Protein-ligand Interaction Profiling Research Articles

Discovery of potential FDA-approved SARS-CoV-2 Papain-like protease inhibitors: A multi-phase in silico approach

Papain-like protease (PLpro) is a crucial enzyme for SARS-CoV-2 replication and immune evasion. Inhibiting PLpro could be a promising strategy to fight against COVID-19. This study aimed to identify potent inhibitors of PLpro among FDA-approved drugs using an in silico approach. The study also aimed to examine and confirm the binding of the selected compounds to the active pocket of PLpro using a multi-phased in silico approach, involving the screening of 3009 FDA-approved drugs to pinpoint the most similar compounds to, TTT, the co-crystallized ligand TTT of PLpro. The selected compounds were subjected to further analysis, including molecular docking, molecular dynamics simulations, MM-GPSA (molecular mechanics generalized Born surface area), and PLIP (Protein-Ligand Interaction Profiler) studies, to examine and confirm their binding to the active pocket of PLpro. Seven candidates (Vismodegib, Celecoxib, Ketoprofen, Indomethacin, Naphazoline, Valdecoxib, and Eslicarbazepine) showed promising in silico activities against the PLpro. The computational analysis confirmed the binding of Celecoxib to the active pocket of PLpro, suggesting its potential in the fight against COVID-19. This study identified seven FDA-approved drugs as potential inhibitors of PLpro, providing a feasible approach for drug repurposing against COVID-19. The results obtained from the in silico approach hold promise, but further in vitro and in vivo studies are warranted to validate the potential of these compounds.

Identification of new potential inhibitors of pteridine reductase-1 (PTR1) via biophysical and biochemical mechanism-based approaches: Step towards the treatment of Leishmaniasis

Leishmaniasis is a parasitic disease, which spreads from the bite of an infected Phlebotomine fly to human hosts. The disease is characterized by a number of clinical manifestations, such as ulcerative lesions at the site of sandfly bite (cutaneous form), inflammation of mucosal membranes (mucosal leishmaniasis) or the deadly visceral form. This study was aimed to target pteridine reductase-1 (PTR1), a member of short chain dehydrogenases, which accounts for the reduction of conjugated and unconjugated pterins in Leishmania parasite. The ptr1-pET28a+-tev construct was expressed using BL21 (DE3) cells, followed by two tandem purification steps including affinity and gel permeation chromatography. In the next phase, functional studies of PTR1 were performed via screening of an in-house library of 500 compounds. The biochemical-mechanism based assay of PTR1 identified 11 hits that were also found to be non-cytotoxic against human fibroblast cell line (BJ) (except compound 6), and thus further studied via computational technique and saturation transfer difference-nuclear magnetic resonance (STD-NMR) spectroscopy. These high throughput techniques identified six compounds 2, 4, 5, 7, 9, and 11 as active, which were then assessed via in-vitro assay. Among them, compounds 2, 4, and 7 showed substantial leishmanicidal activity, comparable to the standard drug, miltefosine (IC50 value: 31.8 ± 0.2 μM). These results narrowed down the search to 3 compounds as potential leads, with prominent protein-ligand interaction profiles. Hence, the respective compounds can be further assessed for their therapeutic potential against leishmaniasis.

Ursolic acid interaction with transcription factors BRAF, V600E, and V600K: a computational approach towards new potential melanoma treatments.

