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1.
Nat Commun ; 15(1): 3684, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38693181

ABSTRACT

The metal-nucleic acid nanocomposites, first termed metal-nucleic acid frameworks (MNFs) in this work, show extraordinary potential as functional nanomaterials. However, thus far, realized MNFs face limitations including harsh synthesis conditions, instability, and non-targeting. Herein, we discover that longer oligonucleotides can enhance the synthesis efficiency and stability of MNFs by increasing oligonucleotide folding and entanglement probabilities during the reaction. Besides, longer oligonucleotides provide upgraded metal ions binding conditions, facilitating MNFs to load macromolecular protein drugs at room temperature. Furthermore, longer oligonucleotides facilitate functional expansion of nucleotide sequences, enabling disease-targeted MNFs. As a proof-of-concept, we build an interferon regulatory factor-1(IRF-1) loaded Ca2+/(aptamer-deoxyribozyme) MNF to target regulate glucose transporter (GLUT-1) expression in human epidermal growth factor receptor-2 (HER-2) positive gastric cancer cells. This MNF nanodevice disrupts GSH/ROS homeostasis, suppresses DNA repair, and augments ROS-mediated DNA damage therapy, with tumor inhibition rate up to 90%. Our work signifies a significant advancement towards an era of universal MNF application.


Subject(s)
Aptamers, Nucleotide , DNA, Catalytic , Stomach Neoplasms , Stomach Neoplasms/metabolism , Stomach Neoplasms/drug therapy , Stomach Neoplasms/genetics , Humans , Aptamers, Nucleotide/chemistry , Aptamers, Nucleotide/metabolism , Cell Line, Tumor , DNA, Catalytic/metabolism , DNA, Catalytic/chemistry , Animals , Receptor, ErbB-2/metabolism , Interferon Regulatory Factor-1/metabolism , Interferon Regulatory Factor-1/genetics , Reactive Oxygen Species/metabolism , Mice , DNA Repair , DNA Damage , Glutathione/metabolism , Glutathione/chemistry , Nucleic Acids/metabolism , Nucleic Acids/chemistry
2.
Pharmaceutics ; 16(2)2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38399330

ABSTRACT

Pinosylvin monomethyl ether (PsMME) is a natural compound known for its valuable bioactive properties, including antioxidant and anti-inflammatory effects. However, PsMME's susceptibility to photodegradation upon exposure to ultraviolet (UV) radiation poses a significant limitation to its applications in the pharmaceutical field. This study, for the first time, introduces a strategy to enhance the photostability of PsMME by employing various nanoformulations. We utilized mesoporous silica nanoparticles (MSNs) coated with polydopamine via a poly(ethylene imine) layer (PDA-PEI-MSNs), thermally carbonized porous silicon nanoparticles (TCPSi), and pure mesoporous polydopamine nanoparticles (MPDA). All these nanocarriers exhibit unique characteristics, including the potential for shielding the drug from UV light, which makes them promising for enhancing the photostability of loaded drugs. Here, these three nanoparticles were synthesized and their morphological and physicochemical properties, including size and ζ-potential, were characterized. They were subsequently loaded with PsMME, and the release profiles and kinetics of all three nanoformulations were determined. To assess their photoprotection ability, we employed gas chromatography with a flame ionization detector (GC-FID) and gas chromatography-mass spectrometry (GC-MS) to assess the recovery percentage of loaded PsMME before and after UV exposure for each nanoformulation. Our findings reveal that MPDA exhibits the highest protection ability, with a remarkable 90% protection against UV light on average. This positions MPDA as an ideal carrier for PsMME, and by extension, potentially for other photolabile drugs as well. As a final confirmation of its suitability as a drug nanocarrier, we conducted cytotoxicity evaluations of PsMME-loaded MPDA, demonstrating dose-dependent drug toxicity for this formulation.

