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Publication Date: 2026
Journal of Molecular Graphics and Modelling (10933263)142
Bioluminescence, the emission of light by living organisms, results from chemiluminescent reactions facilitated by enzymes like luciferases. Among these, NanoLuc (NLuc) stands out due to its exceptional brightness, stability, and compact structure, making it a valuable tool in bioassays and imaging applications. NLuc is a 19.1 kDa monomeric enzyme derived from the deep-sea shrimp Oplophorus gracilirostris. Its structure comprises eleven antiparallel β-strands forming a β-barrel, capped by four α-helices. To enhance its versatility, NLuc has been engineered into split forms. Despite the advancements in split NLuc applications, several impediments exist that can be addressed to improve these systems. Recently the spectacular allosteric mechanisms of NLuc has been reported. Based on that, the enzyme exhibits homotropic negative allostery, where product binding to an allosteric site inhibits substrate binding at the catalytic site. Ongoing research into its structural dynamics and allosteric behaviors continues to expand its potential applications, while efforts to enhance the efficiency of its split forms aim to broaden its utility in complex biological assays. In this in silico assay, we performed dynamic simulations for both the various forms of apo-NLuc and the docking complex with the substrate and product. As a result, we clarify the sources of malfunctions in split NLuc and explore various aspects of split NLuc technologies. We also examine some hypotheses of NLuc mechanisms that display the complex behavior of this luciferase. © 2025
Publication Date: 2025
Biochemical and Biophysical Research Communications (0006291X)758
Alzheimer's disease involves the accumulation of amyloid beta (Aβ) monomers that form oligomers and fibrils in the brain. Studying the Aβ monomer is critical for understanding Aβ assembly and peptide behavior and has implications for drug design. Choosing a starting structure with a higher aggregation tendency for cost-effective MD studies and drug design is crucial. Previous studies have utilized distinct initial conformations, leading to varying results. Hence, this study was conducted to compare different initial conformations using the same MD simulation protocol to investigate the behavior and oligomerization propensity of different starting structures of Aβ during 1μs. The behavior of the monomers and their self-assembly systems were studied thoroughly, and the results revealed that highly helical Aβ monomers which used as starting structures retain high helix content during the simulation, and their tautomerization states did not cause significant changes in the structure. On the other hand, the Aβ extended and S-shaped monomers displayed the fingerprints of the fibril structure, which is believed to be more favorable for self-assembly. Self-assembly behaviors were seen for three S-shaped and three Aβ extended peptides. However, both conformations did not show stable β-sheet intermolecular interaction. For the Aβ16-22 monomer as a fragment of the Aβ that can assemble into fibrils, the impacts of capping and uncapping on the initial structure were also investigated. The results displayed that capped and uncapped structures can form oligomers with β-sheet at termini. However, in the capped state, β-sheet interactions were more stable and remained relatively longer than uncapped. © 2025 Elsevier Inc.
Khani, L.,
Nikfar, N.,
Zakeri, S.,
Rahmati, M.,
Javdan, S.,
Ganjalikhany, M.R.,
Fouladseresht, H.,
Ataei, B.,
Didarian, R.,
Ganjalikhani-hakemi, M. Publication Date: 2025
Infection, Epidemiology And Microbiology (25884115)11(2)pp. 167-178
Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a significant global health threat. The host immune response determines the disease severity, with factors like human leukocyte antigen (HLA) genes, age, sex, and nutritional status influencing outcomes. HLA genes, known for their genetic diversity, are implicated in determining susceptibility and severity of infectious diseases. This study investigated the association between HLA class I genotypes and COVID-19 severity in the Isfahan population, Iran. Materials & Methods:Blood samples were collected from 34 COVID-19 patients with varying levels of disease severity (severe, moderate, and mild). HLA genotyping was performed using polymerase chain reaction-sequence specific primers (PCR-SSP), and in silico analysis assessed the affinity of viral peptides to HLA alleles. Findings: Statistical analyses revealed that HLA-C07 was more prevalent in patients with severe COVID-19, suggesting a potential association between this allele and the disease severity. Furthermore, HLA-A01 was more prevalent among severe cases, while HLA-A02 and HLA-A03 were less frequent, indicating a possible predisposing role for HLA-A01 and protective roles for HLA-A02 and HLA-A*03. Conclusion: These findings highlight the role of HLA molecules in COVID-19 severity and offer insights into genetic factors influencing outcomes. Understanding the association of specific HLA alleles, such as HLA-C07, HLA-A01, HLA-A02, and HLA-A03, with the disease progression lays a foundation for advancing personalized preventive and therapeutic approaches. These results contribute to knowledge on host genetics in infectious diseases, paving the way for further research and therapeutic strategies. © 2025, TMU Press.