Melanoma is one of the cancers with the highest mortality rate for its ability to metastasize. Several targets have undergone investigation for the development of drugs against this pathology. One of the main targets is the kinase BRAF (RAF, rapidly accelerated fibrosarcoma). The most common mutation in melanoma is BRAFV600E and has been reported in 50-90% of patients with melanoma. Due to the relevance of the BRAFV600E mutation, inhibitors to this kinase have been developed, vemurafenib-OMe and dabrafenib. Ursolic acid (UA) is a pentacyclic triterpene with a privileged structure, the pentacycle scaffold, which allows to have a broad variety of biological activity; the most studied is its anticancer capacity. In this work, we reported the interaction profile of vemurafenib-OMe, dabrafenib, and UA, to define whether UA has binding capacity to BRAFWT, BRAFV600E, and BRAFV600K. Homology modeling of BRAFWT, V600E, and V600K; molecular docking; and molecular dynamics simulations were carried out and interactions and residues relevant to the binding of the inhibitors were obtained. We found that UA, like the inhibitors, presents hydrogen bond interactions, and hydrophobic interactions of van der Waals, and π-stacking with I463, Q530, C532, and F583. The ΔG of ursolic acid in complex with BRAFV600K (- 63.31kcal/mol) is comparable to the ΔG of the selective inhibitor dabrafenib (- 63.32kcal/mol) in complex to BRAFV600K and presents a ΔG like vemurafenib-OMe with BRAFWT and V600E. With this information, ursolic acid could be considered as a lead compound for design cycles and to optimize the binding profile and the selectivity towards mutations for the development of new selective inhibitors for BRAFV600E and V600K to new potential melanoma treatments. The homology modeling calculations were executed on the public servers I-TASSER and ROBETTA, followed by molecular docking calculations using AutoGrid 4.2.6, AutoDockGPU 1.5.3, and AutoDockTools 1.5.6. Molecular dynamics and metadynamics simulations were performed in the Desmond module of the academic version of the Schrödinger-Maestro 2020-4 program, utilizing the OPLS-2005 force field. Ligand-protein interactions were evaluated using Schrödinger-Maestro program, LigPlot + , and PLIP (protein-ligand interaction profiler). Finally, all of the protein figures presented in this article were made in the PyMOL program.

8308 Up-regulation of Diacylglycerol kinase gamma (DGKG) in aggressive recurrent pituitary tumors could be targeted by Dasatinib reducing cell proliferation and induced apoptosis

Abstract Disclosure: K. Taniguchi-Ponciano: None. I. Remba: None. M. Loza-Mejia: None. J. Salazar: None. A. Mendez-Perez: None. C. Aguilar-Flores: None. A. Chavez-Gonzalez: None. E. Ortiz-Reyes: None. L. Bonifaz: None. D. Marrero-Rodríguez: None. M. Mercado: None. Pituitary tumors (PT) represent 15% of all intracranial tumors. Some PTs exhibit an aggressive behavior, growing rapidly and invading surrounding tissues, and are frequently resistant to multimodal treatment showing multiple recurrences. Pituitary tumors often recur after initial surgery, particularly when invasive, precluding complete resection of the lesion, which can only be achieved in ∼40-50% of all patients.We have previously characterized transcriptome and exome from 22 tumor lesions from 11 patients by RNA- and DNAseq and methylome profile by microarrays of aggressive, both primary and recurrent PT from the same patient to identify molecular pharmacological targets.Among the differentially expressed genes in most recurrent tumors we found those related to fatty acid biosynthesis and metabolism, phosphatidylinositol, glycerophospholipid and phospholipase D signaling. Importantly, one gene found in most of the lipid-related pathways was diacylglycerol kinase gamma (DGKG). DGKG gene expression was confirmed by immunofluorescence and did not seem to be regulated by DNA methylation. And DGKG showed allelic c.G947A:p.R316K variant in all primary and recurrent tumor tissues analyzed, more research is needed to understand genetic variant impact on protein function. We then performed DGKG molecular docking for FDA-approved drug repurposing. Human DGKG tridimensional model was downloaded from AlphaFold and Autodock Vina, Molegro Virtual Docker, PyMol v2.5.2 program and the Protein-Ligand Interaction Profiler web tool were used. The in silico ADMET profiles were generated in ADMETLab 2.0 using only FDA approved drugs. We identified Dasatinib as a strong candidate for DGKG targeting. We then exposed GH3 cell line to increasing concentrations of Dasatinib (1, 2.5 y 5 μM) using DMSO as vehicle. After cell viability was assessed, approximatively 31% of all live GH3 cells were at proliferative state without any treatment, that was taken as our basal quantity to compare the GH3 cells treated with the TKI’s. Dasatinib reduced approximatively 28% the cell proliferation at 1 μM (p=0.0048), at 2.5 μM reduced nearly 50% of cell proliferation (p=0.003) and at 5 μM inhibited nearly 98% of cell proliferation (p=0.0395) by means of Click-iT EdU Cell proliferation Kit. We then, evaluated Dasatinib apoptosis induction capacity. Interestingly, the 1 μM Dasatinib concentration induced apoptosis (p=0.0001) as concentrations increased, cell death also increased considerably (p=0.0001) measured by Anexin V-FITC and DAPI assay. The RNAseq data from GH3 cells exposed to Dasatinib show diminished gene expression of cell cycle related genes and glycolysis.In conclusion, we observed DGKG upregulated in recurrent aggressive pituitary tumors participating in lipid metabolism pathways and could be targeted by Dasatinib at very low doses. Presentation: 6/3/2024

