Publications by authors named "Masaud Shah"

35 Publications

Endogenous Stem Cell-Based In Situ Tissue Regeneration Using Electrostatically Interactive Hydrogel with a Newly Discovered Substance P Analog and VEGF-Mimicking Peptide.

Small 2021 Sep 4:e2103244. Epub 2021 Sep 4.

Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Korea.

The use of chemoattractants to promote endogenous stem cell-based in situ tissue regeneration has recently garnered much attention. This study is the first to assess the endogenous stem cell migration using a newly discovered substance P (SP) analog (SP1) by molecular dynamics simulations as an efficient chemoattractant. Further, a novel strategy based on electrostatic interaction using cationic chitosan (Ch) and anionic hyaluronic acid (HA) to prepare an SP1-loaded injectable C/H formulation without SP1 loss is developed. The formulation quickly forms an SP1-loaded C/H hydrogel in situ through in vivo injection. The newly discovered SP1 is found to possess human mesenchymal stromal cells (hMSCs) migration-inducing ability that is approximately two to three times higher than that of the existing SP. The designed VEGF-mimicking peptide (VP) chemically reacts with the hydrogel (C/H-VP) to sustain the release of VP, thus inducing vasculogenic differentiation of the hMSCs that migrate toward the C/H-VP hydrogel. Similarly, in animal experiments, SP1 attracts a large number of hMSCs toward the C/H-VP hydrogel, after which VP induces vasculogenic differentiation. Collectively, these findings indicate that SP1-loaded C/H-VP hydrogels are a promising strategy to facilitate endogenous stem cell-based in situ tissue regeneration.
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http://dx.doi.org/10.1002/smll.202103244DOI Listing
September 2021

TPRG1-AS1 induces RBM24 expression and inhibits liver cancer progression by sponging miR-4691-5p and miR-3659.

Liver Int 2021 Jul 30. Epub 2021 Jul 30.

Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea.

Background & Aims: Noncoding RNAs (ncRNAs) play critical roles in hepatocellular carcinoma (HCC) progression. Here, by performing RNA-sequencing (RNA-Seq) profiling, we sought to identify novel ncRNAs that potentially drive the heterogeneous progression of liver cancers.

Methods: RNA-Seq profiles were obtained from 68 HCC specimens and 10 samples of adjacent non-tumour liver tissues. The functional significance of the potential driver ncRNAs was evaluated by cell experiments.

Results: TPRG1-AS1 was identified as a potential driver noncoding RNA that promotes heterogeneous liver cancer progression. TPRG1-AS1 induced tumour suppressor RNA-binding motif protein 24 (RBM24), suppressing tumour growth by activating apoptotic tumour cell death. In addition, we report that TPRG1-AS1 acts as a competing endogenous RNA (ceRNA) for RBM24, sponging miR-4691-5p and miR-3659 to interfere with their binding to RBM24.

Conclusions: We suggest that TPRG1-AS1 is a novel ceRNA sponging miR-4691-5p and miR-3659, resulting in RBM24 expression and suppression of liver cancer growth. Our results provide new insights into the functions of ncRNAs in heterogeneous HCC progression.
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http://dx.doi.org/10.1111/liv.15026DOI Listing
July 2021

USO1 isoforms differentially promote liver cancer progression by dysregulating the ER-Golgi network.

Carcinogenesis 2021 Jul 22. Epub 2021 Jul 22.

Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea.

Alternative splicing of RNA transcripts plays an important role in cancer development and progression. Recent advances in RNA-seq technology have made it possible to identify alternately spliced events in various types of cancer; however, research on hepatocellular carcinoma (HCC) is still limited. Here, by performing RNA-Seq profiling of HCC transcripts at isoform level, we identified tumor-specific and molecular subtype-dependent expression of the USO1 isoforms, which we designated as a normal form USO1-N (XM_001290049) and a tumor form USO1-T (NM_003715). The expression of USO1-T, but not USO1-N, was associated with worse prognostic outcomes of HCC patients. We confirmed that the expression of USO1-T promoted an aggressive phenotype of HCC, both in vitro and in vivo. In addition, structural modeling analyses revealed that USO1-T lacks an ARM10 loop encoded by exon 15, which may weaken the dimerization of USO1 and its tethering to GM130. We demonstrated that USO1-T ensured unstacking of the Golgi and accelerated the trafficking from ER to Golgi and plasma membrane in multiple liver cancer cells. ERK and GRASP65 were found to be involved in the USO1-T mediated Golgi dysfunction. Conclusively, we provide new mechanophysical insights into the USO1 isoforms that differentially regulate the ER-Golgi network, promoting the heterogeneous HCC progression.
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http://dx.doi.org/10.1093/carcin/bgab067DOI Listing
July 2021

Molecular Perspectives of SARS-CoV-2: Pathology, Immune Evasion, and Therapeutic Interventions.

Mol Cells 2021 Jun;44(6):408-421

Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea.

