cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Synthesis, molecular docking of new amide thiazolidine derived from isoniazid and studying their biological activity against cancer cells
Creators: name: Majed, Ahmed A.
name: AL-Duhaidahawi, Dunya
name: Omran, Haider A.
name: Abbas, Sabah
name: Abid, Dawood S.
name: Hmood, Ahmed Y.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: BCL2, an antiapoptotic protein, is overexpressed in many cancers, making it a good cancer treatment target. In 30 years, few BCL2 targeting agents have shown clinical significance. This work designed new amide thiazolidine derived from isoniazid targeting BCL2 and tested them on cancer cell lines, for binding affinities, the novel candidates were docked to the BCL2 target receptor. IC50 of compound A8 46.67 ± 0.9 and 57.14 ± 0.88 μg/ml against PC3 and HEPG2 respectively with docking score −7.6 Kcal/mol with 6GL8 make it the best compound in this series. Melting point, FT-IR, elemental microanalysis (CHN), 1HNMR, and 13CNMR confirmed chemical structures. Communicated by Ramaswamy H. Sarma
Molecular docking, simulations of animal peptides against the envelope protein of Dengue virus
Creators: name: Guntamadugu, Reena
name: Ramakrishnan, Ranjani
name: Darala, Gowtham
name: Kothandan, Sangeetha
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus (HIV), influenza virus and hepatitis C virus. So far, no peptide drug has been approved for antiviral treatment against Dengue virus, and many are under clinical trials. Therefore, developing a reasonable peptide against the Dengue virus Envelope protein structure will be a successful strategy for treating Dengue. Hence, we investigated protein-protein docking interactions between 215 peptides retrieved from the AVP database against the envelope protein using Cluspro and HADDOCK followed by the evaluation of their allegenicity, toxicity and physicochemical characteristics investigation. Further validation of the protein–peptide complexes was performed with Molecular dynamics simulations and Molecular Mechanics Poisson–Boltzmann surface area (MMPBSA) analysis on the hit inhibitors. This study revealed that Indolicidin (−75.026 ± 1.54 KJ/mol) and Human Neutrophil peptide-1 (−71.6551 ± 2.112 KJ/mol) shows higher negative ΔG binding implicating their relative stabilization in the protein–peptide interactions during 100 ns of dynamic simulations. Also, both the peptides exhibited desirable physicochemical properties and were nonallergenic. Hence, we further aim to test these peptides by in vitro and in vivo studies to confirm their efficacy against Dengue virus. Communicated by Ramaswamy H. Sarma
A highly selective and sensitive fluorescence probe for dopamine determination based on a bisquinoline-substituted calix[4]arene carboxylic acid derivative
Creators: name: Sayin, Serkan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences

description: Dopamine (DA) at normal levels in the human body exhibits a high potential for maintaining a proper neuron network. However, their abnormalities in humans can bring out aggressive disorders such as Schizophrenia, hypertension, Tourette’s syndrome, Alzheimer’s disease, bipolar depression, Parkinson’s disease, drug addiction and attention-deficit hyperactivity diseases. Hence, in this study, a bis-quinoline-substituted calix[4] arene carboxylic acid derivative (Quin-Calix-CO2H) at cone conformation was developed as an effective fluorescent sensor for the detection of a catecholamine neurotransmitter (dopamine). The structure of Quin-Calix-CO2H was confirmed using 1H-NMR, 13C-NMR, ESI-MS and elemental analysis techniques. The calixarene-based fluorescent sensor (Quin-Calix-CO2H) has shown fluorescence emission at 404 nm under the excitation of 270 nm. Further, biomolecules binding property of Quin-Calix-CO2H against various biomolecules such as L-cysteine (L-Cys), α-D-glucose (D-Glu), (+)-sodium-L-ascorbate (SAA), urea (UR), L-alanine (L-Ala) and dopamine (DA) exhibited that the fluorescent sensor enables selectively and sensitively detection for DA with a remarkable affinity. The probe Quin-Calix-CO2H has shown fluorescence quenching towards DA concentration ranging from 0 to 4.0 µM with a very low limit of detection (LOD) of 88.5 nmol L−1. In addition, the binding constant and stoichiometry as well as the mechanism of quenching have been also determined from the fluorescence data. Communicated by Ramaswamy H. Sarma