A cadmium-thiocyanate coordination polymer with bridging 2-aminopyridine: Synthesis, characterization DFT studies, Hirshfeld Surface analysis and docking studies

A one-dimensional [Cd(SCN)2]n coordination polymer doubly bridged by 2-aminopyridine has been synthesized via slow evaporation method at low temperature and it was characterized by single-crystal X-ray diffraction, Fourier Transform Infrared (FT-IR) spectroscopy, electronic spectroscopy, thermogravimetric analysis (TGA), and elemental analysis. The polymeric complex crystallizes in the triclinic crystal system with space group P-1. An analysis of the crystal structure as well as Hirshfeld surfaces (HS) associated with 2D fingerprint plots, indicates the existence of C–H· · · π and π-stacking interactions alongside NH—N and NH—S H-bonding interactions contributing to the stabilization of the layered assembly of the compound. Theoretical Density Functional Theory (DFT) Calculations (using different levels of theory) were done on the asymmetric unit of the polymer and a polymer fragment that reflects the coordination environment of Cd2+ in the polymer, to gain more information about the coordination environment of Cd2+ in the polymer. This also permitted a quantification of the interaction energies associated with hydrogen bonding and non-covalent interactions, as well as other quantum chemical parameters. Good consistency was found between the calculated results and the experimental structure. All the levels of theory used predict that the polymer fragment was less stable compared to the asymmetric unit except at the B3LYP/SSD level of theory. Analysis of the HOMO and LUMO was used to explain the charge transfer within the polymer. Thermal analysis of the polymer indicates it decomposes in two steps resulting in a residue indexed to the hexagonal phase of CdS JCPDS [06–0314]. The activity of the metal complex against breast, lung, and liver cancer was measured. The interactions occurring in the docking calculation were examined in detail with PLIP (Protein-Ligand Interaction Profiler) analysis. Lastly, Swiss- ADME (absorption, distribution, metabolism and excretion) analysis was performed to examine the pharmacological properties of the metal complex.

Peripheral (E)-2-[(4-hydroxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one)]-coordinated phthalocyanines with improved enzyme inhibition properties and photophysicochemical behaviors.

In this study, (E)-4-{4-[(1-oxo-3,4-dihydronaphthalen-2(1H)-ylidene)methyl]phenoxy}phthalonitrile (4) and its phthalocyanine derivatives (5-8) were synthesized for the first time. Aggregation behaviors of the novel soluble phthalocyanines in organic solvents were investigated. In addition, the efficiency of 1O2 production of (5) and ZnPc (6) was investigated. The singlet oxygen quantum yields (ΦΔ) for 2HPc (5) and ZnPc (6) were found to be 0.58 and 0.83, respectively. Additionally, novel phthalocyanines (5-8) were investigated for their ability to inhibit enzymes. They exhibited a highly potent inhibition effect on human carbonic anhydrase I and II (hCA I and II) and α-glycosidase (α-Gly) enzymes. Ki values are in the range of 2.60 ± 9.87 to 11.53 ± 6.92 µM, 3.35 ± 0.53 to 15.47 ± 1.20 µM, and 28.60 ± 4.82 to 40.58 ± 7.37 nM, respectively. The calculations of the studied molecule at the B3LYP, HF, and M062X levels in the 6-31G basis sets were made using the Gaussian package program. Afterward, the interactions occurring in the docking calculation against a protein that is the crystal structure of hCA I (PDB ID: 2CAB), the crystal structure of hCA II (PDB ID: 5AML), and the crystal structure of α-Gly (PDB ID: 1R47), were examined. Following that, Protein-Ligand Interaction Profiler (PLIP) analysis was used to look at the interactions that occurred during the docking calculation in further detail.