Jafary, F.,
Moradi, A.,
Ganjalikhany, M.R.,
Hassanpour dehnavi, A.,
Seifati, S.M.,
Khodarahmi, A.,
Hemati, M. Publication Date: 2025
International Journal of Biological Macromolecules (01418130)306
The Warburg effect is detected in numerous types of solid tumors and is characterized by the enhancement of glucose consumption and an increase in the rate of glycolysis in cancer cells. Lactate dehydrogenase A (LDHA) plays a critical role in the Warburg effect and to date, a number of LDHA inhibitors have been identified that act as competitive inhibitors of both the substrate pyruvate and the coenzyme NADH. In our previous study, a set of novel peptides were designed using in silico structure-based method with the aim of inhibiting the activity of LDHA by disrupting the interaction between its enzyme subunits. In the present study employed in vitro and in vivo techniques, to explore the influence of these peptides on the induction of cytotoxicity effect on cancer cell lines. Our findings revealed that the designed peptide effectively inhibits LDHA, leading to the induction of apoptosis and G2/M cell cycle arrest. Finally, we also analyzed the impact of the designed peptide on Balb/c mice, confirming the results of in silico and in vitro studies. Ultimately, the designed peptide had the ability to induce apoptosis in cancer cells by LDHA inhibition. © 2025
Publication Date: 2024
PLoS ONE (19326203)19(7 July)
Cancer control and treatment remain a significant challenge in cancer therapy and recently immune checkpoints has considered as a novel treatment strategy to develop anti-cancer drugs. Many cancer types use the immune checkpoints and its ligand, PD-1/PD-L1 pathway, to evade detection and destruction by the immune system, which is associated with altered effector function of PD-1 and PD-L1 overexpression on cancer cells to deactivate T cells. In recent years, mAbs have been employed to block immune checkpoints, therefore normalization of the anti-tumor response has enabled the scientists to develop novel biopharmaceuticals. In vivo affinity maturation of antibodies in targeted therapy has sometimes failed, and current experimental methods cannot accommodate the accurate structural details of protein-protein interactions. Therefore, determining favorable binding sites on the protein surface for modulator design of these interactions is a major challenge. In this study, we used the in silico methods to identify favorable binding sites on the PD-1 and PD-L1 and to optimize mAb variants on a large scale. At first, all the binding areas on PD-1 and PD-L1 have been identified. Then, using the RosettaDesign protocol, thousands of antibodies have been generated for 11 different regions on PD-1 and PD-L1 and then the designs with higher stability, affinity, and shape complementarity were selected. Next, molecular dynamics simulations and MM-PBSA analysis were employed to understand the dynamic, structural features of the complexes and measure the binding affinity of the final designs. Our results suggest that binding sites 1, 3 and 6 on PD-1 and binding sites 9 and 11 on PD-L1 can be regarded as the most appropriate sites for the inhibition of PD-1-PD-L1 interaction by the designed antibodies. This study provides comprehensive information regarding the potential binding epitopes on PD-1 which could be considered as hotspots for designing potential biopharmaceuticals. We also showed that mutations in the CDRs regions will rearrange the interaction pattern between the designed antibodies and targets (PD-1 and PD-L1) with improved affinity to effectively inhibit protein-protein interaction and block the immune checkpoint. Copyright: © 2024 Abdolmaleki et al.
Publication Date: 2024
Heliyon (24058440)10(23)
Cancer is known as the main cause of mortality in the world, and every year, the rate of incidence and death due to cancer is increasing. Bioactive peptides are one of the novel therapeutic options that are considered a suitable alternative to toxic chemotherapy drugs because they limit side effects with their specific function. In fact, bioactive peptides are short amino acid sequences that obtain diverse physiological functions to maintain human health after being released from parent proteins. This group of biological molecules that can be isolated from different types of natural protein sources has attracted much attention in the field of pharmaceutical and functional foods production. The current article describes the therapeutic benefits of bioactive peptides and specifically and extensively reviews their role in cancer treatment, available sources for discovering anticancer peptides, mechanisms of action, production methods, and existing challenges. © 2024 The Authors
Publication Date: 2023
Scientific Reports (20452322)13(1)
In recent years, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic, and its variants, especially those with higher transmissibility and substantial immune evasion, have highlighted the imperative for developing novel therapeutics as sustainable solutions other than vaccination to combat coronaviruses (CoVs). Beside receptor recognition and virus entry, members of the SARS-CoV-2 replication/transcription complex are promising targets for designing antivirals. Here, the interacting residues that mediate protein–protein interactions (PPIs) of nsp10 with nsp16 and nsp14 were comprehensively analyzed, and the key residues’ interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates both nsp14’s exoribonuclease (ExoN) and nsp16’s 2′O-methyltransferase (2′O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2′O-MTase is responsible for the completion of RNA capping to ensure efficient replication and translation and escape from the host cell’s innate immune system. The results of the PPIs analysis proposed crucial information with implications for designing SARS-CoV-2 antiviral drugs. Based on the predicted shared protein–protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions, a set of dual-target peptide inhibitors was designed. The designed peptides were evaluated by molecular docking, peptide–protein interaction analysis, and free energy calculations, and then further optimized by in silico saturation mutagenesis. Based on the predicted evolutionary conservation of the interacted target residues among CoVs, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors. © 2023, The Author(s).
Jafary, F.,
Joozdani, F.A.,
Shahzamani, K.,
Jafari, S.,
Mirhendi, H.,
Ganjalikhany, M.R. Publication Date: 2023
PLoS ONE (19326203)18(9 September)
During replication, some mutations occur in SARS-CoV-2, the causal agent of COVID-19, leading to the emergence of different variants of the virus. The mutations that accrue in different variants of the virus, influence the virus’ ability to bind to human cell receptors and ability to evade the human immune system, the rate of viral transmission, and effectiveness of vaccines. Some of these mutations occur in the receptor binding domain (RBD) of the spike protein that may change the affinity of the virus for the ACE2 receptor. In this study, several in silico techniques, such as MD and SMD simulations, were used to perform comparative studies to deeply understand the effect of mutation on structural and functional details of the interaction of the spike glycoprotein of SARS-CoV-2, with the ACE2 receptor. According to our results, the mutation in the RBD associated with the Omicron variant increase binding affinity of the virus to ACE2 when compared to wild type and Delta variants. We also observed that the flexibility of the spike protein of the Omicron variant was lower than in comparison to other variants. In summary, different mutations in variants of the virus can have an effect on the binding mechanism of the receptor binding domain of the virus with ACE2. © 2023 Jafary et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Zohrabi, T.,
Azimi-resketi, M.,
Talaei, F.,
Yaghoubi, M.,
Ganjalikhany, M.R.,
Mohamadi farsani, F.,
Eskandarian, A. Publication Date: 2023
Experimental Parasitology (00144894)251
Toxoplasmosis is a serious parasitic infection and novel therapeutic options are highly demanded to effectively eliminate it. In current study, Toxoplasma gondii myosin A, C and F genes were knocked down using small interference RNA (siRNA) method and the parasite survival and virulence was evaluated in vitro and in vivo. The parasites were transfected with specific siRNA, virtually designed for myosin mRNAs, and co-cultured with human foreskin fibroblasts. The transfection rate and the viability of the transfected parasites were measured using flow cytometry and methyl thiazole tetrazolium (MTT) assays, respectively. Finally, the survival of BALB/c mice infected with siRNAs-transfected T. gondii was assessed. It was demonstrated that a transfection rate of 75.4% existed for siRNAs, resulting in 70% (P = 0.032), 80.6% (P = 0.017) and 85.5% (P = 0.013) gene suppression for myosin A, C and F in affected parasites, respectively, which was subsequently confirmed by Western blot analysis. Moreover, lower parasite viability was observed in those with knocked down myosin C with 80% (P = 0.0001), followed by 86.15% (P = 0.004) for myosin F and 92.3% (P = 0.083) for myosin A. Considerably higher mouse survival (about 40 h) was, also, demonstrated in mice challenged with myosin siRNA-transfected T. gondii, in comparison with control group challenged with wild-type parasites. In conclusion, myosin proteins knock down proposes a promising therapeutic strategy to combat toxoplasmosis. © 2023 Elsevier Inc.