Design, characterization and green synthesis of samarium-decorated magnetic Fe3O4 nanoparticles: cytotoxicity and DNA binding studies
Creators: name: Fazlollahi, Masoume
name: Divsalar, Adeleh
name: Masteri-Farahani, Majid
name: Sahebi, Unes
name: Rasouli, Milad
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: In this study, we have successfully synthesized magnetic Fe3O4 nanoparticles adorned with samarium (Sm-MNPs) utilizing ginger extract for the very first time. Furthermore, a comprehensive characterization of the nanoparticles along with an exploration of their physicochemical attributes was conducted. The biological functionalities of the synthesized nanoparticles were investigated through a thorough examination of their interaction with calf thymus DNA (ctDNA) using diverse spectroscopic techniques encompassing ultraviolet–visible (UV–Vis) and fluorescence spectroscopy at varying temperatures. Subsequently, we evaluated the cytotoxicity of the magnetic nanoparticles using a colorectal cancer cell model (HCT116 cells) and a tetrazolium colorimetric assay (MTT assay). The characterization of the ginger extract-coated magnetic nanoparticles (ginger-Sm-MNPs) revealed their superparamagnetic nature, nanocrystalline structure, spherical morphology, hydrodynamic size of 155 nm, and uniform distribution. The outcomes from UV–Vis and fluorescence spectroscopy affirmed the binding of ginger-Sm-MNPs with ctDNA. Additionally, the MTT assay demonstrated that the cytotoxicity of ginger-Sm-MNPs surpassed that of both magnetite nanoparticles and ginger extract. Notably, the inhibitory concentrations (IC50) for the green-synthesized nanoparticles after 24 and 48 h of incubation were determined as 198.1 and 135.8 μg/mL, respectively. In conclusion, our study findings suggest the potential utility of ginger-Sm-MNPs as a promising candidate for various biomedical applications. Communicated by Ramaswamy H. Sarma
A novel approach to design a multiepitope peptide as a vaccine candidate for Bordetella pertussis
Creators: name: Basmenj, Esmaeil Roohparvar
name: Izadkhah, Habib
name: Hosseinpour, Maryam
name: Saburi, Ehsan
name: Ezabadi, Marjan Abhaji
name: Alipourfard, Iraj
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Bordetella pertussis is a very contagious pathogen in humans, causing pertussis disease. Pertussis is one of the 10 leading causes of death due to infectious diseases, especially among infants and children. Antibiotic-resistant strains have recently emerged in this bacterium, and despite the high vaccination coverage, the prevalence of this disease has been increasing recently in both developed and developing countries. The objective of this study is to introduce a novel in silico vaccine candidate aimed at countering B. pertussis effectively. Differing from other comparable studies, this research employed a computational screening methodology to assess the genome of ‘Bordetella pertussis 18323.’ The purpose was to identify an innovative antigen for the development of a vaccine against B. pertussis. Notably, our investigation introduces an innovative antigen distinguished by its elevated immunogenicity score. Importantly, this antigen lacks toxicity and allergenicity, making it recognizable to the immune system and thus capable of inducing a robust immune response. In the subsequent phase, our antigen was utilized to identify potential epitopes conducive to the construction of a B. pertussis vaccine. These epitopes, alongside linkers, his-tag and adjuvants, were amalgamated to form the vaccine candidate. Subsequently, a comprehensive evaluation of the vaccine was conducted, encompassing various computational tests such as secondary and tertiary structure analysis, physicochemical examination, and structural analysis involving docking and molecular dynamics simulations. Importantly, our vaccine successfully passed all in silico tests. Communicated by Ramaswamy H. Sarma
Synthesis, spectrophotometric, pharmacology and theoretical investigation of a new electron transfer complex of 8-hydroxyquinoline with oxalic acid in different polar solvents
Creators: name: Mustafa, Syed Khalid
name: Jame, Rasha
name: Aljohani, Meshari M. H.
name: Omer, Noha
name: Alessa, Ali Hamzah
name: Al-Anazi, Menier
name: Alotaibi, Fatimah A.