In silico analysis of the wild-type and mutant-type of BRCA2 gene

BackgroundThe aim of this study was to conduct an in silico analysis of a novel compound heterozygous variant in breast cancer susceptibility gene 2 (BRCA2) to clarify its structure–function relationship and elucidate the molecular mechanisms underlying triple-negative breast cancer (TNBC).MethodsA tumor biopsy sample was obtained from a 42-year-old Chinese woman during surgery, and a maxBRCA™ test was conducted using the patient’s whole blood. We obtained an experimentally determined 3D structure (1mje.pdb) of the BRCA2 protein from the Protein Data Bank (PDB) as a relatively reliable reference. Subsequently, the wild-type and mutant structures were predicted using SWISS-MODEL and AlphaFold, and the accuracy of these predictions was assessed through the SAVES online server. Furthermore, we utilized a high ambiguity-driven protein–protein docking (HADDOCK) algorithm and protein–ligand interaction profiler (PLIP) to predict the pathogenicity of the mutations and elucidate pathogenic mechanisms that potentially underlies TNBC.ResultsHistological examination revealed that the tumor biopsy sample exhibited classical pathological characteristics of TNBC. Furthermore, the maxBRCA™ test revealed two compound heterozygous BRCA2 gene mutations (c.7670 C > T.pA2557V and c.8356G > A.pA2786T). Through performing in silico structural analyses and constructing of 3D models of the mutants, we established that the mutant amino acids valine and threonine were located in the helical domain and oligonucleotide binding 1 (OB1), regions that interact with DSS1.ConclusionOur analysis revealed that substituting valine and threonine in the helical domain region alters the structure and function of BRCA2 proteins. This mutation potentially affects the binding of proteins and DNA fragments and disrupts interactions between the helical domain region and OB1 with DSS1, potentially leading to the development of TNBC. Our findings suggest that the identified compound heterozygous mutation contributes to the clinical presentation of TNBC, providing new insights into the pathogenesis of TNBC and the influence of compound heterozygous mutations in BRCA2.

Supramolecular clumps of μ2-1,3-acetate bridges of Cd(II)-Salen complex: Synthesis, spectroscopic characterization, crystal structure, DFT quantization's, and antifungal photodynamic therapy

The article divulges the crystal growth, synthesis, and X-ray structure characterization of one centrosymmetric cadmium complex, [Cd{CdL(μ2-1,3-acetate)}2] using Salen ligand (SL). The complex is further characterized using spectroscopic and analytical techniques, including DRS, SEM-EDX, PXRD, and ICP-MS. The crystallographic study showed that the complex has a monoclinic space P21/c. Addison parameters (Ʈ) show the hexagonal geometry of the central Cd(II) metal ion. Hirshfeld surface and 2-D fingerprint confirm supramolecular contacts despite weak C–H⋯O and C–H···π interactions. Energy frameworks, FMOs, global reactivity parameters, MEP, and energy bandgap explain the complex reactivity outlook. The complex inter- and intramolecular bonding interactions were explored through natural bond orbital (NBO), QTAIM, NCI-RDG, Electron Location Function (ELF), and Localized Orbital Locator (LOL) quantization methods. In addition, the complex and its synthetic components in vitro antibacterial efficacy were investigated using Gram-positive and Gram-negative microbial strains. SAR (structure-activity relationship) correlates with biological potency. Molecular docking assessed antimicrobial potency with proteins S. aureus (PDB ID: 1JIJ), C. albicans (PDB ID: 1M7A), E. coli (PDB ID: 1T9U), P. aeruginosa (PDB ID: 2UV0), and A. Niger (PDB ID: 3K4P). The findings are backed by the Protein-Ligand Interaction Profiler (PLIP). The antifungal potency and cell viability test of C. albicans were conducted using photodynamic therapy (APDT).

Trinuclear nickel (II) string complexes and copper (II) coordination polymer with pyrazine modulated unsymmetrical dipyridylamino ligand: Synthesis, structure and bioactivity properties with molecular docking