3.
Front Immunol ; 14: 1253805, 2023.
Article in English | MEDLINE | ID: mdl-37809071

ABSTRACT

Introduction: Stilbenoid compounds have been described to have anti-inflammatory properties in animal models in vivo, and have been shown to inhibit Ca2+-influx through the transient receptor potential ankyrin 1 (TrpA1). Methods: To study how stilbenoid compounds affect inflammatory signaling in vivo, we have utilized the fruit fly, Drosophila melanogaster, as a model system. To induce intestinal inflammation in the fly, we have fed flies with the intestinal irritant dextran sodium sulphate (DSS). Results: We found that DSS induces severe changes in the bacteriome of the Drosophila intestine, and that this dysbiosis causes activation of the NF-κB transcription factor Relish. We have taken advantage of the DSS-model to study the anti-inflammatory properties of the stilbenoid compounds pinosylvin (PS) and pinosylvin monomethyl ether (PSMME). With the help of in vivo approaches, we have identified PS and PSMME to be transient receptor ankyrin 1 (TrpA1)-dependent antagonists of NF-κB-mediated intestinal immune responses in Drosophila. We have also computationally predicted the putative antagonist binding sites of these compounds at Drosophila TrpA1. Discussion: Taken together, we show that the stilbenoids PS and PSMME have anti-inflammatory properties in vivo in the intestine and can be used to alleviate chemically induced intestinal inflammation in Drosophila.


Subject(s)
NF-kappa B , Stilbenes , Animals , NF-kappa B/metabolism , Drosophila/metabolism , Drosophila melanogaster/metabolism , Ankyrins , Intestines , Stilbenes/pharmacology , Anti-Inflammatory Agents/pharmacology , Inflammation/chemically induced , Inflammation/drug therapy
4.
Microbiologyopen ; 12(4): e1371, 2023 08.
Article in English | MEDLINE | ID: mdl-37642487

ABSTRACT

Staphylococcus aureus produces numerous virulence factors that manipulate the immune system, helping the bacteria avoid phagocytosis. In this study, we are investigating three immune evasion molecules called the staphylococcal superantigen-like proteins 1, 5, and 10 (SSL1, SSL5, and SSL10). All three SSLs inhibit vital host immune processes and contribute to S. aureus immune evasion. This study aimed to identify single-chain variable fragment (scFvs) antibodies from synthetic antibody phage libraries, which can recognize either of the three SSLs and could block the interaction between the SSLs and their respective human targets. The antibodies were isolated after three rounds of panning against SSL1, SSL5, and SSL10, and their ability to bind to the SSLs was studied using a time-resolved fluorescence-based immunoassay. We successfully obtained altogether 44 unique clones displaying binding activity to either SSL1, SSL5, or SSL10. The capability of the SSL-recognizing scFvs to inhibit the SSLs' function was tested in an MMP9 enzymatic activity assay, a P-selectin glycoprotein ligand 1 competitive binding assay, and an IgG1-mediated phagocytosis assay. We could show that one scFv was able to inhibit SSL1 and maintain MMP9 activity in a concentration-dependent manner. Finally, the structure of this inhibiting scFv was modeled and used to create putative scFv-SSL1-complex models by protein-protein docking. The complex models were subjected to a 100-ns molecular dynamics simulation to assess the possible binding mode of the antibody.


Subject(s)
Bacteriophages , Immunoglobulin Fragments , Humans , Matrix Metalloproteinase 9 , Staphylococcus aureus , Staphylococcus
5.
Heliyon ; 9(3): e13881, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36895339

ABSTRACT

Purpose: This multidisciplinary study seeks to determine the nature and structure of the informal markets for counterfeit medicines, the co-factors underpinning the demand and supply of counterfeit Western allopathic medicines (WAM), traditional and alternative medicines (TAM), and potential institutional responses in Ghana. Method: This study is based on an interpretive research approach. It deploys a synthesis of a longitudinal ethnographic fieldwork, with multiple repeated visits for observations, analysis of documents, interviews, and focus group discussions. Findings: The study identifies five major inter-related discoveries that point to the need for urgent institutional responses: Approaches to global health governance pay little attention to the complex economic gamut of TAM, including herbal medicines. The rise in necessity entrepreneurship and the availability of easy-to-use packaging and advertising technologies have made TAM a major competitor of WAM. The informal markets for WAM and TAM are structured in ways that allow them to evade formalized interventions and regulations. Standardization allows destructive entrepreneurs to derive advantage from economies of scale and reduce production costs, allowing the sector to flourish with little economic risk while inflicting violence on consumers. Personalization and co-creation of medicine with consumers has the added psychological effect of increasing consumer confidence. This, however, enlists consumers in the market violence against themselves. Social implications: Destructive entrepreneurship, whether inadvertent or criminal creates benefits for groups and individuals but negatively affects public health on various levels. Originality: Mitigation and interventions that ignore the informal TAM market of destructive entrepreneurship only answer a part of the big question of how to guarantee patient/consumer safety from the threats of all counterfeits.