name: Sk, Matiur
name: Islam, Maidul
name: Shakya, Sonam
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Space Science
Physical Sciences not elsewhere classified
Chemical Sciences not elsewhere classified

description: Preparation, characterization, and investigation of a novel organic charge transfer (CT) complex were carried out, with a focus on exploring its antibacterial and antifungal characteristics. Theoretical analysis backs up the experimental findings. CT complex formed was synthesized between 8-hydroxyquinoline (8HQ) and oxalic acid (OA) at RT (room temperature). Different analyses were used to describe the CT complex, including 1H-NMR, FTIR, TGA/DTA, and UV-vis spectra (in different solvents). These indicate that the CT interaction is linked to proton transfer from OA to 8HQ and the subsequent development of ‘N+__H…O-“ type bonding. On the basis of wave number, the CT complex and reactants are distinguished in FTIR spectra. By using Thermo gravimetric Analysis/Differential Thermal Analysis (TGA/DTA) tests, the thermal stability of complicated and thorough corrosion was examined. Through UV-visible spectroscopy, physical characteristics like ECT (interaction energy), RN (resonance energy), ID (ionization potential), f (oscillator strength) and ΔG (free energy) were calculated. The εCT (molar extinction coefficient), the KCT (formation constant), and additional physical properties of this complex were calculated by the Benesi-Hildebrand equation in order to determine its 1:1 stoichiometry. The biological properties are also supported by theoretical study. The protein, Human Serum Albumin (HSA), is observed to bind with CT complex, as shown by molecular docking and the observed binding energy value is −167.04 kcal/mol. Molecular dynamics (MD) simulation 100 ns run was used to refine docking results and binding free energy was calculated using MM-PBSA. This study introduces a novel CT complex, offering fresh perspectives on molecular interactions. Communicated by Ramaswamy H. Sarma
Oxazoline/amide derivatives against M. tuberculosis: experimental, biological and computational investigations
Creators: name: Bajpai, Priyanka
name: Singh, Ankit Kumar
name: Kandagalla, Shivanada
name: Chandra, Phool
name: Sah, Vimlendu Kumar
name: Kumar, Pradeep
name: Grishina, Maria
name: Verma, Om Prakash
name: Pathak, Prateek
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: Tuberculosis (TB) is a treatable contagious disease that continuously kills approximately 2 million people yearly. Different oxazoline/amide derivatives were synthesized, and their anti-tuberculosis activity was performed against different strains of Mtb. This study designed the anti-Mtb compounds based on amide and oxazoline, two different structural moieties. The compounds were further synthesized and characterized by spectral techniques. Their anti-Tb activity was evaluated against strain (M. tuberculosis: H37Rv). Selectivity and binding affinity of all synthesized compounds (2a–2e, 3a–3e) against PanK in Mtb were investigated through molecular docking. Molecular dynamics simulation studies for the promising compounds 2d and 3e were performed for 100 ns. The stability of these complexes was assessed by calculating the root mean square deviation, solvent-accessible surface area, and gyration radius relative to their parent structures. Additionally, free energy of binding calculations were performed. Among all synthesized compounds, 2d and 3e had comparable antitubercular activity against standard drug, validated by their computational and biological study.
Synthesis and computational insights of flavone derivatives as potential estrogen receptor alpha (ER-α) antagonist
Creators: name: Fegade, Bharti. S.
name: Jadhav, Shailaja. B.
name: Chaudhari, Somdatta Y.
name: Tandale, Deepak T.
name: Uttekar, Pravin Shantaram
name: Tabrez, Shams
name: Khan, Mohd Shahnawaz
name: Zaidi, Syed Kashif
name: Mukerjee, Nobendu
name: Ghosh, Arabinda
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Cell Biology
Pharmacology
Chemical Sciences not elsewhere classified
Cancer

description: Hormone-related breast cancer is mostly caused by interactions with estrogen receptor alpha (ER-α), which functions as a transcription factor to control the transcription of numerous genes. Flavones are considered a good substrate for the estrogen receptor. Substitution of the N-heterocyclic ring on the flavon structure may potentiate its anticancer effect. A series of flavon derivatives with an N-heteroaryl ring at the 4' position of the B ring of flavon were designed, prepared and evaluated for in vitro breast cancer activity. Binding interactions of the PzFL, PzF, PiFL, PiF and IFL compounds with ER-α were studied by molecular docking. Molecular dynamics simulation studies were carried out in order to determine the stability and convergence of protein–ligand complexes. The compounds were produced by cyclizing chalcones and chalcones were produced by Claisen–Schmidt condensation of substituted aldehydes and 2-hydroxy acetophenone. Breast cancer activity was evaluated by the MTT assay on MCF-7 cell lines. Also, compounds were studied for their estrogen receptor binding potential on the same cell lines. Molecular docking of compounds showed a good docking score. The molecular dynamics of these compounds expressed stable root mean square deviation, stable radius of gyration and low binding energy, suggesting that ligand bound to protein is quite stable in the complex. MTT assay on MCF-7 cell lines reported PzF and IFL were the most active compounds with lower IC50 values. ER-α binding assay of these compounds revealed the presence of binding interactions with receptors. This study offers a viable reference point for the design of flavon-incorporated N-heterocyclic ring derivatives as breast cancer compounds. Communicated by Ramaswamy H. Sarma
In silico approaches for the identification of novel ULK1 inhibitors: pharmacophore model, molecular docking and molecular dynamics simulations
Creators: name: Yang, Yifan
name: Ji, Cuicui
name: Zhong, Qidi
name: Yan, Hong