The unsymmetrical pyrazine-modulated ligand, N-(pyridine-2-yl)pyrazin-2-amine (Hppza) (1), its 1D straight-chain copper (II) coordination polymer [Cu2(Hppza)2∙(NO3)4]n (2) and trinuclear metal string [Ni3(µ3-ppza)4Cl2] (3) and [Ni3(µ3-ppza)4(NCS)2] (4) complexes have been successfully synthesized and structurally characterized. The free ligand Hppza (1) exhibits anti-syn conformation. In an asymmetric unit of 2, there are two kinds of Cu(II) atoms, both of which have elongated octahedral coordination geometry, and the copper(II) centers are linked by oxygen atoms of one nitrate anion. There are only minor differences in Ni…Ni bond lengths between pyrazine-modulated ligand complexes of [Ni3(μ3-ppza)4×2] (X = Cl− (3), NCS− (4)) and their unmodulated analogs, while the distances between the terminal nickel atoms and the axial ligands 3 and 4 are shorter. The results of magnetic susceptibility measurements showed an antiferromagnetic exchange constant (J) of about J = –199.2 cm–1 for 3 and J = –178.0 cm–1 for 4. The electrochemical properties of nickel strings of Hppza differ significantly from their unmodulated counterparts. The activities of ligands and their metal complexes against various proteins that are AChE (PDB ID: 4M0E), BChE (PDB ID: 5NN0), α-Gly (PDB ID: 1UAS), hCA I (PDB ID: 2CAB), and hCA II (PDB ID: 3DC3) were compared, and then the ADME/T properties of molecules were examined. Afterward, the interactions occurring in the docking calculation were examined in detail with the Protein-Ligand Interaction Profiler (PLIP) service. These complexes were inhibitors of BChE, hCA I and II, α-glycosidase and AChE enzymes for complex 3 and 5 with Ki values of 12.65 and 42.95 μM for hCA I, 3.64 and 15.84 μM for hCA II, 5.44 and 50.07 μM for BChE, 15.85 and 4.77 μM for α-glycosidase and 8.58 and 86.24 μM for AChE, respectively.

In silico docking study of selected compounds for its hepatoprotective activity

Liver fibrosis is a condition characterized by the excessive accumulation of scar tissue in the liver. It is typically caused by chronic liver diseases, such as chronic viral hepatitis (e.g., hepatitis B and C), alcoholic liver disease, non-alcoholic fatty liver disease (NAFLD), autoimmune hepatitis, and certain genetic conditions. Ephrin receptor A2 (EphA2) is identified as potential anti-inflammatory target which influences inflammatory process and immune response, impacting the recruitment and activation of immune cells and as a host cofactor for Hepatitis C Virus (HCV) entry. Andrographolide a diterpenoid lactone, Scoulerine a natural alkaloid possess anti-inflammatory activity. The present work was done to evaluate anti-inflammatory activity of andrographolide and scoulerine using software Autodock 4.2. Phyto-constituents were fetched from the PubChem database. 3D structure of EphA2 were downloaded from Protein Data Bank (PDB). Among two phyto compounds, andrographolide had highest binding energy of -7.58 which is a clear evident of potential anti-inflammatory activity and prevent hepatic fibrosis. The active site of the target protein was predicted by using CASTP (Computed atlas of surface topography of proteins). Protein ligand interaction information is obtained by Protein ligand interaction profiler.

Protein structure prediction based on deep learning: HER2 in complex with a covalent inhibitor

HER2 protein overexpression is associated with the malignant degree and poor prognosis of breast cancer. HER2 levels are elevated in 20% of breast tumors. Several covalent tyrosine kinase inhibitors have been found to reduce tumor cell survival and proliferation in vitro and inhibit downstream HER2 signaling. In the field of protein structure prediction, AlphaFold2, which achieved excellent results in CASP14, can periodically predict protein structures with atomic precision in the absence of similar protein structures. In this study, AlphaFold2 was used to predict the monomeric structure of the HER2 protein. This predicted structure was compared to the conformation of HER2 in complex with a covalent inhibitor, allowing for an examination of the conformational changes induced by the inhibitor. By combining the conformational changes of HER2 protein with the docking results of Protein-Ligand Interaction Profiler, other potential binding sites were identified, which could further reveal the mechanism of drug discovery.

In silico and in vitro evaluation of the anti-virulence potential of patuletin, a natural methoxy flavone, against Pseudomonas aeruginosa.

This study aimed to investigate the potential of patuletin, a rare natural flavonoid, as a virulence and LasR inhibitor against Pseudomonas aeruginosa. Various computational studies were utilized to explore the binding of Patuletin and LasR at a molecular level. Molecular docking revealed that Patuletin strongly interacted with the active pocket of LasR, with a high binding affinity value of -20.96 kcal/mol. Further molecular dynamics simulations, molecular mechanics generalized Born surface area (MM/GBSA), protein-ligand interaction profile (PLIP), and essential dynamics analyses confirmed the stability of the patuletin-LasR complex, and no significant structural changes were observed in the LasR protein upon binding. Key amino acids involved in binding were identified, along with a free energy value of -26.9 kcal/mol. In vitro assays were performed to assess patuletin's effects on P. aeruginosa. At a sub-inhibitory concentration (1/4 MIC), patuletin significantly reduced biofilm formation by 48% and 42%, decreased pyocyanin production by 24% and 14%, and decreased proteolytic activities by 42% and 20% in P. aeruginosa isolate ATCC 27853 (PA27853) and P. aeruginosa clinical isolate (PA1), respectively. In summary, this study demonstrated that patuletin effectively inhibited LasR activity in silico and attenuated virulence factors in vitro, including biofilm formation, pyocyanin production, and proteolytic activity. These findings suggest that patuletin holds promise as a potential therapeutic agent in combination with antibiotics to combat antibiotic-tolerant P. aeruginosa infections.

