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  1. Article: Immunomodulatory Peptides as Vaccine Adjuvants and Antimicrobial Agents.

    Hemmati, Shiva / Saeidikia, Zahra / Seradj, Hassan / Mohagheghzadeh, Abdolali

    Pharmaceuticals (Basel, Switzerland)

    2024  Volume 17, Issue 2

    Abstract: The underdevelopment of adjuvant discovery and diversity, compared to core vaccine technology, is evident. On the other hand, antibiotic resistance is on the list of the top ten threats to global health. Immunomodulatory peptides that target a pathogen ... ...

    Abstract The underdevelopment of adjuvant discovery and diversity, compared to core vaccine technology, is evident. On the other hand, antibiotic resistance is on the list of the top ten threats to global health. Immunomodulatory peptides that target a pathogen and modulate the immune system simultaneously are promising for the development of preventive and therapeutic molecules. Since investigating innate immunity in insects has led to prominent achievements in human immunology, such as toll-like receptor (TLR) discovery, we used the capacity of the immunomodulatory peptides of arthropods with concomitant antimicrobial or antitumor activity. An SVM-based machine learning classifier identified short immunomodulatory sequences encrypted in 643 antimicrobial peptides from 55 foe-to-friend arthropods. The critical features involved in efficacy and safety were calculated. Finally, 76 safe immunomodulators were identified. Then, molecular docking and simulation studies defined the target of the most optimal peptide ligands among all human cell-surface TLRs. SPalf2-453 from a crab is a cell-penetrating immunoadjuvant with antiviral properties. The peptide interacts with the TLR1/2 heterodimer. SBsib-711 from a blackfly is a TLR4/MD2 ligand used as a cancer vaccine immunoadjuvant. In addition, SBsib-711 binds CD47 and PD-L1 on tumor cells, which is applicable in cancer immunotherapy as a checkpoint inhibitor. MRh4-679 from a shrimp is a broad-spectrum or universal immunoadjuvant with a putative Th1/Th2-balanced response. We also implemented a pathway enrichment analysis to define fingerprints or immunological signatures for further in vitro and in vivo immunogenicity and reactogenicity measurements. Conclusively, combinatorial machine learning, molecular docking, and simulation studies, as well as systems biology, open a new opportunity for the discovery and development of multifunctional prophylactic and therapeutic lead peptides.
    Language English
    Publishing date 2024-02-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17020201
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Polypharmacological Cell-Penetrating Peptides from Venomous Marine Animals Based on Immunomodulating, Antimicrobial, and Anticancer Properties.

    Hemmati, Shiva / Rasekhi Kazerooni, Haniyeh

    Marine drugs

    2022  Volume 20, Issue 12

    Abstract: Complex pathological diseases, such as cancer, infection, and Alzheimer's, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into ... ...

    Abstract Complex pathological diseases, such as cancer, infection, and Alzheimer's, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into druggable targets. In this study, 82 marine venomous animal species were retrieved, and 3505 cryptic cell-penetrating peptides (CPPs) were identified in their toxins. A total of 279 safe peptides were further analyzed for antimicrobial, anticancer, and immunomodulatory characteristics. Protease-resistant CPPs with endosomal-escape ability in
    Language English
    Publishing date 2022-12-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2175190-0
    ISSN 1660-3397 ; 1660-3397
    ISSN (online) 1660-3397
    ISSN 1660-3397
    DOI 10.3390/md20120763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Hypericum perforatum

    Mohagheghzadeh, Ala / Badr, Parmis / Mohagheghzadeh, Abdolali / Hemmati, Shiva

    Pharmaceuticals (Basel, Switzerland)

    2023  Volume 16, Issue 6

    Abstract: Any defects in bile formation, secretion, or flow may give rise to cholestasis, liver fibrosis, cirrhosis, and hepatocellular carcinoma. As the pathogenesis of hepatic disorders is multifactorial, targeting parallel pathways potentially increases the ... ...