The outbreak of coronavirus disease 2019 (COVID-19) has not only affected human health but also diverted the focus of research and derailed the world economy over the past year. Recently, vaccination against COVID-19 has begun, but further studies on effective therapeutic agents are still needed. The severity of COVID-19 is attributable to several factors such as the dysfunctional host immune response manifested by uncontrolled viral replication, type I interferon suppression, and release of impaired cytokines by the infected resident and recruited cells. Due to the evolving pathophysiology and direct involvement of the host immune system in COVID-19, the use of immune-modulating drugs is still challenging. For the use of immune-modulating drugs in severe COVID-19, it is important to balance the fight between the aggravated immune system and suppression of immune defense against the virus that causes secondary infection. In addition, the interplaying events that occur during virus-host interactions, such as activation of the host immune system, immune evasion mechanism of the virus, and manifestation of different stages of COVID-19, are disjunctive and require thorough streamlining. This review provides an update on the immunotherapeutic interventions implemented to combat COVID-19 along with the understanding of molecular aspects of the immune evasion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may provide opportunities to develop more effective and promising therapeutics.
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http://dx.doi.org/10.14348/molcells.2021.0026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245319PMC
June 2021

Mutations in the SARS-CoV-2 spike RBD are responsible for stronger ACE2 binding and poor anti-SARS-CoV mAbs cross-neutralization.

Comput Struct Biotechnol J 2020 12;18:3402-3414. Epub 2020 Nov 12.

Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is a novel beta coronavirus. SARS-CoV-2 uses spike glycoprotein to interact with host angiotensin-converting enzyme 2 (ACE2) and ensure cell recognition. High infectivity of SARS-CoV-2 raises questions on spike-ACE2 binding affinity and its neutralization by anti-SARS-CoV monoclonal antibodies (mAbs). Here, we observed Val-to-Lys417 mutation in the receptor-binding domains (RBD) of SARS-CoV-2, which established a Lys-Asp electrostatic interaction enhancing its ACE2-binding. Pro-to-Ala475 substitution and Gly482 insertion in the GSTPCNV-loop of RBD possibly hinders neutralization of SARS-CoV-2 by anti-SARS-CoV mAbs. In addition, we identified unique and structurally conserved conformational-epitopes on RBDs, which can be potential therapeutic targets. Collectively, we provide new insights into the mechanisms underlying the high infectivity of SARS-CoV-2 and development of effective neutralizing agents.
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http://dx.doi.org/10.1016/j.csbj.2020.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657873PMC
November 2020

The αC helix of TIRAP holds therapeutic potential in TLR-mediated autoimmune diseases.

Biomaterials 2020 07 17;245:119974. Epub 2020 Mar 17.

Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea. Electronic address:

Despite being crucial for combating microbes, paradoxical Toll-like receptors (TLRs) signaling have been associated with the aggravation of multiple immune disorders such as systemic lupus erythematosus, psoriasis, rheumatoid arthritis, and nonalcoholic steatohepatitis. The stoichiometry and precise arrangement of the interaction of adapters (via their Toll/interleukin-1 receptor [TIR] domains) are indispensable for the activation of TLRs and of downstream signaling cascades. Among adapters, plasma membrane-anchored MyD88 adaptor-like (MAL) has the potential for BB-loop-mediated self-oligomerization and interacts with other TIR domain-containing adaptors through αC and αD helices. Here, we used information on the MAL-αC interface to exploit its pharmacophores and to design a decoy peptide (MIP2) with broad-range TLR-inhibitory abilities. MIP2 abrogated MyD88- and TRIF-dependent lipopolysaccharide (LPS)-induced TLR4 signaling in murine and human cell lines and manifested a therapeutic potential in models of psoriasis, systemic lupus erythematosus, nonalcoholic steatohepatitis, and sepsis. Levels of hallmark serological and histological biomarkers were significantly restored and the disease symptoms were substantially ameliorated by MIP2 treatment of the animals. Collectively, our biophysical, in vitro, and in vivo findings suggest that MIP2 has broad specificity for TLRs and may be effective in modulating autoimmune complications caused by microbial or environmental factors.
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http://dx.doi.org/10.1016/j.biomaterials.2020.119974DOI Listing
July 2020

A peptide derived from the core β-sheet region of TIRAP decoys TLR4 and reduces inflammatory and autoimmune symptoms in murine models.

EBioMedicine 2020 Feb 1;52:102645. Epub 2020 Feb 1.

Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea. Electronic address:

Background: TLRs are some of the actively pursued drug-targets in immune disorders. Owing to a recent surge in the cognizance of TLR structural biology and signalling pathways, numerous therapeutic modulators, ranging from low-molecular-weight organic compounds to polypeptides and nucleic acid agents have been developed.

Methods: A penetratin-conjugated small peptide (TIP3), derived from the core β-sheet of TIRAP, was evaluated in vitro by monitoring the TLR-mediated cytokine induction and quantifying the protein expression using western blot. The therapeutic potential of TIP3 was further evaluated in TLR-dependent in vivo disease models.

Findings: TIP3 blocks the TLR4-mediated cytokine production through both the MyD88- and TRIF-dependent pathways. A similar inhibitory-effect was exhibited for TLR3 but not on other TLRs. A profound therapeutic effect was observed in vivo, where TIP3 successfully alleviated the inflammatory response in mice model of collagen-induced arthritis and ameliorated the disease symptoms in psoriasis and SLE models.