In-silico Investigations for the Identification of Novel Inhibitors Targeting Hepatitis C Virus RNA-dependent RNA Polymerase.

Hepatitis C is an inflammatory condition of the liver caused by the hepatitis C virus, exhibiting acute and chronic manifestations with severity ranging from mild to severe and lifelong illnesses leading to liver cirrhosis and cancer. According to the World Health Organization's global estimates, a population of about 58 million have chronic hepatitis C virus infection, with around 1.5 million new infections occurring every year. The present study aimed to identify novel molecules targeting the Hepatitis C viral RNA Dependent RNA polymerases, which play a crucial role in genome replication, mRNA synthesis, etc. Methods: Structure-based virtual screening of chemical libraries of small molecules was done using AutoDock/Vina. The top-ranking pose for every ligand was complexed with the protein and used for further protein-ligand interaction analysis using the Protein-ligand interaction Profiler. Molecules from virtual screening were further assessed using the pkCSM web server. The proteinligand interactions were further subjected to molecular dynamics simulation studies to establish dynamic stability. Molecular docking-based virtual screening of the database of small molecules, followed by screening based on pharmacokinetic and toxicity parameters, yielded eight probable RNA Dependent RNA polymerase inhibitors. The docking scores for the proposed candidates ranged from - 8.04 to -9.10 kcal/mol. The potential stability of the ligands bound to the target protein was demonstrated by molecular dynamics simulation studies. Data from exhaustive computational studies proposed eight molecules as potential anti-viral candidates, targeting Hepatitis C viral RNA Dependent RNA polymerases, which can be further evaluated for their biological potential.

In vitro and in silico correlation of benzoxazole-based thiazolidinone hybrids derivatives: A promising acetylcholinesterase and butyrylcholinesterase inhibitors

Benzoxazole-based thiazolidinone hybrids derivatives (1–19) were afforded and further subjected to in vitro acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition studies for the first time. All these analogues were found to display good inhibition against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE)enzymes with IC50 values 4.20 ± 1.10 µM to 43.20 ± 4.50 µM (against AChE) and 3.80 ± 1.20 µM to 34.50 ± 3.30 µM (against BuChE) as compared to standard donepezil having IC50 values of 21.86 ± 0.40 µM (against AChE) and 32.47 ± 2.30 µM (against BuChE) respectively. Specifically, compound 16, characterized by a 3,4-dichloro substitution on ring B and 2–OH and 4-CF3 substitutions on ring C, along with compound 13, having 2,4-diCl on ring B and 2-OH and 4-CF3 on ring C, were identified as the most potent inhibitors of the targeted AChE and BuChE enzymes, even manifolds more potent than standard donepezil drug. The structures of all synthesized analogues were verified through the utilization of multiple spectroscopic techniques, including HREI-MS and NMR (1H NMR and 13C NMR). The structure-activity relationship (SAR) demonstrated that analogs bearing electron withdrawing groups such as –CF3, –Cl and -NO2 groups displayed superior AChE and BuChE activities. In the molecular docking analysis of the most potent analogs, a favorable protein-ligand interaction (PLI) profile was observed with the respective targets (AChE and BuChE). These interactions encompassed crucial bonding types such as hydrogen bonding, π-π interactions, π-π stacking, and hydrophobic interactions.