    Abstract Any defects in bile formation, secretion, or flow may give rise to cholestasis, liver fibrosis, cirrhosis, and hepatocellular carcinoma. As the pathogenesis of hepatic disorders is multifactorial, targeting parallel pathways potentially increases the outcome of therapy.
    Language English
    Publishing date 2023-06-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph16060887
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Viral Prefusion Targeting Using Entry Inhibitor Peptides: The Case of SARS-CoV-2 and Influenza A virus.

    Behzadipour, Yasaman / Hemmati, Shiva

    International journal of peptide research and therapeutics

    2022  Volume 28, Issue 1, Page(s) 42

    Abstract: In this study, peptide entry inhibitors against the fusion processes of severe acute respiratory syndrome coronavirus-2 (SCV2) and influenza A virus (IAV) were designed and evaluated. Fusion inhibitor peptides targeting the conformational shift of the ... ...

    Abstract In this study, peptide entry inhibitors against the fusion processes of severe acute respiratory syndrome coronavirus-2 (SCV2) and influenza A virus (IAV) were designed and evaluated. Fusion inhibitor peptides targeting the conformational shift of the viral fusion protein were designed based on the relatively conserved sequence of HR2 from SCV2 spike protein and the conserved fusion peptide from hemagglutinin (HA) of IAV. Helical HR2 peptides bind more efficiently to HR1 trimer, while helical amphipathic anti-IAV peptides have higher cell penetration and endosomal uptake. The initial sequences were mutated by increasing the amphipathicity, using helix favoring residues, and residues likely to form salt- and disulfide-bridges. After docking against their targets, all anti-SCV2 designed peptides bonded with the HR1 3-helical bundle's hydrophobic crevice, while AntiSCV2P1, AntiSCV2P3, AntiSCV2P7, and AntiSCV2P8 expected to form coiled coils with at least one of the HR1 strands. Four of the designed anti-IAV peptides were cell-penetrating (AntiIAVP2, AntiIAVP3, AntiIAVP4, AntiIAVP7). All of them interacted with the fusion peptide of HA and some of the residues in the conserved hydrophobic pocket of HA2 in H1N1, H3N1, and H5N1 subtypes of IAV. AntiIAVP3 and AntiIAVP4 peptides had the best binding to HA2 conserved hydrophobic pocket, while, AntiIAVP2 and AntiIAVP6 showed the best binding to the fusion peptide region. According to analyses for in-vivo administration, AntiSCV2P1, AntiSCV2P7, AntiIAVP2, and AntiIAVP7 were the best candidates. AntiSCV2 and AntiIAV peptides were also conjugated using an in vivo cleavable linker sensitive to TMPRSS2 applicable as a single therapeutic in coinfections or uncertain diagnosis.
    Supplementary information: The online version contains supplementary material available at 10.1007/s10989-021-10357-y.
    Language English
    Publishing date 2022-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2192632-3
    ISSN 1573-3904 ; 1573-3149
    ISSN (online) 1573-3904
    ISSN 1573-3149
    DOI 10.1007/s10989-021-10357-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Polypharmacological Cell-Penetrating Peptides from Venomous Marine Animals Based on Immunomodulating, Antimicrobial, and Anticancer Properties

    Hemmati, Shiva / Rasekhi Kazerooni, Haniyeh

    Mar Drugs. 2022 Dec. 04, v. 20, no. 12

    2022  

    Abstract: Complex pathological diseases, such as cancer, infection, and Alzheimer’s, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into ... ...

