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Durdagi, S.

Publications and source records attributed to Durdagi, S..

18 recordsLinked to original sources

Targeting Ubiquitin-Specific Protease 7 (USP7): A Pharmacophore-Guided Drug Repurposing and Physics-Based Molecular Simulations Study

Ubiquitin-Specific Protease 7 (USP7) has emerged as a critical therapeutic target in cancer due to its regulatory roles of tumor suppressors, oncoproteins, and epigenetic modifiers. In this study, we present a comprehensive drug repurposing strategy to identify potential USP7 inhibitors from a curated library of 6,654 FDA-approved and investigational small molecules. Using structure-based pharmacophore models derived from USP7-inhibitor crystal structures, we conducted virtual screening to select candidates with favorable pharmacophoric alignment. The top 100 hits were subjected to short 10 ns molecular dynamics (MD) simulations and MM/GBSA binding energy calculations, narrowing down to 36 promising ligands. These were further evaluated through longer (100 ns) MD simulations, binding energy refinement, ligand clustering based on molecular fingerprints, and cancer-specific activity predictions using a binary QSAR model. Twelve compounds demonstrated favorable binding profiles, structural diversity, and high predicted anticancer activity, such as xantifibrate, etofylline clofibrate, and carafiban. This multi-tiered hybrid virtual screening pipeline highlights the potential of drug repurposing for the rapid identification of USP7 inhibitors, offering a cost-effective path toward novel anticancer therapeutics.

bioinformatics↗

Development of Machine Learning-based QSAR Models for the Designing of Novel Anti-cancer Therapeutics Against Malignant Glioma

In the early drug design and discovery phase, virtual screening of diverse small molecule libraries is crucial. Machine learning (ML)-based algorithms have made this process easier and faster. In this study, we have applied ML-based algorithms to generate the QSAR models for virtual screening. The aim of study is to design the statistically significant models for the screening of small molecule libraries to identify the novel hits against IDH1 mutant receptor crucial for glioblastoma multiforme (GBM). To construct the models, we have used both cell lines data (U87 and U251 cells) and the inhibitors of IDH1 mutant reported in the literature and used the pIC50 activity data to train our models. Furthermore, ligand-based 3D QSAR models and structure-based pharmacophore models were also constructed and validated.

bioinformatics↗

Employing Steered MD Simulations for Effective Virtual Screening: Active Pharmacophore Search by Dynamic Corrections to target MKK3-MYC Interactions

The intricate relationship between mitogen-activated protein kinase 3 (MKK3) and MYC proto-oncogene protein (MYC) activation holds deep implications for the progression of cancer, particularly in the context of triple negative breast cancer (TNBC). Despite significant progress, the challenge of discovering effective MYC-targeted drugs persists, demanding innovative approaches to control MYC-dependent malignancies. A promising avenue in this pursuit involves disrupting the protein-protein interactions (PPIs) between MKK3 and MYC. The significance of this interaction is emphasized by the activation of MYC by MKK3 in diverse cell types, presenting a novel perspective for therapeutic interventions in MYC-driven pathways. In the current study, a novel in silico strategy to screen small molecule libraries that target the MKK3-MYC interaction was conducted. Dynamic structure-based pharmacophore models were developed and utilized for screening the small molecule libraries, enabling the identification of compounds exhibiting favorable alignment with the defined pharmacophore features. Subsequently, physics-based simulations approaches were conducted on these selected hit molecules. Steered molecular dynamics (sMD) simulations were utilized to assess the correlation between the necessary forces to dissociate candidate hit ligands from the binding pocket and their corresponding average binding free energies (MM/GBSA). Comparative analysis of the average binding free energies of the identified hits obtained from the small molecule libraries represent that the identified compounds have promising predicted binding affinities compared to the reference molecule SGI-1027. Therefore, these findings may signify a crucial advancement in our ability to control MYC activation in cancer.

bioinformatics↗

Targeting miRNA for Colorectal Cancer: In Silico Identification and Physics-based De Novo Modeling of Oncogenic miR-135b for Small Molecule RNA Therapy

Colorectal cancer is one of the leading causes of cancer deaths worldwide. In the current study, we have identified miR-135b, a microRNA to be differentially expressed in colorectal cancer, through an analysis of the differentially expressed miRNAs from the Gene Expression Omnibus database. Subsequently, the target genes associated with miR-135b were pinpointed, and pathway and functional enrichment analyses were performed to gain a comprehensive understanding of the underlying biological processes involved. A de novo three-dimensional model of its tertiary structure was developed for small-molecule targeting at the Dicer cleavage site. Dicer binds to the terminal loop region of the pre-miRNA and cleaves to generate double stranded miRNA duplex. The miRNA duplex is unwound, one of the strands, guide miRNA, is loaded into the RNA-induced silencing complex (RISC) for miRNA-mRNA target interaction and post-transcriptional gene silencing. Following results from molecular docking simulations initiated with the ChemDiv miRNA-targeted small molecule library ([~]20.000 compounds), top-scoring compounds commercial analogues were then searched within the ZINC library using SwissSimilarity. These analogues were docked to the Dicer cleavage site and their optimized docking scores were obtained. These top-scoring molecules were then subject to all-atom molecular dynamics simulations and post-simulation analyses were conducted to assess the dynamic interactions between the miRNA and the selected hit ligands.