name: Wang, Juan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: The serine/threonine kinase unc-51-like autophagy activating kinase 1 (ULK1) has been regarded as an attractive target for tumor therapy. In this study, in silico approaches, such as the pharmacophore-based virtual screening strategy, molecular docking and molecular dynamics (MD) simulations, were applied to develop novel potential ULK1 inhibitors. The pharmacophore models based on known aminopyrimidine ULK1 inhibitors were constructed to screen the dataset of 1.68 million compounds, which were obtained via screening the 2.30 million compounds in ChEMBL database by Lipinski’s rule of five. Seven novel compounds and 1 known ULK1 inhibitor stand out for the strong virtual biological activity by molecular docking, cluster analysis, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculation and Absorption Distribution Metabolism Excretion Toxicity (ADMET) prediction. Their results of MD included principal component analysis (PCA) and Free Energy Landscapes surface (FELs) indicated that the protein–ligand complex was stable in simulated trajectories of 100 ns. The binding free energy (BFE) calculations showed that a total of 6 novel compounds (CL130, CL834, CL961, CL966, CL163 and CL329) with the stable binding state and stronger BFE (−61.17 to −37.01 kcal/mol) than that of original ligand 3RF (−36.66 kcal/mol). With reference to the ULK1 inhibition of 3RF (IC50 = 160 nM), it can be inferred that these compounds could be used as a new type of potential ULK1 inhibitors and be worthy of further investigation for tumor treatments. Communicated by Ramaswamy H. Sarma
Spectroscopy and dynamics of beta-lactoglobulin complexed with rifampicin
Creators: name: Sharma, Sudhanshu
name: Takkella, Dineshbabu
name: Vishwakarma, Jyoti
name: Gavvala, Krishna
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer

description: In this paper, we report the binding interaction of milk protein, beta-lactoglobulin (BLG), with an antibiotic against tuberculosis, rifampicin (RIF). BLG intrinsic fluorescence from tryptophan (Trp) amino acids was monitored to understand protein-drug interactions. Binding parameters and stoichiometry were estimated with the help of fluorescence spectral changes. Synchronous fluorescence spectroscopy was employed to exclusively monitor the Trp and Tyrosine (Tyr) environment in the presence of RIF. With the help of steady state fluorescence at different temperatures supported by time-resolved fluorescence, we confirmed that the protein forms a static complex with RIF. Thermodynamic parameters, ΔH and ΔS values, showed the involvement of hydrophobic forces between the RIF and BLG. Competitive displacement assay with ANS confirmed the BLG calyx as the binding site for RIF. Energy transfer mechanism from Trp to RIF was attributed to the fluorescence changes in protein upon complexation. The Förster resonance energy transfer (FRET) was used to find distance, energy transfer efficiency and rate of energy transfer between donor (BLG) and acceptor (RIF). Fourier-transform infrared (FTIR) spectroscopy was utilized for estimating changes in the secondary structure of BLG induced by RIF. Molecular docking was used to visualise the binding location of RIF on BLG. Molecular dynamics (MD) simulation studies showed a consistent binding interactions between BLG and RIF during the 100 ns simulation period and this well supported the increased beta sheet content in FTIR. Overall our results establish the potential of intrinsic fluorescence of BLG in combination with biophysical tools to rationalize drug-protein interactions. Communicated by Ramaswamy H. Sarma Characteristic binding analysis of rifampicin with beta-lactoglobulin by spectroscopy, molecular docking and molecular dynamics simulation
Screening of potential inhibitors of Leishmania major N-myristoyltransferase from Azadirachta indica phytochemicals for leishmaniasis drug discovery by molecular docking, molecular dynamics simulation and density functional theory methods
Creators: name: Tewari, Disha
name: Rawat, Kalpana
name: Bisht, Amisha
name: Almoyad, Mohammad Ali Abdullah
name: Wahab, Shadma
name: Chandra, Subhash
name: Pande, Veena
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Leishmaniasis is one of the most neglected parasitic diseases worldwide. The toxicity of current drugs used for its treatment is a major obstacle to their effectiveness, necessitating the discovery and development of new therapeutic agents for better disease control. In Leishmania parasites, N-Myristoyltransferase (NMT) has been identified as a promising target for drug development. Thus, exploring well-known medicinal plants such as Azadirachta indica and their phytochemicals can offer a diverse range of treatment options, potentially leading to disease prevention and control. To assess the therapeutic potential of these compounds, their ADMET prediction and drug-likeness properties were analyzed. The top 4 compounds were selected which had better and significantly low binding energy than the reference molecule QMI. Based on the binding energy score of the top compounds, the results show that Isonimocinolide has the highest binding affinity (-9.8 kcal/mol). In addition, a 100 ns MD simulation of the four best compounds showed that Isonimocinolide and Nimbolide have good stability with LmNMT. These compounds were then subjected to MMPBSA (last 30 ns) calculation to analyze protein-ligand stability and dynamic behavior. Nimbolide and Meldenin showed lowest binding free energy i.e. −84.301 kJ/mol and −91.937 kJ/mol respectively. DFT was employed to calculate the HOMO-LUMO energy gap, global reactivity parameters, and molecular electrostatic potential of all hit molecules. The promising results obtained from MD simulations and MMPBSA analyses provide compelling evidence for the potential use of these compounds in future drug development efforts for the treatment of leishmaniasis. Communicated by Ramaswamy H. Sarma
Structure-based virtual screening and molecular docking approaches to identify potential inhibitors against KIF2C to combat glioma
Creators: name: Hussein, Deema
name: Saka, Mohamad
name: Baeesa, Saleh
name: Bangash, Mohammed
name: Alghamdi, Fahad
name: Al Zughaibi, Torki
name: AlAjmi, Mohamed F.