    Abstract Complex pathological diseases, such as cancer, infection, and Alzheimer’s, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into druggable targets. In this study, 82 marine venomous animal species were retrieved, and 3505 cryptic cell-penetrating peptides (CPPs) were identified in their toxins. A total of 279 safe peptides were further analyzed for antimicrobial, anticancer, and immunomodulatory characteristics. Protease-resistant CPPs with endosomal-escape ability in Hydrophis hardwickii, nuclear-localizing peptides in Scorpaena plumieri, and mitochondrial-targeting peptides from Synanceia horrida were suitable for compartmental drug delivery. A broad-spectrum S. horrida-derived antimicrobial peptide with a high binding-affinity to bacterial membranes was an antigen-presenting cell (APC) stimulator that primes cytokine release and naïve T-cell maturation simultaneously. While antibiofilm and wound-healing peptides were detected in Synanceia verrucosa, APC epitopes as universal adjuvants for antiviral vaccination were in Pterois volitans and Conus monile. Conus pennaceus-derived anticancer peptides showed antiangiogenic and IL-2-inducing properties with moderate BBB-permeation and were defined to be a tumor-homing peptide (THP) with the ability to inhibit programmed death ligand-1 (PDL-1). Isoforms of RGD-containing peptides with innate antiangiogenic characteristics were in Conus tessulatus for tumor targeting. Inhibitors of neuropilin-1 in C. pennaceus are proposed for imaging probes or therapeutic delivery. A Conus betulinus cryptic peptide, with BBB-permeation, mitochondrial-targeting, and antioxidant capacity, was a stimulator of anti-inflammatory cytokines and non-inducer of proinflammation proposed for Alzheimer’s. Conclusively, we have considered the dynamic interaction of cells, their microenvironment, and proportional-orchestrating-host- immune pathways by multi-target-directed CPPs resembling single-molecule polypharmacology. This strategy might fill the therapeutic gap in complex resistant disorders and increase the candidates’ clinical-translation chance.
    Keywords Conus ; Pterois volitans ; Scorpaena plumieri ; Synanceia horrida ; Synanceia verrucosa ; T-lymphocytes ; animals ; antigen-presenting cells ; antimicrobial peptides ; antioxidant activity ; artificial intelligence ; cytokines ; death ; drugs ; epitopes ; neoplasms ; vaccination
    Language English
    Dates of publication 2022-1204
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2175190-0
    ISSN 1660-3397
    ISSN 1660-3397
    DOI 10.3390/md20120763
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Hypericum perforatum L. and the Underlying Molecular Mechanisms for Its Choleretic, Cholagogue, and Regenerative Properties

    Ala Mohagheghzadeh / Parmis Badr / Abdolali Mohagheghzadeh / Shiva Hemmati

    Pharmaceuticals, Vol 16, Iss 887, p

    2023  Volume 887

    Abstract: Any defects in bile formation, secretion, or flow may give rise to cholestasis, liver fibrosis, cirrhosis, and hepatocellular carcinoma. As the pathogenesis of hepatic disorders is multifactorial, targeting parallel pathways potentially increases the ... ...

    Abstract Any defects in bile formation, secretion, or flow may give rise to cholestasis, liver fibrosis, cirrhosis, and hepatocellular carcinoma. As the pathogenesis of hepatic disorders is multifactorial, targeting parallel pathways potentially increases the outcome of therapy. Hypericum perforatum has been famed for its anti-depressive effects. However, according to traditional Persian medicine, it helps with jaundice and acts as a choleretic medication. Here, we will discuss the underlying molecular mechanisms of Hypericum for its use in hepatobiliary disorders. Differentially expressed genes retrieved from microarray data analysis upon treatment with safe doses of Hypericum extract and intersection with the genes involved in cholestasis are identified. Target genes are located mainly at the endomembrane system with integrin-binding ability. Activation of α5β1 integrins, as osmo-sensors in the liver, activates a non-receptor tyrosine kinase, c-SRC, which leads to the insertion of bile acid transporters into the canalicular membrane to trigger choleresis. Hypericum upregulates CDK6 that controls cell proliferation, compensating for the bile acid damage to hepatocytes. It induces ICAM1 to stimulate liver regeneration and regulates nischarin, a hepatoprotective receptor. The extract targets the expression of conserved oligomeric Golgi (COG) and facilitates the movement of bile acids toward the canalicular membrane via Golgi-derived vesicles. In addition, Hypericum induces SCP2, an intracellular cholesterol transporter, to maintain cholesterol homeostasis. We have also provided a comprehensive view of the target genes affected by Hypericum ’s main metabolites, such as hypericin, hyperforin, quercitrin, isoquercitrin, quercetin, kaempferol, rutin, and p -coumaric acid to enlighten a new scope in the management of chronic liver disorders. Altogether, standard trials using Hypericum as a neo-adjuvant or second-line therapy in ursodeoxycholic-acid-non-responder patients define the future trajectories of cholestasis treatment ...
    Keywords bile acid ; bioactive compounds ; cholesterol ; p -coumaric acid ; hypericin ; hyperforin ; Medicine ; R ; Pharmacy and materia medica ; RS1-441
    Subject code 616
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Characterization of a Stable Form of Carboxypeptidase G2 (Glucarpidase), a Potential Biobetter Variant, From Acinetobacter sp. 263903-1.