Publication Date: 2023
Process Biochemistry (18733298)130pp. 245-255
Human Follistatin-like 1, is a protein with multiple disulfide bonds involved in important physiological processes. The current research aimed to evaluate the relationship between the reduction of disulfide bonds and the function of human FSTL1. Human FSTL1 was expressed in a bacterial expression system, purified, and reduced using 4–16 mM dithiothreitol (DTT). The results showed that the proliferation in the presence of the reduced human FSTL1 with 16 mM was better than that of the non-reduced protein. While circular dichroism spectroscopy showed that the content of the secondary structure of human FSTL1 did not change significantly, fluorescence spectroscopy studies show that the surface hydrophobicity of human FSTL1 decreased after reduction of disulfide bonds. Molecular dynamics studies showed that the radius of gyration decreased in the presence of 16 mM DTT. Our results showed that the reduction of disulfide bonds in human FSTL1 increased the hydrophilicity of the surface and might have a compensatory effect on the decrease in the hydrophilicity caused by the lack of post-translational modifications in the bacterial expression system. The present study may be useful for future pathological studies. © 2023 Elsevier Ltd
Dehbashi, M.,
Hojati najafabadi, Z.,
Bashi naeini, M.M.,
Ganjalikhany, M.R.,
Cho, W.C.,
Shimosaka, A.,
Navabi, P.,
Ganjalikhani-hakemi, M. Publication Date: 2021
Frontiers in Oncology (2234943X)11
For many years, high-affinity subunit of IL-2 receptor (CD25) has been considered as a promising therapeutic target for different pathologic conditions like allograft rejection, autoimmunity, and cancers. Although CD25 is transiently expressed by newly-activated T cells, it is the hallmark of regulatory T (Treg) cells which are the most important immunosuppressive elements in tumor microenvironment. Thus, Tregs can be considered as a potential target for chimeric antigen receptor (CAR)-based therapeutic approaches. On the other hand, due to some profound adverse effects pertaining to the use of CAR T cells, CAR NK cells have caught researchers’ attention as a safer choice. Based on these, the aim of this study was to design and develop a CAR NK cell against CD25 as the most prominent biomarker of Tregs with the prospect of overcoming immune escape mechanism in solid and liquid cancers. In the current study, an anti-CD25 CAR was designed and evaluated by comprehensive in silico analyses. Then, using lentiviral transduction system, NK-92 cell line was engineered to express this anti-CD25 CAR construct. In vitro functional analyses of anti-CD25 CAR for its reactivity against CD25 antigen as well as for cytotoxicity and cytokine production assays against CD25 bearing Jurkat cell line were done. In silico analyses demonstrated that the anti-CD25 CAR transcript and scFv protein structures were stable and had proper interaction with the target. Also, in vitro analyses showed that the anti-CD25 CAR-engineered NK-92 cells were able to specifically detect and lyse target cells with an appropriate cytokine production and cytotoxic activity. To conclude, the results showed that this novel CAR NK cell is functional and warrant further investigations. © Copyright © 2021 Dehbashi, Hojati, Motovali-bashi, Ganjalikhany, Cho, Shimosaka, Navabi and Ganjalikhani-Hakemi.
Publication Date: 2021
Iranian Journal Of Basic Medical Sciences (20083874)24(4)pp. 360-368
Objective(s): IL-2Rα plays a critical role in maintaining immune function. However, expression and secretion of CD25 in various malignant disorders and autoimmune diseases are now well established. Thus, CD25 is considered an important target candidate for antibody-based therapy. This study aimed to find the most suitable linker peptide to construct a functional anti-CD25 single-chain fragment variable (scFv) by bioinformatics studies and its production in a bacterial expression system. Materials and Methods: Here, the 3D structures of the scFvs with different linkers were predicted and molecular dynamics simulation was performed to compare their structures and dynamics. Then, interactions between five models of scFv and human CD25 were calculated via molecular docking. According to MD and docking results, the anti-CD25 scFvs with (Gly4Ser)3 linker were constructed and cloned into pET-22b(+). Then, recombinant plasmids were transformed into Escherichia coli Bl21 (DE3) for expression using IPTG and lactose as inducers. Anti-CD25 scFv was purified from the periplasm and detected by SDS-PAGE and Western blot. Afterward, functionality was evaluated using ELISA. Results: In silico analysis showed that the model containing (Gly4Ser)3 as a linker has more stability compared with other linkers. The results of SDS-PAGE, Western blot, and ELISA confirmed the accuracy of anti-CD25 scFv production and its ability to bind to the human CD25. Conclusion: Conclusively, our work provides a theoretical and experimental basis for production of an anti-CD25 scFv, which may be applied for various malignant disorders and autoimmune diseases. © 2021 Mashhad University of Medical Sciences. All rights reserved.