6.
Elife ; 112022 12 07.
Article in English | MEDLINE | ID: mdl-36475542

ABSTRACT

Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression of this protein and development of drug resistance. We thus pursued an alternative strategy that led us to the discovery of TS-dimer destabilizers. These compounds bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. A structural, spectroscopic, and kinetic investigation has provided evidence and quantitative information on the effects of the interaction of these small molecules with hTS. Focusing on the best among them, E7, we have shown that it inhibits hTS in cancer cells and accelerates its proteasomal degradation, thus causing a decrease in the enzyme intracellular level. E7 also showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.


Subject(s)
Ovarian Neoplasms , Thymidylate Synthase , Female , Animals , Mice , Humans , Binding Sites , Thymidylate Synthase/chemistry , Thymidylate Synthase/metabolism , Fluorouracil/pharmacology , Ovarian Neoplasms/drug therapy , Enzyme Inhibitors/pharmacology
7.
Biomedicines ; 10(11)2022 Nov 01.
Article in English | MEDLINE | ID: mdl-36359299

ABSTRACT

The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.

8.
J Comput Aided Mol Des ; 36(7): 507-520, 2022 07.
Article in English | MEDLINE | ID: mdl-35809194

ABSTRACT

Enterococcus faecalis, a gram-positive bacterium, is among the most common nosocomial pathogens due to its limited susceptibility to antibiotics and its reservoir of the genes coding for virulence factors. Bacterial enzymes such as kinases and phosphorylases play important roles in diverse functions of a bacterial cell and, thus, are potential antibacterial drug targets. In Gram-positive bacteria, HPr Kinase/Phosphorylase (HPrK/P), a bifunctional enzyme is involved in the regulation of carbon catabolite repression by phosphorylating/dephosphorylating the histidine-containing phosphocarrier protein (HPr) at Ser46 residue. Deficiencies in HPrK/P function leads to severe defects in bacterial growth. This study aimed at identifying novel inhibitors of E. faecalis HPrK/P from a commercial compound library using structure-based virtual screening. The hit molecules were purchased and their effect on enzyme activity and growth of resistant E. faecalis was evaluated in vitro. Furthermore, docking and molecular dynamics simulations were performed to study the interactions of the hit compounds with HPrK/P. Among the identified hit molecules, two compounds inhibited the phosphorylation of HPr as well as significantly reduced the growth of resistant E. faecalis in vitro. These identified potential HPrK/P inhibitors open new research avenues towards the development of novel antimicrobials against resistant Gram-positive bacteria.


Subject(s)
Anti-Infective Agents , Bacterial Proteins , Enterococcus faecalis , Anti-Infective Agents/pharmacology , Bacterial Proteins/antagonists & inhibitors , Enterococcus faecalis/drug effects , Enterococcus faecalis/enzymology , Phosphorylases/antagonists & inhibitors , Phosphorylation , Protein Serine-Threonine Kinases/antagonists & inhibitors
9.
Eur J Pharm Sci ; 175: 106220, 2022 Aug 01.
Article in English | MEDLINE | ID: mdl-35618201

ABSTRACT

With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC50 < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.


Subject(s)
Zika Virus Infection , Zika Virus , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Humans , Peptide Hydrolases , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins , Zika Virus/chemistry , Zika Virus/metabolism , Zika Virus Infection/drug therapy
10.
ChemMedChem ; 17(5): e202100714, 2022 03 04.
Article in English | MEDLINE | ID: mdl-34978160

ABSTRACT

Due to the ever-increasing antimicrobial resistance there is an urgent need to continuously design and develop novel antimicrobial agents. Inspired by the broad antibacterial activities of various heterocyclic compounds such as 2-quinolone derivatives, we designed and synthesized new methyl-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alaninate-1,2,3-triazole derivatives via 1,3-dipolar cycloaddition reaction of 1-propargyl-2-quinolone-L-alaninate with appropriate azide groups. The synthesized compounds were obtained in good yield ranging from 75 to 80 %. The chemical structures of these novel hybrid molecules were determined by spectroscopic methods and the antimicrobial activity of the compounds was investigated against both bacterial and fungal strains. The tested compounds showed significant antimicrobial activity and weak to moderate antifungal activity. Despite the evident similarity of the quinolone moiety of our compounds with fluoroquinolones, our compounds do not function by inhibiting DNA gyrase. Computational characterization of the compounds shows that they have attractive physicochemical and pharmacokinetic properties and could serve as templates for developing potential antimicrobial agents for clinical use.