    Sadeghian, Issa / Hemmati, Shiva

    Molecular biotechnology

    2021  Volume 63, Issue 12, Page(s) 1155–1168

    Abstract: Carboxypeptidase G2 (CPG2) is a bacterial enzyme widely used to detoxify methotrexate (MTX) and in enzyme/prodrug therapy for cancer treatment. However, several drawbacks, such as instability, have limited its efficiency. Herein, we have evaluated the ... ...

    Abstract Carboxypeptidase G2 (CPG2) is a bacterial enzyme widely used to detoxify methotrexate (MTX) and in enzyme/prodrug therapy for cancer treatment. However, several drawbacks, such as instability, have limited its efficiency. Herein, we have evaluated the properties of a putative CPG2 from Acinetobacter sp. 263903-1 (AcCPG2). AcCPG2 is compared with a CPG2 derived from Pseudomonas sp. strain RS-16 (PsCPG2), available as an FDA-approved medication called glucarpidase. After modeling AcCPG2 using the I-TASSER program, the refined model was validated by PROCHECK, VERIFY 3D and according to the Z score of the model. Using computational analyses, AcCPG2 displayed higher thermodynamic stability and a lower aggregation propensity than PsCPG2. AcCPG2 showed an optimum pH of 7.5 against MTX and was stable over a pH range of 5-10. AcCPG2 exhibited optimum activity at 50 °C and higher thermal stability at a temperature range of 20-70 °C compared to PsCPG2. The K
    MeSH term(s) Acinetobacter/enzymology ; Amino Acid Sequence ; Enzyme Stability ; Folic Acid/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Methotrexate/metabolism ; Models, Molecular ; Pseudomonas/enzymology ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Sequence Alignment ; Temperature ; Thermodynamics ; gamma-Glutamyl Hydrolase/chemistry ; gamma-Glutamyl Hydrolase/genetics ; gamma-Glutamyl Hydrolase/isolation & purification ; gamma-Glutamyl Hydrolase/metabolism
    Chemical Substances Recombinant Proteins ; Folic Acid (935E97BOY8) ; gamma-Glutamyl Hydrolase (EC 3.4.19.9) ; Methotrexate (YL5FZ2Y5U1)
    Language English
    Publishing date 2021-07-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1193057-3
    ISSN 1559-0305 ; 1073-6085
    ISSN (online) 1559-0305
    ISSN 1073-6085
    DOI 10.1007/s12033-021-00370-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Glucarpidase (carboxypeptidase G2): Biotechnological production, clinical application as a methotrexate antidote, and placement in targeted cancer therapy.

    Moradbeygi, Fatemeh / Ghasemi, Younes / Farmani, Ahmad Reza / Hemmati, Shiva

    Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    2023  Volume 166, Page(s) 115292

    Abstract: Patients receiving high-dose methotrexate (HDMTX) for malignancies are exposed to diverse complications, including nephrotoxicity, hepatotoxicity, mucositis, myelotoxicity, neurological symptoms, and death. Glucarpidase is a recombinant carboxypeptidase ... ...