bioinformatics↗

DIFFERENTIAL SCANNING CALORIMETRY: A SUITABLE METHODOLOGY TO PROBLEM THE BINDING PROPERTIES OF BCL-2 INHIBITORS

The Differential Scanning Calorimeter (DSC) technique is commonly used for quantitative analysis of protein stability, and it is one of the methods used to quantify protein-ligand interactions. DSC provides denaturation curves that can be a source of data on binding constants. B-cell leukemia/lymphoma-2 (BCL-2) is an antiapoptotic protein, one of the overexpressed proteins in cancer cells. Here, binding constants for BCL-2 of nine BCL-2 inhibitors were evaluated by utilization of DSC measurements. The binding free energies of suggested inhibitors of BCL-2 were measured by melting temperature, Tm, and heat capacity, Cp. Evaluated BCL-2 binding parameters of candidate molecules agreed with our previously reported biological assays and molecular simulations indicating that the DSC method could be applied for the determination of free energies of enzyme inhibitors with high accuracy. Therefore, our results showed that this fast and relatively cheap technique can be conducted in high throughput drug screening analyses to compare the binding affinity of a set of compounds against a specific target protein. BCL-2 and most of its inhibitors have hydrophobic cavities, and a definite percent of dimethyl sulfoxide (DMSO) was advised to increase the solubility. Our work also suggests that the presence of the recommended high concentration of DMSO as the solvent significantly changes the affinity of the inhibitors to BCL-2, revealing similar DSC curves for all inhibitors.

biophysics↗

Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations

CCR5 is one of the co-receptors for HIV-1 entry into host cells and is class A GPCR. This receptor has vital roles in the immune system and is involved in the pathogenesis of different diseases. Various studies were conducted to understand its activation mechanism including structural studies in which inactive and active states of the receptor were determined in complex with various binding partners. These determined structures provided opportunities to perform molecular dynamics simulations (MD) and analyze conformational changes observed in protein structures. The atomic level dynamical studies allow us to explore the effects of ionizable residues in the receptor. Here, our aim was to investigate the changes observed in the conformation of CCR5 when it is in complex with inhibitor maraviroc (MRV), an approved anti-HIV drug or HIV-1 envelope protein GP120 in comparison to when the receptor was in apo form. In our simulations, we considered both ionized and protonated states of ionizable binding site residue GLU2837.39 in CCR5 as the protonation state of this residue was considered ambiguously in previous studies. Our simulation results suggested that in fact, the change in the protonation state of GLU2837.39 caused interaction profiles to be different between CCR5 and its binding partners, GP120 or MRV. We observed that when the protonated state of GLU2837.39 was considered in complex with envelope protein GP120, there were substantial structural changes in CCR5 indicating it adopts more of an active-like conformation. On the other hand, CCR5 when it was in complex with MRV always adopted inactive conformation regardless of the protonation state. Hence, CCR5 coreceptor displays conformational heterogeneity not only based on its binding partner but also on the state of the protonation state of a binding site residue GLU2837.39. This outcome is also in accordance with some studies showing that GP120 binding could activate signaling pathways. Additionally, this outcome could also have critical implications for the discovery of novel CCR5 inhibitors to be used as anti-HIV drugs by in silico methods such as molecular docking since consideration of the protonated state of GLU2837.39 could be required.

biophysics↗

Utilizing Heteroatom Types and Numbers from Extensive Ligand Libraries to Develop Novel hERG Blocker QSAR Models Using Machine Learning-based Classifiers

The human Ether-a-go-go Related Gene (hERG) channel plays a crucial role in membrane repolarization. Any disruptions in its function can lead to severe cardiovascular disorders like long QT syndrome (LQTS), which increases the risk of serious cardiovascular problems such as tachyarrhythmia and sudden cardiac death. Drug-induced LQTS is a significant concern and has resulted in drug withdrawals in the past. The main objective of this research study is to pinpoint crucial heteroatoms present in ligands that initiate interactions leading to effective blocking of the hERG channel. To achieve this aim, ligand-based quantitative structure-activity relationships (QSAR) models were constructed using extensive ligand libraries, considering the heteroatom types and numbers, and their associated hERG channel blockage pIC50 values. Machine learning-assisted QSAR models were developed to analyze the key structural components influencing compound activity. Among various methods, the KPLS method proved to be the most efficient, allowing the construction of models based on eight distinct fingerprints. The study delved into investigating the influence of heteroatoms on the activity of hERG blockers, revealing their significant role. Furthermore, by quantifying the effect of heteroatom types and numbers on ligand activity at the hERG channel, six compound pairs were selected for molecular docking. Subsequent molecular dynamics (MD) simulations and MM/GBSA calculations per residue were performed to comprehensively analyze the interactions of the selected pair compounds.