Interpretation: Our data suggest that TIP3 may be a potential lead candidate for the development of effective therapeutics against TLR-mediated autoimmune disorders.

Funding: This work was supported by the National Research Foundation of Korea (NRF-2019M3A9A8065098, 2019M3D1A1078940 and 2019R1A6A1A11051471). The funders did not have any role in the design of the present study, data collection, data analysis, interpretation, or the writing of the manuscript.
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http://dx.doi.org/10.1016/j.ebiom.2020.102645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997517PMC
February 2020

In-silico design of peptide inhibitors of K-Ras target in cancer disease.

J Biomol Struct Dyn 2020 Nov 23;38(18):5488-5499. Epub 2019 Dec 23.

Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan.

Cancer is a leading cause of death, over one million individuals analyzed, and around 500,000 deaths happen due to cancer every year alone in the United States. The Ras is a significant protein in the signaling transduction pathways and has a leading role in cell proliferation. Above 30% of all human tumors arises due to the mutations in genes that encode a Ras protein that operate signaling cascades necessary for malignant transformation, tumor angiogenesis, and metastasis. The Ras gene family comprised of 36 total genes in human. The N-Ras, K-Ras, and H-Ras are accounted for to assume noticeable function in human cancer. The mutation in K-Ras protein is most commonly found in tumors. K-Ras is the most crucial driver in lung and pancreatic cancers. Among the mutations of N-Ras, H-Ras, and K-Ras, the mutant K-Ras is the most prevalent target for the development of Lungs, colon, and pancreatic cancers. The study aimed to develop the peptide inhibitors of the K-Ras G12D. The crystal structure of the mutant K-Ras/R11.1.6 G12D complex was retrieved from the protein databank. The protein R11.1.6 directly blocks interaction with Raf and diminishes signaling through the Raf-MEK-ERK signaling pathway. Here, in this study, we designed novel peptides from the truncated reference peptide (R11.1.6) through residue scan methodology. The top ten designed peptides (based on binding free energies) were subjected to molecular dynamics simulations using AMBER to evaluate stability. Our results indicate that the top ten selected peptides have strong interactions with K-Ras than the reference peptide (R11.1.6) and have the potency to prevent the binding of Raf and K-Ras.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2019.1704880DOI Listing
November 2020

Pneumococcal VncR Strain-Specifically Regulates Capsule Polysaccharide Synthesis.

Front Microbiol 2019 1;10:2279. Epub 2019 Oct 1.

School of Pharmacy, Sungkyunkwan University, Suwon, South Korea.

Capsular polysaccharides (CPS), a major virulence factor in , become thicker during blood invasion while not during asymptomatic nasopharyngeal colonization. However, the underlying mechanism controlling this differential pneumococcal CPS regulation remain unclear. Here, we show how VncR, the response regulator of the vancomycin resistance locus ( operon), regulates CPS expression in mutants in three serotype (type 2, 3, and 6B) backgrounds upon exposure to serum lactoferrin (LF). Comparative analysis of CPS levels in the wild type (WT) of three strains and their isogenic mutants after LF exposure revealed a strain-specific alteration in CPS production. Consistently, VncR-mediated strain-specific CPS production is correlated with pneumococcal virulence, . Electrophoretic mobility-shift assay and co-immunoprecipitation revealed an interaction between VncR and the promoter () in the presence of serum. In addition, analysis uncovered this protein-DNA interaction, suggesting that VncR binds with the , and recognizes the strain-specific significance of the tandem repeats in . Taken together, the interaction of VncR and after serum exposure plays an essential role in regulating differential strain-specific CPS production, which subsequently determines strain-specific systemic virulence. This study highlights how host protein LF contributes to pneumococcal VncR-mediated CPS production. As CPS plays a significant role in immune evasion, these findings suggest that drugs designed to interrupt the VncR-mediated CPS production could help to combat pneumococcal infections.
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http://dx.doi.org/10.3389/fmicb.2019.02279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781885PMC
October 2019

Linear and Rationally Designed Stapled Peptides Abrogate TLR4 Pathway and Relieve Inflammatory Symptoms in Rheumatoid Arthritis Rat Model.

J Med Chem 2019 07 8;62(14):6495-6511. Epub 2019 Jul 8.

Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea.

A mounting evidence exists for the despicable role of the aberrant immune response in the pathogenesis of rheumatoid arthritis (RA), where toll-like receptor 4 (TLR4) can activate synovial fibroblasts that lead to the chronic inflammation and joint destruction, thus making TLR4 a potent drug target in RA. We report that novel TLR4-antagonizing peptide, PIP2, inhibits the induction of inflammatory biomarkers in vitro as well as in vivo. Systemically, PIP2 inhibits the lipopolysaccharide (LPS)-elicited TNF-α, IL-6, and IL-12p40 in a mouse model. The rationally designed cyclic derivative, cPIP2, is capable of inhibiting LPS-induced proinflammatory cytokines at significantly lower concentration as compared to PIP2 (PIP2 IC = 20 μM, cPIP2 IC = 5 μM). Finally, cPIP2 was able to relieve the inflammatory symptoms and synovial tissue destruction in the RA rat model. Cumulatively, these data suggest that PIP2 and cPIP2 hold strong promise for the development of peptide-based immunotherapeutics that could be of great value in curbing TLR-related immune complications including RA.
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http://dx.doi.org/10.1021/acs.jmedchem.9b00061DOI Listing
July 2019

EPHB6 mutation induces cell adhesion-mediated paclitaxel resistance via EPHA2 and CDH11 expression.