Subject(s)
Anti-Infective Agents , Quinolones , Anti-Bacterial Agents/chemistry , Anti-Infective Agents/pharmacology , Antifungal Agents/chemistry , Hydroxyquinolines , Microbial Sensitivity Tests , Molecular Structure , Quinolones/pharmacology , Structure-Activity Relationship , Triazoles/chemistry
12.
J Biomol Struct Dyn ; 39(13): 4936-4948, 2021 08.
Article in English | MEDLINE | ID: mdl-32579061

ABSTRACT

The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C-S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptide Hydrolases , Protease Inhibitors/pharmacology
13.
Eur J Pharm Sci ; 155: 105537, 2020 Dec 01.
Article in English | MEDLINE | ID: mdl-32890663

ABSTRACT

Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 µM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies.


Subject(s)
HIV Fusion Inhibitors , HIV Infections , HIV-1 , Binding Sites , CCR5 Receptor Antagonists/pharmacology , HIV Infections/drug therapy , Humans , Ligands , Receptors, CCR5
14.
Int J Biol Macromol ; 153: 399-411, 2020 Jun 15.
Article in English | MEDLINE | ID: mdl-32151723

ABSTRACT

(Chymo)trypsin-like serine fold proteases belong to the serine/cysteine proteases found in eukaryotes, prokaryotes, and viruses. Their catalytic activity is carried out using a triad of amino acids, a nucleophile, a base, and an acid. For this superfamily of proteases, we propose the existence of a universal 3D structure comprising 11 amino acids near the catalytic nucleophile and base - Nucleophile-Base Catalytic Zone (NBCZone). The comparison of NBCZones among 169 eukaryotic, prokaryotic, and viral (chymo)trypsin-like proteases suggested the existence of 15 distinct groups determined by the combination of amino acids located at two "key" structure-functional positions 54T and 55T near the catalytic base His57T. Most eukaryotic and prokaryotic proteases fell into two major groups, [ST]A and TN. Usually, proteases of [ST]A group contain a disulfide bond between cysteines Cys42T and Cys58T of the NBCZone. In contrast, viral proteases were distributed among seven groups, and lack this disulfide bond. Furthermore, only the [ST]A group of eukaryotic proteases contains glycine at position 43T, which is instrumental for activation of these enzymes. In contrast, due to the side chains of residues at position 43T prokaryotic and viral proteases do not have the ability to carry out the structural transition of the eukaryotic zymogen-zyme type.


Subject(s)
Models, Molecular , Serine Endopeptidases/chemistry , Amino Acids/chemistry , Amino Acids/genetics , Binding Sites , Protein Conformation , Serine Endopeptidases/genetics
15.
Eur J Pharmacol ; 873: 172962, 2020 Apr 15.
Article in English | MEDLINE | ID: mdl-32001220

ABSTRACT

Hops (Humulus lupulus L.), a major component of beer, contain potentially neuroactive compounds that made it useful in traditional medicine as a sleeping aid. The present study aims to investigate the individual components in hops acting as allosteric modulators in GABAA receptors and bring further insight into the mode of action behind the sedative properties of hops. GABA-potentiating effects were measured using [3H]ethynylbicycloorthobenzoate (EBOB) radioligand binding assay in native GABAA receptors. Flumazenil sensitivity of GABA-potentiating effects, [3H]Ro 15-4513, and [3H]flunitrazepam binding assays were used to examine the binding to the classical benzodiazepines site. Humulone (alpha acid) and 6-prenylnaringenin (prenylflavonoid) were the most potent compounds displaying a modulatory activity at low micromolar concentrations. Humulone and 6-prenylnaringenin potentiated GABA-induced displacement of [3H]EBOB binding in a concentration-dependent manner where the IC50 values for this potentiation in native GABAA receptors were 3.2 µM and 3.7 µM, respectively. Flumazenil had no significant effects on humulone- or 6-prenylnaringenin-induced displacement of [3H]EBOB binding. [3H]Ro 15-4513 and [3H]flunitrazepam displacements were only minor with humulone but surprisingly prominent with 6-prenylnaringenin despite its flumazenil-insensitive modulatory activity. Thus, we applied molecular docking methods to investigate putative binding sites and poses of 6-prenylnaringenin at the GABAA receptor α1ß2γ2 isoform. Radioligand binding and docking results suggest a dual mode of action by 6-prenylnaringenin on GABAA receptors where it may act as a positive allosteric modulator at α+ß- binding interface as well as a null modulator at the flumazenil-sensitive α+γ2- binding interface.