Publication Date: 2021
Scientific Reports (20452322)11(1)
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry of viral genome to the host cell. Therefore, blocking the virus-cell interaction could be a potential target for the prevention of viral infection. The binding of SARS-CoV-2 to ACE2 is a protein–protein interaction, and so, analyzing the structure of the spike glycoprotein of SARS-CoV-2 and its underlying mechanism to bind the host cell receptor would be useful for the management and treatment of COVID-19. In this study, we performed comparative in silico studies to deeply understand the structural and functional details of the interaction between the spike glycoprotein of SARS-CoV-2 and its cognate cellular receptor ACE2. According to our results, the affinity of the ACE2 receptor for SARS-CoV-2 was higher than SARS-CoV. According to the free energy decomposition of the spike glycoprotein-ACE2 complex, we found critical points in three areas which are responsible for the increased binding affinity of SARS-CoV-2 compared with SARS-CoV. These mutations occurred at the receptor-binding domain of the spike glycoprotein that play an essential role in the increasing the affinity of coronavirus to ACE2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from − 2 kcal mol−1 in SARS-COV to − 6 kcal mol−1 in SARS-COV-2. The results demonstrated that some mutations in the receptor-binding motif could be considered as a hot-point for designing potential drugs to inhibit the interaction between the spike glycoprotein and ACE2. © 2021, The Author(s).
Bidram, M.,
Zhao, Y.,
Shebardina, N.G.,
Baldin, A.V.,
Bazhin, A.V.,
Ganjalikhany, M.R.,
Zamyatnin, A.A.,
Ganjalikhani-hakemi, M. Publication Date: 2021
Vaccines (2076393X)9(10)
Malignant melanoma is one of the most aggressive forms of cancer and the leading cause of death from skin tumors. Given the increased incidence of melanoma diagnoses in recent years, it is essential to develop effective treatments to control this disease. In this regard, the use of cancer vaccines to enhance cell-mediated immunity is considered to be one of the most modern immunotherapy options for cancer treatment. The most recent cancer vaccine options are mRNA vaccines, with a focus on their usage as modern treatments. Advantages of mRNA cancer vaccines include their rapid production and low manufacturing costs. mRNA-based vaccines are also able to induce both humoral and cellular immune responses. In addition to the many advantages of mRNA vaccines for the treatment of cancer, their use is associated with a number of challenges. For this reason, before mRNA vaccines can be used for the treatment of cancer, comprehensive information about them is required and a large number of trials need to be conducted. Here, we reviewed the general features of mRNA vaccines, including their basis, stabilization, and delivery methods. We also covered clinical trials involving the use of mRNA vaccines in melanoma cancer and the challenges involved with this type of treatment. This review also emphasized the combination of treatment with mRNA vaccines with the use of immune-checkpoint blockers to enhance cell-mediated immunity. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Publication Date: 2021
RSC Advances (20462069)11(19)pp. 11048-11056
Protein kinases play a significant role in cellular activation procedures by exhibiting a vivid selection in the target, as well as recognizing and phosphorylating them. Extracellular signal-regulated kinase 2 (ERK2) is one of the main kinases in the mitogen-activated protein kinase (MAPK) signaling cascade and engages in dynamically regulating the activities of signaling proteins and physiological processes, including cell proliferation, differentiation, adhesion, migration, and survival. Predicting collective dynamic and structural motions in biological macromolecules is pivotal to obtain a better understanding of the majority of biological processes. Here, through molecular dynamic simulation and normal mode analysis, we investigated ERK2 conformations, in the forms of active (phosphorylated), inactive (unphosphorylated), and in a complex with its substrate, ribosomal protein S6 kinase alpha-1 (RSK1), to determine functional characteristics. Our finding demonstrated that ERK2 plays a switch role in the regulation of pathways. In the case that this protein kinase is in the active form, all critical regions shift to be prepared to accept the substrate and catalytic action. Meanwhile, inactive ERK2 shows contrasting results in which all motions tend to close the catalytic site and cease the phosphorylation action in the MAPK cascade. These findings are in line with those from other similar studies and provide us with novel molecular target regions and recent details on how this mechanism works. © The Royal Society of Chemistry 2021.
Publication Date: 2020
International Journal of Peptide Research and Therapeutics (15733149)26(3)pp. 1513-1522
Fusion (F) and Hemagglutinin-neuraminidase (HN) glycoproteins of Newcastle disease virus containing important epitopes play crucial role in stimulation of humoral and cell-mediated immunity of the host. In the present study we analyzed and compared genetic diversity of F and HN sequences related to long-term circulating sub-genotype VIIj isolates to genotype VII and II strains. In addition, F and HN epitope prediction was performed using IEDB, NetMHC 4.0 and NetMHC II 3.1 servers. Molecular docking analysis was also conducted for VIIj and LaSota isolates interacting MHC I and II molecules. Results indicated that certain specific mutations were occurred in Fusion and Hemagglutinin-neuraminidase proteins of VIIj sub-genotype. Epitope prediction study revealed that the unique variations were located on the antigenic site regions of F and HN glycoproteins. Furthermore, docking interaction analysis showed surprising results, in which defined antigenic site residues of VIIj isolates interacted to MHC molecules with higher affinity levels rather than LaSota strains used as vaccines. Our in silico results suggest that by applying certain epitope sequences inducing both immune responses, vaccination failures may be reduced and challenged vaccinated host cells may stop viral shedding beside protection from Newcastle disease infection. Thus, we recommend the introduced antigenic sites of VIIj sub-genotype in this paper would act as the great targets for epitope-based vaccine design in the region. © 2019, Springer Nature B.V.