Exp Mol Med 2019 06 3;51(6):1-12. Epub 2019 Jun 3.

Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea.

Mutations affect gene functions related to cancer behavior, including cell growth, metastasis, and drug responses. Genome-wide profiling of cancer mutations and drug responses has identified actionable targets that can be utilized for the management of cancer patients. Here, the recapitulation of pharmacogenomic data revealed that the mutation of EPHB6 is associated with paclitaxel resistance in cancer cells. Experimental data confirmed that the EPHB6 mutation induces paclitaxel resistance in various cancer types, including lung, skin, and liver cancers. EPHB6 mutation-induced paclitaxel resistance was mediated by an interaction with EPHA2, which promotes c-Jun N-terminal kinase (JNK)-mediated cadherin 11 (CDH11) expression. We demonstrated that EPHB6-mutated cells acquire cell adhesion-mediated drug resistance (CAM-DR) in association with CDH11 expression and RhoA/focal adhesion kinase (FAK) activation. Targeted inhibition of EPHA2 or CDH11 reversed the acquired paclitaxel resistance, suggesting its potential clinical utility. The present results suggest that the EPHB6 mutation and its downstream EPHA2/JNK/CDH11/RhoA/FAK signaling axis are novel diagnostic and therapeutic targets for overcoming paclitaxel resistance in cancer patients.
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http://dx.doi.org/10.1038/s12276-019-0261-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547695PMC
June 2019

Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2.

Proteins 2019 10 13;87(10):837-849. Epub 2019 Jun 13.

State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Half of the world population is infected by the Gram-negative bacterium Helicobacter pylori (H. pylori). It colonizes in the stomach and is associated with severe gastric pathologies including gastric cancer and peptic ulceration. The most virulent factor of H. pylori is the cytotoxin-associated gene A (CagA) that is injected into the host cell. CagA interacts with several host proteins and alters their function, thereby causing several diseases. The most well-known target of CagA is the tumor suppressor protein ASPP2. The subdomain I at the N-terminus of CagA interacts with the proline-rich motif of ASPP2. Here, in this study, we carried out alanine scanning mutagenesis and an extensive molecular dynamics simulation summing up to 3.8 μs to find out hot spot residues and discovered some new protein-protein interaction (PPI)-modulating molecules. Our findings are in line with previous biochemical studies and further suggested new residues that are crucial for binding. The alanine scanning showed that mutation of Y207 and T211 residues to alanine decreased the binding affinity. Likewise, dynamics simulation and molecular mechanics with generalized Born surface area (MMGBSA) analysis also showed the importance of these two residues at the interface. A four-feature pharmacophore model was developed based on these two residues, and top 10 molecules were filtered from ZINC, NCI, and ChEMBL databases. The good binding affinity of the CHEMBL17319 and CHEMBL1183979 molecules shows the reliability of our adopted protocol for binding hot spot residues. We believe that our study provides a new insight for using CagA as the therapeutic target for gastric cancer treatment and provides a platform for a future experimental study.
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http://dx.doi.org/10.1002/prot.25748DOI Listing
October 2019

Oceans as a Source of Immunotherapy.

Mar Drugs 2019 May 10;17(5). Epub 2019 May 10.

Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea.

Marine flora is taxonomically diverse, biologically active, and chemically unique. It is an excellent resource, which offers great opportunities for the discovery of new biopharmaceuticals such as immunomodulators and drugs targeting cancerous, inflammatory, microbial, and fungal diseases. The ability of some marine molecules to mediate specific inhibitory activities has been demonstrated in a range of cellular processes, including apoptosis, angiogenesis, and cell migration and adhesion. Immunomodulators have been shown to have significant therapeutic effects on immune-mediated diseases, but the search for safe and effective immunotherapies for other diseases such as sinusitis, atopic dermatitis, rheumatoid arthritis, asthma and allergies is ongoing. This review focuses on the marine-originated bioactive molecules with immunomodulatory potential, with a particular focus on the molecular mechanisms of specific agents with respect to their targets. It also addresses the commercial utilization of these compounds for possible drug improvement using metabolic engineering and genomics.
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http://dx.doi.org/10.3390/md17050282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562586PMC
May 2019

Toll-like receptor-induced cytokines as immunotherapeutic targets in cancers and autoimmune diseases.

Semin Cancer Biol 2020 08 2;64:61-82. Epub 2019 May 2.

Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea. Electronic address:

Immune cells of the myeloid and lymphoid lineages express Toll-like receptors (TLRs) to recognize pathogenic components or cellular debris and activate the immune system through the secretion of cytokines. Cytokines are signaling molecules that are structurally and functionally distinct from one another, although their secretion profiles and signaling cascades often overlap. This situation gives rise to pleiotropic cell-to-cell communication pathways essential for protection from infections as well as cancers. Nonetheless, deregulated signaling can have detrimental effects on the host, in the form of inflammatory or autoimmune diseases. Because cytokines are associated with numerous autoimmune and cancerous conditions, therapeutic strategies to modulate these molecules or their biological responses have been immensely beneficial over the years. There are still challenges in the regulation of cytokine function in patients, even in those who take approved biological therapeutics. In this review, our purpose is to discuss the differential expression patterns of TLR-regulated cytokines and their cell type specificity that is associated with cancers and immune-system-related diseases. In addition, we highlight key structural features and molecular recognition of cytokines by receptors; these data have facilitated the development and approval of several biologics for the treatment of autoimmune diseases and cancers.
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http://dx.doi.org/10.1016/j.semcancer.2019.05.002DOI Listing
August 2020

Recent clinical trends in Toll-like receptor targeting therapeutics.

Med Res Rev 2019 05 18;39(3):1053-1090. Epub 2018 Nov 18.

Department of Molecular Science and Technology, Ajou University, Suwon, Korea.

Toll-like receptors (TLRs) are germline-encoded receptors that are central to innate and adaptive immune responses. Owing to their vital role in inflammation, TLRs are rational targets in clinics; thus, many ligands and biologics have been reported to overcome the progression of various inflammatory and malignant conditions and support the immune system. For each TLR, at least one, and often many, drug formulations are being evaluated. Ligands reported as stand-alone drugs may also be reported based on their use in combinatorial therapeutics as adjuvants. Despite their profound efficacy in TLR-modulation in preclinical studies, multiple drugs have been terminated at different stages of clinical trials. Here, TLR modulating drugs that have been evaluated in clinical trials are discussed, along with their mode of action, suggestive failure reasons, and ways to improve the clinical outcomes. This review presents recent advances in TLR-targeting drugs and provides directions for more successful immune system manipulation.
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http://dx.doi.org/10.1002/med.21553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6587958PMC
May 2019

Structural-dynamic insights into the cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides.

J Biomol Struct Dyn 2019 09 5;37(15):4035-4050. Epub 2018 Dec 5.

a State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , China.

() is one of the most extensively studied Gram-negative bacteria due to its implication in gastric cancer. The oncogenicity of is associated with cytotoxin-associated gene A (CagA), which is injected into epithelial cells lining the stomach. Both the - and -termini of CagA are involved in the interaction with several host proteins, thereby disrupting vital cellular functions, such as cell adhesion, cell cycle, intracellular signal transduction, and cytoskeletal structure. The -terminus of CagA interacts with the tumor-suppressing protein, apoptosis-stimulating protein of p53 (ASPP2), subsequently disrupting the apoptotic function of tumor suppressor gene p53. Here, we present the in-depth molecular dynamic mechanism of the CagA-ASPP2 interaction and highlight hot-spot residues through mutagenesis. Our findings are in agreement with previous studies and further suggest other residues that are crucial for the CagA-ASPP2 interaction. Furthermore, the ASPP2-binding pocket possesses potential druggability and could be engaged by decoy peptides, identified through a machine-learning system and suggested in this study. The binding affinities of these peptides with CagA were monitored through extensive computational procedures and reported herein. While CagA is crucial for the oncogenicity of , our designed peptides possess the potential to inhibit CagA and restore the tumor suppressor function of ASPP2.
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http://dx.doi.org/10.1080/07391102.2018.1537895DOI Listing
September 2019

Adenylate kinase potentiates the capsular polysaccharide by modulating Cps2D in Streptococcus pneumoniae D39.

Exp Mol Med 2018 09 5;50(9):1-14. Epub 2018 Sep 5.

School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea.

Streptococcus pneumoniae is a polysaccharide-encapsulated bacterium. The capsule thickens during blood invasion compared with the thinner capsules observed in asymptomatic nasopharyngeal colonization. However, the underlying mechanism regulating differential CPS expression remains unclear. CPS synthesis requires energy that is supplied by ATP. Previously, we demonstrated a correlation between ATP levels and adenylate kinase in S. pneumoniae (SpAdK). A dose-dependent induction of SpAdK in serum was also reported. To meet medical needs, this study aimed to elucidate the role of SpAdK in the regulation of CPS production. CPS levels in S. pneumoniae type 2 (D39) increased proportionally with SpAdK levels, but they were not related to pneumococcal autolysis. Moreover, increased SpAdK levels resulted in increased total tyrosine kinase Cps2D levels and phosphorylated Cps2D, which is a regulator of CPS synthesis in the D39 strain. Our results also indicated that the SpAdK and Cps2D proteins interact in the presence of Mg-ATP. In addition, in silico analysis uncovered the mechanism behind this protein-protein interaction, suggesting that SpAdK binds with the Cps2D dimer. This established the importance of the ATP-binding domain of Cps2D. Taken together, the biophysical interaction between SpAdK and Cps2D plays an important role in enhancing Cps2D phosphorylation, which results in increased CPS synthesis.
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http://dx.doi.org/10.1038/s12276-018-0141-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123713PMC
September 2018

Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism.

Sci Rep 2017 09 12;7(1):11362. Epub 2017 Sep 12.

Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea.