In silico identification and characterization of small molecule binding to the CD1d immunoreceptor

CD1 immunoreceptors are a non-classical major histocompatibility complex (MHC) that present antigens to T cells to elucidate immune responses against disease. The antigen repertoire of CD1 has been composed primarily of lipids until recently when CD1d-restricted T cells were shown to be activated by non-lipidic small molecules, such as phenyl pentamethyl dihydrobenzofuran sulfonate (PPBF) and related benzofuran sulfonates. To date structural insights into PPBF/CD1d interactions are lacking, so it is unknown whether small molecule and lipid antigens are presented and recognized through similar mechanisms. Furthermore, it is unknown whether CD1d can bind to and present a broader range of small molecule metabolites to T cells, acting out functions analogous to the MHC class I related protein MR1. Here, we perform in silico docking and molecular dynamics simulations to structurally characterize small molecule interactions with CD1d. PPBF was supported to be presented to T cell receptors through the CD1d F’ pocket. Virtual screening of CD1d against more than 17,000 small molecules with diverse geometry and chemistry identified several novel scaffolds, including phytosterols, cholesterols, triterpenes, and carbazole alkaloids, that serve as candidate CD1d antigens. Protein-ligand interaction profiling revealed conserved residues in the CD1d F’ pocket that similarly anchor small molecules and lipids. Our results suggest that CD1d could have the intrinsic ability to bind and present a broad range of small molecule metabolites to T cells to carry out its function beyond lipid antigen presentation. Communicated by Ramaswamy H. Sarma

Evaluation of therapeutic potentials of some bioactive compounds in selected African plants targeting main protease (Mpro) in SARS-CoV-2: a molecular docking study

BackgroundCoronavirus disease 2019 (COVID-19) is an infectious disease brought on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a global treat in early 2020. Despite worldwide research proving different medications used to treat COVID-19, the infection still affects the human race; we need to continue researching the virus to protect humanity and reduce the complications that some medications might cause. This study focuses on finding another promising therapeutic compound against SARS-CoV-2. Twenty-four (24) bioactive compounds were selected from the following African plants' Adansonia digitata L, Aframomum melegueta K. Schum, Ageratum conyzoides (L.) L, and Boswellia dalzielii, and Remdesivir was used as the control medication. The PubChem web server acquired the 3D structures of bioactive compounds in the plant and the control medication. The SARS-CoV-2 main protease (Mpro) crystal structure was obtained using the Protein Data Bank (PDB). Using the SwissADME web server, the bioactive compounds' drug-likeness was assessed, and AutoDock was employed for the molecular docking with the Mpro. The Proteins Plus and Protein–Ligand Interaction Profiler web servers were used to analyse the docked complexes. Furthermore, the admetSAR website was utilized to predict the ligands' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.ResultsBased on the drug-likeness screening, Rutin violated more than one of the Lipinski rules of five, while Remdesivir violated two. Molecular docking analysis results indicated that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene exhibited a stronger binding affinity with Mpro, with binding scores of − 7.1, − 7.1, − 8.0, − 7.3, − 7.2, − 6.8, and − 6.5 kcal/mol, respectively, compared to Remdesivir's binding score of − 6.3 kcal/mol. Consequently, binding scores of bioactive compounds suggest their potential biological activity against the SARS-CoV-2 main protease. Additionally, these bioactive compounds exhibited favourable ADMET properties. Vitexin also has a plasma protein binding below 90%, a promising medication distribution feature.ConclusionsThis study shows that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene have better binding affinities with Mpro than Remdesivir. Molecular dynamics simulation in vitro and in vivo investigation is required to support this study.

Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes.

Protein properties and interactions have been widely investigated by using external labels. However, the micromolar sensitivity of the current dyes limits their applicability due to the high material consumption and assay cost. In response to this challenge, we synthesized a series of cyanine5 (Cy5) dye-based quencher molecules to develop an external dye technique to probe proteins at the nanomolar protein level in a high-throughput one-step assay format. Several families of Cy5 dye-based quenchers with ring and/or side-chain modifications were designed and synthesized by introducing organic small molecules or peptides. Our results showed that steric hindrance and electrostatic interactions are more important than hydrophobicity in the interaction between the luminescent negatively charged europium-chelate-labeled peptide (Eu-probe) and the quencher molecules. The presence of substituents on the quencher indolenine rings reduces their quenching property, whereas the increased positive charge on the indolenine side chain improved the interaction between the quenchers and the luminescent compound. The designed quencher structures entirely altered the dynamics of the Eu-probe (protein-probe) for studying protein stability and interactions, as we were able to reduce the quencher concentration 100-fold. Moreover, the new quencher molecules allowed us to conduct the experiments using neutral buffer conditions, known as the peptide-probe assay. These improvements enabled us to apply the method in a one-step format for nanomolar protein-ligand interaction and protein profiling studies instead of the previously developed two-step protocol. These improvements provide a faster and simpler method with lower material consumption.