Subject(s)
Flavonoids/pharmacology , GABA Modulators/pharmacology , Humulus/chemistry , Receptors, GABA-A/drug effects , Animals , Azides/metabolism , Benzodiazepines/metabolism , Binding, Competitive/drug effects , Cyclohexenes/pharmacology , Dose-Response Relationship, Drug , Flumazenil/pharmacology , Flunitrazepam/metabolism , GABA Modulators/metabolism , Male , Molecular Docking Simulation , Plant Extracts/chemistry , Plant Extracts/pharmacology , Radioligand Assay , Rats , Rats, Sprague-Dawley , Receptors, GABA-A/metabolism , Terpenes/pharmacology
16.
Biomolecules ; 9(4)2019 03 28.
Article in English | MEDLINE | ID: mdl-30925835

ABSTRACT

Tumorigenesis in humans is a multistep progression that imitates genetic changes leading to cell transformation and malignancy. Oncogenic kinases play a central role in cancer progression, rendering them putative targets for the design of anti-cancer drugs. The presented work aims to identify the potential multi-target inhibitors of oncogenic receptor tyrosine kinases (RTKs) and serine/threonine kinases (STKs). For this, chemoinformatics and structure-based virtual screening approaches were combined with an in vitro validation of lead hits on both cancerous and non-cancerous cell lines. A total of 16 different kinase structures were screened against ~739,000 prefiltered compounds using diversity selection, after which the top hits were filtered for promising pharmacokinetic properties. This led to the identification of 12 and 9 compounds against RTKs and STKs, respectively. Molecular dynamics (MD) simulations were carried out to better comprehend the stability of the predicted hit kinase-compound complexes. Two top-ranked compounds against each kinase class were tested in vitro for cytotoxicity, with compound F34 showing the most promising inhibitory activity in HeLa, HepG2, and Vero cell lines with IC50 values of 145.46 µM, 175.48 µM, and 130.52 µM, respectively. Additional docking of F34 against various RTKs was carried out to support potential multi-target inhibition. Together with reliable MD simulations, these results suggest the promising potential of identified multi-target STK and RTK scaffolds for further kinase-specific anti-cancer drug development toward combinatorial therapies.


Subject(s)
Antineoplastic Agents/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Kinase Inhibitors/pharmacology , Protein Kinases/metabolism , Animals , Antineoplastic Agents/chemistry , Cell Proliferation/drug effects , Cell Survival/drug effects , Chlorocebus aethiops , Drug Evaluation, Preclinical , Drug Screening Assays, Antitumor , HeLa Cells , Hep G2 Cells , Humans , Molecular Structure , Protein Kinase Inhibitors/chemistry , Vero Cells
17.
Molecules ; 24(2)2019 Jan 17.
Article in English | MEDLINE | ID: mdl-30658387

ABSTRACT

This Special Issue contains thirteen articles that provide a vivid snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges [...].


Subject(s)
Drug Design , Models, Molecular , Drug Evaluation, Preclinical , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Receptors, G-Protein-Coupled/metabolism
18.
Virulence ; 9(1): 724-737, 2018 12 31.
Article in English | MEDLINE | ID: mdl-29473457

ABSTRACT

Coagulation, complement, and innate immunity are tightly interwoven and form an alliance that can be traced back to early eukaryotic evolution. Here we employed an ecoimmunological approach using Tissue Factor Pathway Inhibitor (TFPI)-1-derived peptides from the different classes of vertebrates (i.e. fish, reptile, bird, and mammals) and tested whether they can boost killing of various human bacterial pathogens in plasma. We found signs of species-specific conservation and diversification during evolution in these peptides that significantly impact their antibacterial activity. Though all peptides tested executed bactericidal activity in mammalian plasma (with the exception of rodents), no killing was observed in plasma from birds, reptiles, and fish, pointing to a crucial role for the classical pathway of the complement system. We also observed an interference of these peptides with the human intrinsic pathway of coagulation though, unlike complement activation, this mechanism appears not to be evolutionary conserved.