Middle East respiratory syndrome coronavirus (MERS-CoV) has evolved to navigate through the sophisticated network of a host's immune system. The immune evasion mechanism including type 1 interferon and protein kinase R-mediated antiviral stress responses has been recently attributed to the involvement of MERS-CoV protein 4a (p4a) that masks the viral dsRNA. However, the structural mechanism of how p4a recognizes and establishes contacts with dsRNA is not well explained. In this study, we report a dynamic mechanism deployed by p4a to engage the viral dsRNA and make it unavailable to the host immune system. Multiple variants of p4a-dsRNA were created and investigated through extensive molecular dynamics procedures to highlight crucial interfacial residues that may be used as potential pharmacophores for future drug development. The structural analysis revealed that p4a exhibits a typical αβββα fold structure, as found in other dsRNA-binding proteins. The α1 helix and the β1-β2 loop play a crucial role in recognizing and establishing contacts with the minor grooves of dsRNA. Further, mutational and binding free energy analyses suggested that in addition to K63 and K67, two other residues, K27 and W45, might also be crucial for p4a-dsRNA stability.
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http://dx.doi.org/10.1038/s41598-017-11736-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596018PMC
September 2017

Toll-like Receptor-Dependent Negative Effects of Opioids: A Battle between Analgesia and Hyperalgesia.

Front Immunol 2017 31;8:642. Epub 2017 May 31.

Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.

Our understanding of the pathophysiology of the pathological pain and the pharmacology of analgesic treatments has progressed tremendously over the past two decades. Among the well-documented pro-algesic factors, glia and other toll-like receptors (TLRs)-expressing cells in the neuroimmune interface have been recognized for their role in the development of neuropathic pain and for compromising the analgesic effects of opioids. Here, we comprehensively review the molecular mechanisms of pain initiation and progression, the role of TLRs in these processes, and the molecular mechanisms of morphine and morphine-3-glucuronide in TLR-dependent central immune signaling. The data reviewed here suggest that, while targeting glia to treat neuropathic pain, both analgesic and analgesia-opposing effects of opioids must be considered by acknowledging their role in TLR-mediated signaling.
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http://dx.doi.org/10.3389/fimmu.2017.00642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450035PMC
May 2017

TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation.

Biomaterials 2017 05 20;126:49-60. Epub 2017 Feb 20.

Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea. Electronic address:

Negative regulation of Toll-like receptor-4 (TLR4) is anticipated to control the pathogen-induced exaggerated immune response. However, effective TLR4 antagonists with scarce off-target effects are yet to be developed. To fill this void, we sought to design small peptide-inhibitors of the TLR4/MD2-LPS interaction. Here we report novel TLR4-antagonistic peptides (TAP), identified through phage display, endowed with the LPS-induced proinflammation inhibition, and confirmed in mice. TAPs-attributed TLR4-antagonism were initially evaluated through NF-κB inhibition in HEK-blue hTLR4 and RAW264.7 cells, and further reinforced by the downregulation of MAPKs (mitogen-activated protein kinases), NF-κB, interleukin 6, and suppression of the oxidative-stress products and iNOS in macrophages and human peripheral blood mononuclear cells (hPBMCs). Among these, TAP2 specifically halted the TLR4, but not other TLRs signaling, which was further confirmed by the biophysical kinetic assay. Finally, TAP2 diminished LPS-elicited systemic cytokine response in vivo, suggesting that TAPs, specifically TAP2, have the potential to treat TLR4-mediated immune ailments.
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http://dx.doi.org/10.1016/j.biomaterials.2017.02.023DOI Listing
May 2017

A structural insight into the negative effects of opioids in analgesia by modulating the TLR4 signaling: An in silico approach.

Sci Rep 2016 12 16;6:39271. Epub 2016 Dec 16.

Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.

Opioids are considered the gold standard therapy for pain. However, TLR-dependent negative effects in analgesia have highlighted the complexities in the pharmacodynamics of opioids. While successive studies have reported that morphine and Morphine-3-glucuronide (M3G) activate the TLR4 pathway, the structural details of this mechanism are lacking. Here, we have utilized various computational tools to reveal the structural dynamics of the opioid-bound TLR4/MD2 complex, and have proposed a potential TLR4 activation mechanism. Our results support previous findings, and include the novel insight that the stable binding of morphine and naloxone, but not M3G, in the MD2 cavity, is TLR4 dependent. Morphine interacts with MD2 near its Phe126 loop to induce the active conformation (MD2); however, this binding is likely reversible, and the complex gains stability upon interaction with TLR4. M3G also induces the MD2 state, with both the Phe126 loop and the H1 loop being involved in MD2-M3G complex stability. Remarkably, naloxone, which requires TLR4 interaction for complex stability, switches the conformation of the gating loop to the inactive state (MD2°). Cumulatively, our findings suggest that ligand binding and receptor clustering occur successively in opioid-induced TLR4 signaling, and that MD2 plasticity and pocket hydrophobicity are crucial for the recognition and accommodation of ligands.
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http://dx.doi.org/10.1038/srep39271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159903PMC
December 2016

Advances in Antiviral Therapies Targeting Toll-like Receptors.

Expert Opin Investig Drugs 2016 29;25(4):437-53. Epub 2016 Feb 29.

a Department of Molecular Science and Technology , Ajou University , Suwon , Korea.