Researching of resistance to etravirine in some HIV-1 low-level viremia strains by in-silico methods

Abstract Objectives Human immunodeficiency virus (HIV) is a significant infection that attacks immune system cells and integrates its genetic material into host cells. Left untreated, it leads to acquired immunodeficiency syndrome (AIDS). Antiretroviral therapy (ART) is used to control HIV infection. Etravirine (ETR) is an important non-nucleoside reverse transcriptase inhibitor (NNRTI) utilized in the treatment of HIV. Low-level viremia (LLW) is a serious clinical condition, and the underlying mechanisms remain incompletely understood. The aim of our study is to analyze and elucidate the resistance status of Lys104Gln, Lys102Gln, Lys101Arg-Lys104Arg, Ser191Phe, Ile94Leu-Lys104Arg, Lys104Glu-His235Leu, Ala98Ser and Val179Ile mutations using in-silico methods, which are identified as low-level viremic strains, because their resistance status to ETR is unknown. Methods Homology modeling was performed using the Swiss Model program. Molecular docking of ETR with the reverse transcriptase (RT) enzyme was conducted using the CB-Dock program developed by AutoDock Vina. Protein-ligand interaction analysis was carried out using the protein-ligand interaction profiler (PLIP). Results A98S and V179I mutations altered the physicochemical properties of the region, resulting in changes to the conformational structure of the NNRTI hydrophobic pocket compared to the wild-type and consequently decreased docking scores. Conclusions Based on the evaluation of literature data and in-silico analyses, it is believed that A98S and V179I mutations may alter the conformational structure of the hydrophobic pocket where ETR binds, potentially resulting in low-level resistance against ETR.

Phenothiazine-based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi.

Phenothiazine derivatives can unselectively inhibit the trypanothione-dependent antioxidant system enzyme trypanothione reductase (TR). A virtual screening of 2163 phenothiazine derivatives from the ZINC15 and PubChem databases docked on the active site of T. cruzi TR showed that 285 compounds have higher affinity than the natural ligand trypanothione disulfide. 244 compounds showed higher affinity toward the parasite's enzyme than to its human homolog glutathione reductase. Protein-ligand interaction profiling predicted that the main interactions for the top scored compounds were with residues important for trypanothione disulfide binding: Phe396, Pro398, Leu399, His461, Glu466, and Glu467, particularly His461, which participates in catalysis. Two compounds with the desired profiles, ZINC1033681 (Zn_C687) and ZINC10213096 (Zn_C216), decreased parasite growth by 20 % and 50 %, respectively. They behaved as mixed-type inhibitors of recombinant TR, with Ki values of 59 and 47 μM, respectively. This study provides a further understanding of the potential of phenothiazine derivatives as TR inhibitors.

Bioinformatics analysis of wild-type ParC and S79F, S79Y mutations in Streptococcus pneumoniae.

S79Y and S79F mutations in ParC at the fluoroquinolone binding site confer resistance to quinolones in Streptococcus pneumoniae. The aim of this study was to perform bioinformatics analysis of wild-type and mutant ParC identified in S. pneumoniae strains. Homology models were created with Swiss Model, and the UCSF Chimera was used for the analysis and evaluation of the models. Molecular docking studies and protein-ligand interaction analysis were performed using CB-Dock developed by AutoDock Vina and Protein Ligand Interaction Profiler (PLIP), respectively. According to the homology modeling results, changes were observed in the physicochemical properties. Both mutant types showed a decrease in hydrophobicity (S79F: 2.0, S79Y: 0.5 - Kyte-Doolittle) and an increase in regional volume (S79F: 95 Å3, S79Y: 100 Å3). The docking scores for the wild-type, S79F, and S79Y types were 6.3, 4.9, and 5.0, respectively. The decrease in docking scores indicates weaker binding in the mutant types. The results of the PLIP analysis indicate that new bonds were formed, and the bond types changed in both mutant types, while some bonds disappeared. It is believed that the change in physicochemical properties caused by the mutation altered the conformation of the quinolone binding region and the bond types, numbers, and proximities of the amino acids involved in the interaction with the active substance. The results obtained from the modeling performed in this study with visualization and analysis of possible conformational, hydrophobic, and volumetric changes of only ParC mutations provided data and literature support to elucidate the mechanism. The molecular docking and PLIP results obtained in this study support both the homology modeling results and the fact that S79F and S79Y have been shown to be resistant in the literature.