Publication Date: 2020
Iranian Journal Of Biotechnology (23222921)18(4)pp. 124-131
Background: Reteplase, the recombinant form of tissue plasminogen activator, is a thrombolytic drug with outstanding characteristics, while demonstrating limited solubility and reduced plasminogen activation. Previously, we in silico designed a variant of Reteplase with positively supercharged surface, which showed promising stability, solubility and activity. This study was devoted to evaluation of the utility of supercharging technique for enhancing these characteristics in Reteplase. Objective: To test the hypothesis that reinforced surface charge of a rationally-designed Reteplase variant will not compromise its stability, will increase its solubility, and will enhance its plasminogen cleavage activity. Materials and Methods: Supercharged Reteplase coding sequence was cloned in pDest527 vector and expressed in E. coli BL21 (DE3). The expressed protein was extracted by cell disruption. Inclusion bodies were solubilized using guanidine hydrochloride, followed by dialysis for protein refolding. After confirmation with SDS-PAGE and western blotting, extracted proteins were assayed for solubility and tested for bioactivity. Results: SDS-PAGE and western blot analysis confirmed the successful expression of Reteplase. Western blot experiments showed most of Reteplase expressed in the insoluble form. Plasminogen cleavage assay showed significantly higher activity of the supercharged variant than the wild type protein (P < 0.001). The stability of the supercharged variant was also comparable to the wild type. Conclusion: Our findings, i.e. the contribution of the surface supercharging technique to retained stability, enhanced plasminogen cleavage activity, while inefficiently changed solubility of Reteplase, contain implications for future designs of soluble variants of this fibrinolytic protein drug. © 2020 The Author(s); Published by National Institute of Genetic Engineering and Biotechnology.
Publication Date: 2020
Research In Pharmaceutical Sciences (17355362)15(2)pp. 164-173
Background and purpose: Tobacco etch virus (TEV) protease is a protease with high sequence specificity which is useful for the cleavage of fusion proteins. A major limitation of this enzyme is its relatively poor solubility. This study aimed to investigate the effects of some suggested mutations by online tools and molecular dynamics simulation to improve the solubility of TEV protease in vitro. Experimental approach: We designed a rational multi-stage process to determine the solubilizing mutations of TEV protease. At the first stage, all the possible mutations were predicted using online tools such as PoPMuSiC and Eris servers, in which five mutations include N23F, N23L, Q74L, Q74V, and Q74I were suggested for further studies. In the next step, the three dimensional structure of the wild type (WT) and the best mutations were subjected to molecular dynamic simulations to evaluate the dynamic behaviour of the obtained structures. The selected mutation was introduced into the structure using site-directed mutagenesis and expressed in Escherichia coli BL21DE3. After purification, solubility and activity of the purified mutant and WT-TEV proteases were assayed. Findings /Results: By considering the analysis of various factors such as structural and solubility properties, one mutant, N23F, was selected for in vitro studies which led to a 1.5 times increase in the solubility compared to the WT while its activity was decreased somewhat. Conclusion and implications: We propose N23F mutation, according to computational and experimental analyses for TEV proteases which resulted in a 150% increase in solubility compared to the WT. © 2020 Wolters Kluwer Medknow Publications. All rights reserved.
Publication Date: 2019
International Journal Of Cancer Management (25384422)12(4)
Background: DNA topoisomerase II alpha (Top2-α) enzyme is an important target for many anticancer drugs. A variety of TOP2A genomic variants has been found associated with the development of drug resistance to this enzyme. Methods: Here, we have characterized 2 non-synonymous single nucleotide polymorphisms (nsSNPs) including rs762022284 and rs764177670 in TOP2A gene, which could affect its response to Amsacrine and Mitoxantrone as important inhibitors of the enzyme. The nsSNPs were genotyped in the Iranian population and the data were analyzed, using PLINK and PICcalc programs. Results: Genotyping data indicated the allele frequency of 0.30 (PIC = 0.42) and 0.05 (PIC = 0.09) for rs762022284 and rs764177670, respectively. Conclusions: The data suggested that the presence of rs762022284 and rs764177670 nsSNPs could affect Top2-α response to Amsacrine and Mitoxantrone, indicating the necessity of consideration of population-dependent genotypes in cancer chemotherapy, using these drugs. © 2019, Author(s).
Publication Date: 2019
Research In Pharmaceutical Sciences (17355362)14(4)pp. 359-368
Reteplase (recombinant plasminogen activator, r-PA) is a thrombolytic agent recombined from tissue-type plasminogen activator (t-PA), which has several prominent features such as strong thrombolytic ability and E. coli expressibility. Despite these outstanding features, it demonstrates reduced fibrin binding affinity, reduced stimulation of protease activity, and lower solubility, hence higher aggregation propensity, compared to t-PA. The present study was devoted to design r-PA variants with comparable structural stability, enhanced biological activity, and high solubility. For this purpose, computational molecular modeling techniques were utilized. The supercharging technique was applied for r-PA to designing new species of the protein. Based on the results from in silico evaluation of selected mutations in comparison to the wild-type r-PA, the designed supercharged mutant (S7 variant) exhibited augmented stability, decreased solvation energy, as well as enhanced binding affinity to fibrin. The data also implied increased plasminogen cleavage activity of the new variant. These findings have implications to therapies which involve removal of intravascular blood clots, including the treatment of acute myocardial infarction. © 2019 Wolters Kluwer Medknow Publications. All rights reserved.