Introduction: Organisms have evolved a rapid and non-specific way to defend themselves via Toll-like receptors (TLRs), which recognize specific signatures present on invading microbes and viruses. Once detected, these receptors flood the cell with cytokines and IFNs that not only help to eradicate the invading viruses but also activate the adaptive immune response. Owing to difficulties in viral detection, a whole class of TLRs is dedicated to sensing viral nucleic acids, while other TLRs detect viral coat proteins and aid in establishing antiviral immunity. To protect humans better, TLRs and their downstream mediators can be used as potential drug targets, which can be either activated or inhibited, to counter viral infections.

Areas Covered: The current review focuses on TLR-targeting investigational drugs developed to treat viral diseases and virus-induced complications.

Expert Opinion: TLRs are a good choice for eradicating viral infections because they can fine-tune the immune response. However, TLRs should be exploited carefully, as there have been instances where their activation has led to unwanted responses in terms of both immune and viral activation. Therefore, more focus should be placed on novel drugs that can induce significant and long-term immunity, while concomitantly alleviating side effects.
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http://dx.doi.org/10.1517/13543784.2016.1154040DOI Listing
December 2016

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes.

PLoS One 2016 20;11(1):e0147240. Epub 2016 Jan 20.

Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.

The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox2(0bp)) or 3 base pairs (Oct4/Sox2(3bp)) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox2(0bp) and Oct4/Sox2(3bp) complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147240PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720428PMC
August 2016

Middle East respiratory syndrome coronavirus: transmission, virology and therapeutic targeting to aid in outbreak control.

Exp Mol Med 2015 Aug 28;47:e181. Epub 2015 Aug 28.

Department of Molecular Science and Technology, Ajou University, Suwon, Korea.

Middle East respiratory syndrome coronavirus (MERS-CoV) causes high fever, cough, acute respiratory tract infection and multiorgan dysfunction that may eventually lead to the death of the infected individuals. MERS-CoV is thought to be transmitted to humans through dromedary camels. The occurrence of the virus was first reported in the Middle East and it subsequently spread to several parts of the world. Since 2012, about 1368 infections, including ~487 deaths, have been reported worldwide. Notably, the recent human-to-human 'superspreading' of MERS-CoV in hospitals in South Korea has raised a major global health concern. The fatality rate in MERS-CoV infection is four times higher compared with that of the closely related severe acute respiratory syndrome coronavirus infection. Currently, no drug has been clinically approved to control MERS-CoV infection. In this study, we highlight the potential drug targets that can be used to develop anti-MERS-CoV therapeutics.
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http://dx.doi.org/10.1038/emm.2015.76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558490PMC
August 2015

In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response.

Sci Rep 2015 Aug 20;5:13446. Epub 2015 Aug 20.

Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.

The high-risk human papillomavirus E6 (hrHPV E6) protein has been widely studied due to its implication in cervical cancer. In response to viral threat, activated kinases phosphorylate the IRF3 autoinhibitory domain, inducing type1 interferon production. HPV circumvents the antiviral response through the possible E6 interaction with IRF3 and abrogates p53's apoptotic activity by recruiting E6-associated protein. However, the molecular mechanism of IRF3 inactivation by hrHPV E6 has not yet been delineated. Therefore, we explored this mechanism through in silico examination of protein-protein and protein-ligand docking, binding energy differences, and computational alanine mutagenesis. Our results suggested that the LxxLL motifs of IRF3 binds within the hydrophobic pocket of E6, precluding Ser-patch phosphorylation, necessary for IRF3 activation and interferon induction. This model was further supported by molecular dynamics simulation. Furthermore, protein-ligand docking and drug resistance modeling revealed that the polar patches in the pocket of E6, which are crucial for complex stability and ligand binding, are inconsistent among hrHPV species. Such variabilities pose a risk of treatment failure owing to point mutations that might render drugs ineffective, and allude to multi-drug therapy. Overall, this study reveals a novel perspective of innate immune suppression in HPV infections and suggests a plausible therapeutic intervention.
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http://dx.doi.org/10.1038/srep13446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542336PMC
August 2015

Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection.

Sci Rep 2015 Jan 7;5:7657. Epub 2015 Jan 7.

Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, Korea.

TLR4 in complex with MD2 senses the presence of lipid A (LA) and initiates a signaling cascade that curb the infection. This complex is evolutionarily conserved and can initiate the immune system in response to a variety of LAs. In this study, molecular dynamics simulation (25 ns) was performed to elucidate the differential behavior of TLR4/MD2 complex in response to Rhodobacter sphaeroides lipid A (RsLA). Penta-acyl chain-containing RsLA is at the verge of agonist (6 acyl-chains) and antagonist (4 acyl-chains) structure, and activates the TLR4 pathway in horses and hamsters, while inhibiting in humans and murine. In the time-evolved coordinates, the promising factors that dictated the differential response included the local and global mobility pattern of complexes, solvent-accessible surface area of ligand, and surface charge distributions of TLR4 and MD2. We showed that the GlcN1-GlcN2 backbone acquires agonist (3FXI)-like configurations in horses and hamsters, while acquiring antagonist (2E59)-like configurations in humans and murine systems. Moreover, analysis of F126 behavior in the MD2 F126 loop (amino acids 123-129) and loop EF (81-89) suggested that certain sequence variations also contribute to species-specific response. This study underlines the TLR4 signaling mechanism and provides new therapeutic opportunities.
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http://dx.doi.org/10.1038/srep07657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288214PMC
January 2015

Screening and design of anti-diabetic compounds sourced from the leaves of neem (Azadirachta indica).