bioinformatics↗

Dynamic Structure-based Pharmacophore Models for Virtual Screening of Small Molecule Libraries Targeting the YB-1

In drug discovery, ligand-based techniques offer rapid screening, whereas structure-based approaches provide deeper insights but are time-consuming. Hybrid methods like structure-based pharmacophore models combine advantages for accurate screening of large ligand libraries. However, there are substantial limits to build structure-based pharmacophore models. Static models relying on a single co-crystallized structure or docking pose often fall short in capturing the dynamic nature of binding interactions. In this study, we present dynamic structure-based pharmacophore models, aimed at better representing physiological conditions and addressing these challenges. The urgent need for improved cancer treatment has led to the search for new chemotherapeutic strategies. Y box binding protein 1 (YB-1) is a multifunctional protein associated with tumor progression and treatment resistance in various cancers. For the first time in the literature, our study utilizes a known small molecule YB-1 inhibitor (SU056) bound to the active regions of the RNA-binding sites to develop dynamic structure-based pharmacophores. These models were then used in the screening of large ligand libraries.

biophysics↗

Rapid and High Resolution Ambient Temperature Structure Determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish Light Source (Turkish DeLight). The complete dataset was collected in 18.5 mins with resolution extending to 2.39 [A] and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

biophysics↗

Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source: Turkish DeLight

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g. proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryo-crystallography has never been performed in Turkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, Istanbul, Turkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

biophysics↗

Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in-silico drug screening studies has been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with 9 drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.

molecular biology↗

Receptor-wide Determinants of G Protein Coupling Selectivity in Aminergic GPCRs

G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed an extensive phylogenetic analysis and identified specifically conserved residues for the receptors having similar coupling profiles in each aminergic receptor. By integrating our methodology of differential evolutionary conservation of G protein-specific amino acids with structural analyses, we identified selective activation networks for Gs, Gi1, Go, and Gq. To validate that these networks could determine coupling selectivity we further analyzed Gs specific activation network and associated it with the larger TM6 tilt which is a signature of Gs-coupled receptors. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7x41 plays an important role in both receptor activation and Gs coupling selectivity by inducing a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called "sequential switches of activation" describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms and G protein contact.

evolutionary biology↗

Molecular simulations reveal the impact of RAMP1 on ligand binding and dynamics of CGRPR heterodimer

The release of the neuropeptide of calcitonin gene-related peptide (CGRP) plays a key role in the mechanisms of migraine pathology and pain perception as it causes vasodilatation, neurogenic inflammation, mast cell degranulation, sensory signal activation and peripheral sensitivity. Although the findings on the effectiveness of CGRP-targeted therapies in migraine provide new information about the pathophysiology of migraine, questions remain on how the CGRP mechanisms fit into the overall migraine theory. The cryo-EM structure of Gs-protein complexed human CGRP receptor (CGRPR) with bound endogenous CGRP neuropeptide paved the way of understanding the insights into the CGRP receptor function. With several molecular modeling approaches, molecular dynamics (MD) simulations and post-MD analyzes, we aimed to investigate the importance of RAMP1 in the stability of calcitonin receptor-like receptor (CLR). Moreover, we compared the binding modes of the CGRP neuropeptide and CGRPR antagonists (i.e., telcagepant and rimegepant) within the presence or absence of RAMP1. We also investigated the global and local effects of bound molecules on CGRPR as well as their effects on the CLR-RAMP1 interaction interfaces. Results showed that although these molecules stay stable at the ectodomain binding site, they can also bind to the orthosteric ligand binding pocket and form the crucial interactions occurred in the CGRP agonism, which may be interpreted as non-specificity of the ligands, however, most of these interactions at orthosteric site are not sustainable or weak. Particularly, RAMP1 may also be important for the stability of TM domain of CLR hereby stabilizing the orthosteric binding pocket.

biophysics↗

The neutralization effect of Montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies

Small molecule inhibitors have previously been investigated in different studies as possible therapeutics in the treatment of SARS-CoV-2. In the current drug repurposing study, we identified the leukotriene (D4) receptor antagonist Montelukast as a novel agent that simultaneously targets two important drug targets of SARS-CoV-2. We initially demonstrated the dual inhibition profile of Montelukast through multiscale molecular modeling studies. Next, we characterized its effect on both targets by different in vitro experiments including the Fluorescent Resonance Energy Transfer (FRET)-based main protease enzyme inhibition assay, surface plasmon resonance (SPR) spectroscopy, pseudovirus neutralization on HEK293T / hACE2, and virus neutralization assay using xCELLigence MP real time cell analyzer. Our integrated in silico and in vitro results confirmed the dual potential effect of the Montelukast both on virus entry into the host cell (Spike/ACE2) and on the main protease enzyme inhibition. The virus neutralization assay results showed that while no cytotoxicity of the Montelukast was observed at 12 M concentration, the cell index time 50 (CIT50) value was delayed for 12 hours. Moreover, it was also shown that Favipiravir, a well-known antiviral used in COVID-19 therapy, should be used by 16-fold higher concentrations than Montelukast in order to have the same effect of Montelukast. The rapid use of new small molecules in the pandemic is very important today. Montelukast, whose pharmacokinetic and pharmacodynamic properties are very well characterized and has been widely used in the treatment of asthma since 1998, should urgently be completed in clinical phase studies and if its effect is proven in clinical phase studies, it should be used against COVID-19.

biophysics↗

Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growth in vivo

Eukaryotic elongation factor 2 kinase (eEF-2K), an unusual alpha kinase, is involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is indicated as one of the critical drivers of breast cancer and associated with poor clinical prognosis, representing a potential molecular target. The crystal structure of eEF-2K is unknown and there is no potent and effective eEF-2K inhibitor reported for clinical applications. To meet this challenge, we designed and synthesized several generations of potential inhibitor compounds and performed in silico studies. The effect of the inhibitors at the binding pocket of eEF-2K is analyzed after developing a 3D target model by homology modeling approaches using a domain of another -kinase called myosin heavy-chain kinase A (MHCKA) that is closely resembling eEF-2K. Our results showed that compounds with coumarin-chalcone cores have a high predicted binding affinity for binding to eEF-2K. Following in vitro studies, we identified a compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and inhibited proliferation of various breast cancer cells with different features (BT20, MDA-MB-231, MDA-MB-436 and MCF-7) by induction of apoptosis while sparing normal cells. In vivo systemic administration of the the lead inhibitor encapsulated in single lipid-based nanoparticles twice a week significantly supressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice. In conclusion, our study provides the first in vivo effective small molecule eEF-2K inhibitor that may be used for molecularly targeted precison medicine strategies in breast cancer or other eEF-2K-dependent tumors.

cancer biology↗

Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray crystallography. We employed detailed molecular simulations of selected known main protease inhibitors with the structures and compared binding modes and energies. The combined structural biology and molecular modeling studies not only reveal the dynamics of small molecules targeting main protease but will also provide invaluable opportunities for drug repurposing and structure-based drug design studies against SARS-CoV-2. One Sentence SummaryRadiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19.

biophysics↗

Structural and functional characterization of allatostatin receptor type-C of Thaumetopoea pityocampa revealed the importance of Q2716.55 residue in G protein-dependent activation pathway

Insect neuropeptide receptors are among the potential targets for designing next-generation pesticides. Activation of allatostatin receptor type C (AstR-C), a G Protein-coupled receptor (GPCR), upon stimulation with its endogenous ligand, allatostatin C (AST-C), leads to the inhibition of juvenile hormone (JH) secretion that consequently regulates physiology of insects. Here we conducted in silico and in vitro approaches to characterize the structure and function of AstR-C of Thaumetopoea pityocampa (T.pit), a well-known pest in Mediterranean countries. The sequence of AstR-C and AST-C were derived from whole genome sequencing (WGS) data. Resonance energy transfer (RET) methods were used to investigate the downstream effectors of the receptor and the temporal kinetics of G protein activation. Three-dimensional (3D) structure of AstR-C constructed via homology modeling methods was subjected to molecular dynamics (MD) simulations and docking studies to identify the orthosteric pocket. Our results showed that T.pit AstR-C couples to Gi/o subtype of G proteins at sub-nanomolar ranges of the the ligand with the G protein recruitment and activation kinetics of [~]4 and 6 seconds, respectively, when 1 nM AST-C is administered. At the increasing concentration of native ligand, {beta}arrestin was shown to be recruited at nanomolar ranges the ligand. Docking and MD simulation studies revealed the importance of extracellular loop 2 (ECL2) in T.pit AstRC/AST-C interaction, and combination of in silico and in vitro methods supported the accuracy of the built model and the predicted orthosteric pocket. Q2716.55 (Ballesteros-Weinstein generic numbering) was found to have a substantial role in G protein dependent activation of AstR-C possibly via contributing to the flexibility of the structure.

bioinformatics↗

Development of Small Molecule MEIS Inhibitors that modulate HSC activity

Meis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34low cells) and human (CD34+, CD133+, and ALDHhi cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1, Hif-2 and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.

molecular biology↗