Publication Date: 2019
Critical Reviews in Eukaryotic Gene Expression (10454403)29(2)pp. 177-187
The vast majority of drugs act through binding to their protein targets. Prediction of the interaction between small molecules and these receptors is a key element in the process of drug discovery. Advances in structural biology have enabled us to resolve the three-dimensional structure of proteins, which are the targets of the drugs. Pharmacogenetics also helped researchers to study the structural variations arise from the single nucleotide polymorphisms (SNPs) and to survey the effects these variations in drug design and development. These improvements led to the identification of structural changes caused by SNPs, which affect the drug interaction with their receptors, called drug response. In this study, the interaction between androgen receptor and bicalutamide was investigated using a computational analysis. The results of these analyses were then used for identification of nonsynonymous SNPs that are potentially involved in drug response alterations. The data show that amino acids Met895, Trp741, Arg752, Ile899, Leu707, Gly708, Gln711, Met745, Met749, Thr877, Phe764, Met742, Asn705 and Leu704 are the main residues involved in the interaction between androgen receptor and bicalutamide. The occurrence of nonsynonymous polymorphisms I843T, L708R, H690P, I870M, N757S, L713F, G744E, L678P, M788V, M781I, A722T, H875Y, I842V, and F827L in this receptor greatly affected its interaction with bicalutamide, and they were able to cause drug resistance. The results of this study could be useful in predicting the response to treatment in patients receiving bicalutamide. © 2019 Begell House, Inc.
Publication Date: 2019
Scientific Reports (20452322)9(1)
Lactate dehydrogenase A (LDHA) is a critical metabolic enzyme belonging to a family of 2-hydroxy acid oxidoreductases that plays a key role in anaerobic metabolism in the cells. In hypoxia condition, the overexpression of LDHA shifts the metabolic pathway of ATP synthesis from oxidative phosphorylation to aerobic glycolysis and the hypoxia condition is a common phenomenon occurred in the microenvironment of tumor cells; therefore, the inhibition of LDHA is considered to be an excellent strategy for cancer therapy. In this study, we employed in silico methods to design inhibitory peptides for lactate dehydrogenase through the disturbance in tetramerization of the enzyme. Using peptide as an anti-cancer agent is a novel approach for cancer therapy possessing some advantages with respect to the chemotherapeutic drugs such as low toxicity, ease of synthesis, and high target specificity. So peptides can act as appropriate enzyme inhibitor in parallel to chemical compounds. In this study, several computational techniques such as molecular dynamics (MD) simulation, docking and MM-PBSA calculation have been employed to investigate the structural characteristics of the monomer, dimer, and tetramer forms of the enzyme. Analysis of MD simulation and protein-protein interaction showed that the N-terminal arms of each subunit have an important role in enzyme tetramerization to establish active form of the enzyme. Hence, N-terminal arm can be used as a template for peptide design. Then, peptides were designed and evaluated to obtain best binders based on the affinity and physicochemical properties. Finally, the inhibitory effect of the peptides on subunit association was measured by dynamic light scattering (DLS) technique. Our results showed that the designed peptides which mimic the N-terminal arm of the enzyme can successfully target the C-terminal domain and interrupt the bona fide form of the enzyme subunits. The result of this study makes a new avenue to disrupt the assembly process and thereby oppress the function of the LDHA. © 2019, The Author(s).
Publication Date: 2019
PLoS ONE (19326203)14(5)
EGFR (epidermal growth factor receptor) plays the critical roles in the vital cell activities, proliferation, differentiation, migration and survival in response to polypeptide growth factor ligands. Aberrant activation of this receptor has been demonstrated in many human cancers, particularly in non-small cell lung carcinoma (NSCLC). L858R point mutation is the most common oncogenic mutation in EGFR tyrosine kinase domain in patients with EGFR-mutated NSCLC. A feedback inhibitor of EGFR is MIG6 molecule which binds peptide-substrate binding site of the receptor and leads to degradation of activated EGFR. In this in silico study, the peptide-substrate binding site of EGFRL858R mutant has been targeted to inhibit it using molecular docking, MD simulation and MM-PBSA method. Finally, physicochemical properties of the designed peptides have been evaluated. A peptide library was provided composed of 31 peptides which were designed based on the MIG6 structure. The results indicated that, two peptides were able to inhibit EGFRL858R mutant selectively. This computational study could be helpful in designing novel inhibitory peptides to inhibit oncogenic EGFR mutants which do not respond to available EGFR TKIs. © 2019 Tavakoli, Ganjalikhany. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Publication Date: 2018
Journal of Cellular Biochemistry (07302312)119(2)pp. 1780-1790
Renilla Luciferase (RLuc) is a blue light emitter protein which can be applied as a valuable tool in medical diagnosis. But due to lack of the crystal structure of RLuc-ligand complex, the functional motions and catalytic mechanism of this enzyme remain largely unknown. In the present study, the active site properties and the ligand-receptor interactions of the native RLuc and its red-shifted light emitting variant (Super RLuc 8) were investigated using molecular docking approach, molecular dynamics (MD) analysis, and MM-PBSA method. The detailed analysis of the main clusters led to identifying a lid-like structure and its functional motions. Furthermore, an induced-fit mechanism is proposed where ligand-binding induces conformational changes of the active site. Our findings give an insight into the deeper understanding of RLuc conformational changes during binding steps and ligand-receptor pattern. Moreover, our work broaden our understanding of how active site geometry is adjusted to support the catalytic activity and red-shifted light emission in Super RLuc 8. © 2017 Wiley Periodicals, Inc.