    Abstract Patients receiving high-dose methotrexate (HDMTX) for malignancies are exposed to diverse complications, including nephrotoxicity, hepatotoxicity, mucositis, myelotoxicity, neurological symptoms, and death. Glucarpidase is a recombinant carboxypeptidase G2 (CPG2) that converts MTX into nontoxic metabolites. In this study, the role of vector type, gene optimization, orientation, and host on the expression of CPG2 is investigated. The effectiveness of various therapeutic regimens containing glucarpidase is classified and perspectives on the dose adjustment based on precision medicine are provided. Conjugation with cell-penetrating peptides, human serum albumin, and polymers such as PEG and dextran for delivery, higher stability, and production of the biobetter variants of CPG2 is highlighted. Conjugation of CPG2 to F(ab՜)
    MeSH term(s) Humans ; Methotrexate/therapeutic use ; gamma-Glutamyl Hydrolase/genetics ; gamma-Glutamyl Hydrolase/therapeutic use ; Prodrugs ; Antidotes ; Neoplasms ; Antibodies/therapeutic use ; Polymers/therapeutic use
    Chemical Substances Methotrexate (YL5FZ2Y5U1) ; glucarpidase (2GFP9BJD79) ; gamma-Glutamyl Hydrolase (EC 3.4.19.9) ; Prodrugs ; Antidotes ; Antibodies ; Polymers
    Language English
    Publishing date 2023-08-12
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 392415-4
    ISSN 1950-6007 ; 0753-3322 ; 0300-0893
    ISSN (online) 1950-6007
    ISSN 0753-3322 ; 0300-0893
    DOI 10.1016/j.biopha.2023.115292
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Humanizing plant-derived snakins and their encrypted antimicrobial peptides.

    Ghanbarzadeh, Zohreh / Hemmati, Shiva / Mohagheghzadeh, Abdolali

    Biochimie

    2022  Volume 199, Page(s) 92–111

    Abstract: Due to safety restrictions, plant-derived antimicrobial peptides (AMPs) need optimization to be consumed beyond preservatives. Herein, 175 GASA-domain-containing snakins were analyzed. Factors including charge, hydrophobicity, helicity, hydrophobic ... ...

    Abstract Due to safety restrictions, plant-derived antimicrobial peptides (AMPs) need optimization to be consumed beyond preservatives. Herein, 175 GASA-domain-containing snakins were analyzed. Factors including charge, hydrophobicity, helicity, hydrophobic moment (μH), folding enthalpy, folding heat capacity, folding free energy, therapeutic index, allergenicity, and bitterness were considered. The most optimal snakins for oral consumption as preservatives were from Cajanus cajan, Cucumis melo, Durio zibethinus, Glycine soja, Herrania umbratica, and Ziziphus jujuba. Virtual digestion of snakins predicted ACE1 and DPPIV inhibitory as dominant effects upon oral use with antihypertensive and antidiabetic properties. To be applied as a therapeutic in parenteral administration, snakins were browsed for short 20-mer encrypted fragments that were non-toxic or with eliminated toxicity using directed mutagenesis yet retaining the AMP property. The most promising 20-mer AMPs were Mr-SNK2-1a in Morella rubra with BBB permeation, Na-SNK2-2a(C
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Antimicrobial Cationic Peptides/chemistry ; Antimicrobial Cationic Peptides/pharmacology ; Antimicrobial Peptides ; Gram-Negative Bacteria ; Hydrophobic and Hydrophilic Interactions ; Microbial Sensitivity Tests ; Plants
    Chemical Substances Anti-Bacterial Agents ; Antimicrobial Cationic Peptides ; Antimicrobial Peptides
    Language English
    Publishing date 2022-04-26
    Publishing country France
    Document type Journal Article
    ZDB-ID 120345-9
    ISSN 1638-6183 ; 0300-9084
    ISSN (online) 1638-6183
    ISSN 0300-9084
    DOI 10.1016/j.biochi.2022.04.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: A comprehensive in silico characterization of bacterial signal peptides for the excretory production of

    Owji, Hajar / Hemmati, Shiva

    3 Biotech

    2018  Volume 8, Issue 12, Page(s) 488

    Abstract: ... Anabaena ... ...

    Abstract Anabaena variabilis
    Language English
    Publishing date 2018-11-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-018-1517-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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