Bioinformation 2013 27;9(20):1031-5. Epub 2013 Dec 27.

Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan.

Diabetes Mellitus is affecting people of all age groups worldwide. Many synthetic medicines available for type 2 diabetes mellitus in the market. However, there is a strong requirement for the development of better anti-diabetes compounds sourced especially from natural sources like medicinal plants. The extracts from the leaves of neem (Azadirachta indica) is traditionally known to have anti-diabetes properties. Therefore, there is an increased interest to identify potential compounds identified from neem leaf extracts showing predicted binding property with the known diabetes mellitus type 2 protein enzyme target phosphoenol-pyruvate carboxykinase(PEPCK). The structure data for compounds found in the leaf extract of neem was screened against PEPCK using molecular docking simulation and screening techniques. Results show that the compound 3-Deacetyl-3-cinnamoyl-azadirachtin possesses best binding properties with PEPCK. This observation finds application for further consideration in in vitro and in vivo validation.
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http://dx.doi.org/10.6026/97320630091031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910360PMC
February 2014

Interactions of ketoamide inhibitors on HCV NS3/4A protease target: molecular docking studies.

Mol Biol Rep 2014 Jan;41(1):337-45

HCV infection in more than 200 million individuals worldwide is a principal health problem. Prior to the development of HCV protease inhibitor combination therapy, HCV infected patients were treated with pegylated interferon-α and ribavirin. The adverse side effects associated with this type of treatment may lead to the discontinuation of treatment in certain number of patients. Currently, the inhibitors of NS3/4A Protease were found promising candidates for the treatment of HCV infection. There are several inhibitors of HCV NS3/4A protease that are passing through clinical improvement showing good potency against HCV infections in a number of patients. To further recognize binding interactions and activity trend, the molecular docking studies were performed on a number of HCV NS3/4A protease ketoamide inhibitors via MOE docking protocol. The docking analysis resulted in the detection of important ligand interactions with respect to binding site of target protein and produced good correlation coefficient (r2 = 0.690) between docking score and biological activities. These molecular docking results should, in our view, contribute for further optimization of ketoamide derivatives as NS3/4A protease inhibitors.
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http://dx.doi.org/10.1007/s11033-013-2867-xDOI Listing
January 2014

Molecular docking study of P4-Benzoxaborolesubstituted ligands as inhibitors of HCV NS3/4A protease.

Bioinformation 2013 19;9(6):309-14. Epub 2013 Mar 19.

Department of Biochemistry, UCS, Shankar, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan.

NS3/4A protease is an important emerging target for the cure of hepatitis C. There are many inhibitors of HCV NS3/4A protease that are passing through the clinical improvement indicating momentous reduction in the viral infection rate of patients. In this study molecular docking via MOE-Dock program was used to evaluate binding interactions of ligands with HCV NS3/4A protease. The docking and experimental results were found in good correlation. The best conformations of ligands were analyzed for binding interactions with the residues of binding cavity of NS3/4A protease. The valuable binding interactions and docking scores were observed for compounds 01, 05, 06, 07, 08 and 09.
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http://dx.doi.org/10.6026/97320630009309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607190PMC
April 2013

Interaction and inhibition of dengue envelope glycoprotein with mammalian receptor DC-sign, an in-silico approach.

PLoS One 2013 18;8(3):e59211. Epub 2013 Mar 18.

Bioinformatics Research Laboratory, National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.

Membrane fusion is the central molecular event during the entry of enveloped viruses into cells. The critical agents of this process are viral surface proteins, primed to facilitate cell bilayer fusion. The important role of Dendritic-cell-specific ICAM3-grabbing non-integrin (DC-SIGN) in Dengue virus transmission makes it an attractive target to interfere with Dengue virus Propagation. Receptor mediated endocytosis allows the entry of virions due to the presence of endosomal membranes and low pH-induced fusion of the virus. DC-SIGN is the best characterized molecule among the candidate protein receptors and is able to mediate infection with the four serotypes of dengue virus (DENV). Unrestrained pair wise docking was used for the interaction of dengue envelope protein with DC-SIGN and monoclonal antibody 2G12. Pre-processed the PDB coordinates of dengue envelope glycoprotein and other candidate proteins were prepared and energy minimized through AMBER99 force field distributed in MOE software. Protein-protein interaction server, ZDOCK was used to find molecular interaction among the candidate proteins. Based on these interactions it was found that antibody successfully blocks the glycosylation site ASN 67 and other conserved residues present at DC-SIGN-Den-E complex interface. In order to know for certain, the exact location of the antibody in the envelope protein, co-crystallize of the envelope protein with these compounds is needed so that their exact docking locations can be identified with respect to our results.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059211PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601059PMC
September 2013
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