Subject(s)
Blood Coagulation , Complement System Proteins , Evolution, Molecular , Immunity, Innate , Lipoproteins/genetics , Vertebrates , Animals , Blood Bactericidal Activity , Humans
19.
Front Immunol ; 9: 3000, 2018.
Article in English | MEDLINE | ID: mdl-30619353

ABSTRACT

Human papillomavirus (HPV) induced cervical cancer is the second most common cause of death, after breast cancer, in females. Three prophylactic vaccines by Merck Sharp & Dohme (MSD) and GlaxoSmithKline (GSK) have been confirmed to prevent high-risk HPV strains but these vaccines have been shown to be effective only in girls who have not been exposed to HPV previously. The constitutively expressed HPV oncoproteins E6 and E7 are usually used as target antigens for HPV therapeutic vaccines. These early (E) proteins are involved, for example, in maintaining the malignant phenotype of the cells. In this study, we predicted antigenic peptides of HPV types 16 and 18, encoded by E6 and E7 genes, using an immunoinformatics approach. To further evaluate the immunogenic potential of the predicted peptides, we studied their ability to bind to class I major histocompatibility complex (MHC-I) molecules in a computational docking study that was supported by molecular dynamics (MD) simulations and estimation of the free energies of binding of the peptides at the MHC-I binding cleft. Some of the predicted peptides exhibited comparable binding free energies and/or pattern of binding to experimentally verified MHC-I-binding epitopes that we used as references in MD simulations. Such peptides with good predicted affinity may serve as candidate epitopes for the development of therapeutic HPV peptide vaccines.


Subject(s)
Antigens, Viral/immunology , Histocompatibility Antigens Class I/metabolism , Papillomavirus Infections/prevention & control , Papillomavirus Vaccines/immunology , Uterine Cervical Neoplasms/prevention & control , Antigens, Viral/chemistry , Antigens, Viral/metabolism , Computational Biology/methods , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/immunology , DNA-Binding Proteins/metabolism , Epitope Mapping/methods , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/immunology , Epitopes, B-Lymphocyte/metabolism , Epitopes, T-Lymphocyte/chemistry , Epitopes, T-Lymphocyte/immunology , Epitopes, T-Lymphocyte/metabolism , Female , Histocompatibility Antigens Class I/chemistry , Histocompatibility Antigens Class I/immunology , Human papillomavirus 16/immunology , Human papillomavirus 18/immunology , Humans , Molecular Dynamics Simulation , Oncogene Proteins, Viral/chemistry , Oncogene Proteins, Viral/immunology , Oncogene Proteins, Viral/metabolism , Papillomavirus E7 Proteins/chemistry , Papillomavirus E7 Proteins/immunology , Papillomavirus E7 Proteins/metabolism , Papillomavirus Infections/immunology , Papillomavirus Infections/virology , Papillomavirus Vaccines/chemistry , Repressor Proteins/chemistry , Repressor Proteins/immunology , Repressor Proteins/metabolism , Structural Homology, Protein , Uterine Cervical Neoplasms/immunology , Uterine Cervical Neoplasms/virology , Vaccines, Subunit/chemistry , Vaccines, Subunit/immunology
20.
Adv Healthc Mater ; 6(21)2017 Nov.
Article in English | MEDLINE | ID: mdl-28892296

ABSTRACT

Approaches to increase the efficiency in developing drugs and diagnostics tools, including new drug delivery and diagnostic technologies, are needed for improved diagnosis and treatment of major diseases and health problems such as cancer, inflammatory diseases, chronic wounds, and antibiotic resistance. Development within several areas of research ranging from computational sciences, material sciences, bioengineering to biomedical sciences and bioimaging is needed to realize innovative drug development and diagnostic (DDD) approaches. Here, an overview of recent progresses within key areas that can provide customizable solutions to improve processes and the approaches taken within DDD is provided. Due to the broadness of the area, unfortunately all relevant aspects such as pharmacokinetics of bioactive molecules and delivery systems cannot be covered. Tailored approaches within (i) bioinformatics and computer-aided drug design, (ii) nanotechnology, (iii) novel materials and technologies for drug delivery and diagnostic systems, and (iv) disease models to predict safety and efficacy of medicines under development are focused on. Current developments and challenges ahead are discussed. The broad scope reflects the multidisciplinary nature of the field of DDD and aims to highlight the convergence of biological, pharmaceutical, and medical disciplines needed to meet the societal challenges of the 21st century.


Subject(s)
Models, Biological , Computational Biology , Drug Delivery Systems , Drug Design , Humans , Molecular Docking Simulation , Nanomedicine , Nanotechnology , Neoplasms/diagnosis , Proteins/chemistry , Proteins/metabolism , Quantitative Structure-Activity Relationship
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