Publication Date: 2017
Current Cancer Drug Targets (15680096)17(7)pp. 657-668
Background: DNA topoisomerase II-α (Top2-α), an essential enzyme for the management of DNA during replication, transcription, recombination, and chromatin remodeling, is one of the most important anticancer targets. Numerous molecules have been designed as Top2-α inhibitors. However, several studies have shown that polymorphisms and mutations in Top2 have conferred resistance to most of these anticancer drugs. The aim of this study was to computationally examine the mechanisms by which genomic variations in Top2-α could affect its resistance to Amsacrine and Mitoxantrone as important inhibitors of the enzyme. Results: The results showed that variants K529E, R568H, R568G and T530M could affect Top2-α inhibition by Amsacrine causing possible drug-resistant. Moreover, R487K, and Y481C variants could change the response of the enzyme to Mitoxantrone. Conclusion: These results could facilitate the prediction and development of more effective drugs for Top2-α variants, making the cancer chemotherapy more effective. © 2017 Bentham Science Publishers.
Publication Date: 2016
Network Modeling Analysis in Health Informatics and Bioinformatics (21926670)5(1)
An in silico study was conducted to identify antigens with potential possibility of being a vaccine against type 1 diabetes mellitus (T1DM). A molecular mimicry between protein 2C of coxsackievirus B4 and autoantigen glutamic acid decarboxylase 65 is a significant factor in the pathogenesis of T1DM. The aim of this study was to predict the protein 2C of coxsackievirus B4 epitopes and design a vaccine against T1DM. Several web servers were used to predict continuous B cell epitopes and 8 peptides (P1–P8) were selected. Then the 3D structure of P2C was built by structural modeling using Robetta and the structure was subjected to 10 ns molecular dynamics simulation by Amber to obtain an average structure in an explicit water system. Molecular mimicry theory was confirmed by local structural alignment of modeled structure protein 2C with glutamic acid decarboxylase 65 using Swiss pdb viewer. Then conformational B cell epitope web servers were used to identify discontinuous B cells epitopes. PDBsum was used for the analysis of the protein 2C secondary structure. Finally, T cells epitopes have been predicted by the immune epitope database analysis resource (IEDB). In silico analysis of the sequence and structure retrieved by mentioned methods and web servers, revealed that two out of 8 peptides (P2 and P7 epitopes) are the best choices for the vaccine design. These results suggest that epitopes and structural features of the protein 2C of coxsackievirus B4 can be predicted and this information could be used to make novel vaccines for control of T1DM. © 2016, Springer-Verlag Wien.
Sadeghi, M.,
Ranjbar, B.,
Ganjalikhany, M.R.,
Khan, F.M.,
Schmitz, U.,
Wolkenhauer, O.,
Gupta, S.K. Publication Date: 2016
PLoS ONE (19326203)11(12)
Technological and methodological advances in multi-omics data generation and integration approaches help elucidate genetic features of complex biological traits and diseases such as prostate cancer. Due to its heterogeneity, the identification of key functional components involved in the regulation and progression of prostate cancer is a methodological challenge. In this study, we identified key regulatory interactions responsible for primary to metastasis transitions in prostate cancer using network inference approaches by integrating patient derived transcriptomic and miRomics data into gene/miRNA/transcription factor regulatory networks. One such network was derived for each of the clinical states of prostate cancer based on differentially expressed and significantly correlated gene, miRNA and TF pairs from the patient data. We identified key elements of each network using a network analysis approach and validated our results using patient survival analysis. We observed that HOXD10, BCL2 and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN and JUNB are playing a central role. Benefiting integrative networks our analysis suggests that some of these molecules were targeted by several overexpressed miRNAs which may have a major effect on the dysregulation of these molecules. For example, in the metastatic tumors five miRNAs (miR-671-5p, miR-665, miR-663, miR-512-3p and miR-371-5p) are mainly responsible for the dysregulation of STAT3 and hence can provide an opportunity for early detection of metastasis and development of alternative therapeutic approaches. Our findings deliver new details on key functional components in prostate cancer progression and provide opportunities for the development of alternative therapeutic approaches. © 2016 Sadeghi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Publication Date: 2016
Medicinal Chemistry Research (10542523)25(6)pp. 1250-1259
Topoisomerases are enzymes that resolve winding problem of DNA during cellular processes. Because of essential roles of these enzymes in maintenance of cell function, topoisomerases are important targets for cancer chemotherapy. To date, several topoisomerase inhibitors have been introduced and applied as drugs in the treatment of cancer. Topoisomerase II α (Top2-α), a subclass of topoisomerase II enzymes, functions as the target for several anticancer agents and a variety of mutations in this protein have been associated with the development of drug resistance. Mitoxantrone and Amsacrine are among two important inhibitors of Top2 enzymes used in cancer chemotherapy. In this study, we used computational methods to analysis interactions between these compounds and Top2-α in order to identify the most important residues involved in the enzyme inhibition. In order to obtain reliable results, several docking studies have been performed on the human Top2-β to reproduce binding modes which are observed in the crystal form of Top2-β complexed with Mitoxantrone and Amsacrine. Since human Top2-β is the closest homologue to Top2-α, same docking parameters have been used for docking of Top2-α with mentioned drugs. The data also showed that the main residues involved in the interaction between Top2-α and Mitoxantrone were Lys489, Asp504, Glu506, Gly488, Ile490 and Leu491. For Top2α-Amsacrine complex, the interaction was mainly through Arg487, Glu506, Gly488, Lys489, Asn504 and Ala505. These findings clarify the mechanisms of action for these drugs and may facilitate future drug development and cancer treatment. © 2016, Springer Science+Business Media New York.
