIK1L, and STK35L3. (0.04 MB DOC)

Ensembl accession identifiers of STK35L1, STK35L2 (PDIK1L), and STK35L3 genes in different organisms. * NCBI accession id. # Species specific paralogs. (0.12 MB DOC)

Expression analysis of STK35. Expression analysis of STK35. To verify the expression of STK35 mRNA, RNA and cDNA were prepared from endothelial cells. 455 bp and 755 bp PCR products (Lane 2 and 3) were amplified with STK35 specific primers from cDNA pools. No PCR product was amplified in negative control (reverse transcriptase polymerase was exclud...

In platelets stimulated by thrombin to secrete and aggregate, cofilin is rapidly dephosphorylated leading to its activation. Cofilin by severing existing actin filaments and stimulating F-actin polymerization on newly created barbed ends dynamizes the actin cytoskeleton. We previously found that cofilin dephosphorylation is Ca(2+)-dependent and occ...

Lysophosphatidic acid (LPA) is a ligand for LPA(1-3) of the endothelial differentiation gene family G-protein-coupled receptors, and LPA(4-8) is related to the purinergic family G-protein-coupled receptor. Because the structure-activity relationship (SAR) of GPR92/LPA(5) is limited and whether LPA is its preferred endogenous ligand has been questio...

Protein kinases form a superfamily of highly diverged proteins that mediate wide array of the signal transduction in eukaryotic cells; by modification of substrate activity, protein kinases also control many other cellular processes, including metabolism, transcription, cell cycle progression, cytoskeletal rearrangement and cell movement, apoptosis...