Publication Date: 2015
Computational Biology and Chemistry (14769271)59pp. 185-198
It has been previously shown that the inhibition of mitogen activated protein kinase kinase (MEK) contributes to apoptosis and suppression of different cancer cells. Correspondingly, a number of MEK1/2 inhibitors have been designed and evaluated since 2001. However, they did not satisfy essential pharmacokinetic (PK) and pharmacodynamic (PD) properties thus, almost most of them were terminated in pre-clinical or clinical studies. This study aims to design new specific MEK1/2 inhibitors with improved PK/PD profiles to be used as alternative cancer medications. In first part of this study, a comprehensive screening, for the first time, was done on well-known MEK1/2 inhibitors using a number of computational programs such as AutoDock Tools 4.2 (ADT) and AutoDock Vina. Therefore a valuable training dataset as well as a reliable pharmacophore model were provided which were then used to design new inhibitors. According to the results of training dataset, Trametinib was determined as the best inhibitor provided, so far. So, Trametinib was used as the lead structure to design new inhibitors in this study. In second part of this investigation, a set of new allosteric MEK1/2 inhibitors were designed significantly improving the binding energy as well as the ADMET properties, suggesting more specific and stable ligand-receptor complexes. Consequently, the structures 14 and 15 of our inhibitors, as the most potent structures, are great substituents for Trametinib to be used and evaluated in clinical trials as alternative cancer drugs. © 2015 Elsevier Ltd. All rights reserved.
Publication Date: 2012
PLoS ONE (19326203)7(7)
Candida antarctica lipase B (CALB) belongs to psychrophilic lipases which hydrolyze carboxyl ester bonds at low temperatures. There have been some features reported about cold-activity of the enzyme through experimental methods, whereas there is no detailed information on its mechanism of action at molecular level. Herein, a comparative molecular dynamics simulation and essential dynamics analysis have been carried out at three temperatures (5, 35 and 50°C) to trace the dominant factors in the psychrophilic properties of CALB under cold condition. The results clearly describe the effect of temperature on CALB with meaningful differences in the flexibility of the lid region (α5 helix), covering residues 141-147. Open- closed conformations have been obtained from different sets of long-term simulations (60 ns) at 5°C gave two reproducible distinct forms of CALB. The starting open conformation became closed immediately at 35 and 50°C during 60 ns of simulation, while a sequential open-closed form was observed at 5°C. These structural alterations were resulted from α5 helical movements, where the closed conformation of active site cleft was formed by displacement of both helix and its side chains. Analysis of normal mode showed concerted motions that are involved in the movement of both α5 and α10 helices. It is suggested that the functional motions needed for lypolytic activity of CALB is constructed from short-range movement of α5, accompanied by long-range movement of the domains connected to the lid region. © 2012 Ganjalikhany et al.
Azizi, A.,
Ranjbar, B.,
Khajeh, K.,
Ghodselahi, T.,
Hoornam, S.,
Mobasheri, H.,
Ganjalikhany, M.R. Publication Date: 2011
International Journal of Biological Macromolecules (01418130)49(4)pp. 652-656
The stability of enzymes with no reduction in their catalytic activity still remains a critical issue in industrial applications. Naturally occurring osmolytes are commonly used as protein stabilizers. In this study we have investigated the effects of sorbitol and trehalose on the structural stability and activity of Pseudomonas cepacia lipase (PCL), using UV-visible, circular dichroism (CD) and fluorescence spectroscopy. Surface plasmon resonance (SPR) technique was used to trace changes in the refractive index and dielectric constant of the environment. The results revealed that catalytic activity and intrinsic fluorescence intensity of PCL increased in the presence of both osmolytes. Far-UV CD spectra indicated that the protein has undergone some conformational changes upon interacting with these osmolytes. Increasing the concentration of sorbitol led to changes in the refractive index and consequently the dielectric constant of environment; whereas in the case of trehalose, such changes were not significant. Unfavorable interactions of trehalose with protein surface induced higher preferential exclusion from the enzyme-water interface than that of sorbitol. Results of this report could give further insights about the stabilization mechanism of osmolytes. © 2011 Elsevier B.V.
Tohidi moghadam, T.,
Ranjbar, B.,
Khajeh, K.,
Etezad, S.M.,
Khalifeh, K.,
Ganjalikhany, M.R. Publication Date: 2011
International Journal of Biological Macromolecules (01418130)49(4)pp. 629-636
Gold nanorods, with their unique morphology and optical properties have offered new prospects for biomedical and biosensing applications. Herein, the interaction between gold nanorods and a model protein has been monitored using spectroscopic techniques. The enzyme retains high fraction of its native structure with a slight increase in the helical content at the expense of β-turns. Kinetic investigations revealed notable increase of enzyme affinity for substrate without significant decrease in the Vmax. Emission spectra of tryptophan residues in the presence of chaotropic agent highlighted the maintenance of internal quenching due to the induced compactness. Comparison of the gold nanorod treated lysozyme with free enzyme revealed higher thermodynamic stability under denaturing condition. Results from this study encourage the possibility of utilizing gold nanorods as promising nanocarrier candidates for a new generation of drug delivery applications. © 2011 Elsevier B.V.
Publication Date: 2010
Journal of Molecular Catalysis - B Enzymatic (13811177)62(2)pp. 127-132
Firefly luciferase is widely used in many analytical techniques. However, the enzyme is unstable, so that its relative inactivation results in low sensitivity of those techniques. In this study, we have investigated the effects of MgSO4 and trehalose on the structural stability and function of luciferase from Photinus pyralis using circular dichroism (CD), conventional and stopped-flow fluorescence spectroscopy and bioluminescence assay. The secondary structural content, compactness and its melting temperature are also studied, which showed that the stability of luciferase increased in the presence of additives. Measurements of refolding rate constants under conditions that favor folding, show that MgSO4 accelerates the folding of enzyme, on the contrary, refolding rate constant decreases in the presence of trehalose which can be attributed to its high viscosity. Finally, combined with remaining activity assay we concluded that magnesium sulfate and trehalose can be used for short- and long-term stabilization, respectively. © 2009 Elsevier B.V. All rights reserved.