name: Haque, Shafiul
name: Rehman, Md Tabish
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Glioma, a kind of malignant brain tumor, is extremely lethal. Kinesin family member 2C (KIF2C) was found to have an aberrant expression in several cancer types, including lung cancer and glioma. KIF2C may therefore be a useful therapeutic target for the treatment of glioma. In the current study, new drug candidates that may function as KIF2C enzyme inhibitors were discovered. MTi OpenScreen was used to carry out the structure-based virtual screening of an inbuilt drug library containing 150,000 compounds. These compounds belong to different classes, such as natural product-based compounds (NP-lib), purchasable approved drugs (Drugs-lib), and food constituents compound collection (FOOD-lib). Based on their binding affinities, a total of 84 compounds were further pushed to calculate ADMET properties. The compounds (16) meeting the ADMET cutoff ranges were then further docked to the receptor to find their plausible binding modes using the Glide tool’s standard precision (SP) technique. The docking results were examined using the Glide gscore, and the best binding compounds (Rimacalib and Sarizotan) were chosen to test their stability with KIF2C protein through molecular dynamics (MD) simulation. Similarly, Principal Component Analysis and cross-correlation matrix were also examined. The MM/GBSA binding free energies showed a considerable energy contribution in the binding of hits with the KIF2C. Collectively, these findings strongly suggest the potential of the lead compounds to inhibit the biological function of KIF2C, emphasizing the need for further investigation in this area. Communicated by Ramaswamy H. Sarma
Developing reliable classification of dual IDO1/TDO inhibitors using data fusion and majority voting
Creators: name: Ghaemi, Zahra
name: Asadollahi-Baboli, M.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Hematology

description: Indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO) are promising dual-targeting inhibitors in cancer and neurodegenerative diseases treatment. Data fusion of receptor-based and ligand-based information of dual IDO1/TDO inhibitors were employed for active/inactive classification performance. A reliable decision making procedure was used here to identify active/inactive dual IDO1/TDO inhibitors using majority voting method and pools of individual classifications instead of individual models. All classification models were validated using prediction set, cross-validation and y-scrambling tests. The classification outcomes indicate that the sensitivity, specificity, precision, accuracy, G-mean and F1 score values increases up to ∼90% using data fusion and majority voting method. Compare to individual classification models with a single prediction point, the majority voting method has more reliable results due to the integration of the pool of individual classification models. This classification strategy may lead to more reliable identification of active/inactive dual-targeting inhibitors in cancer immunotherapy. Communicated by Ramaswamy H. Sarma
Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori
Creators: name: Kashyap, Dharmendra
name: Koirala, Suman
name: Roy, Rajarshi
name: Saini, Vaishali
name: Varshney, Nidhi
name: Bagde, Pranit Hemant
name: Samanta, Sunanda
name: Kar, Parimal
name: Jha, Hem Chandra
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Cancer is a condition in which a few of the body’s cells grow beyond its control and spread to other outward regions. Globally, gastric cancer (GC) is third most common cause of cancer-related mortality and the fourth most common kind of cancer. Persistent infection of VacA-positive Helicobacter pylori (H. pylori) modulates cellular physiology and leads to GC. About ∼70% of H. pylori are positive for vacuolating cytotoxin-A (VacA), and it infects ∼80–90% of world populations. Herein, for first time, we repurposed FDA-approved gram-negative antibiotics, which are feasible alternatives to existing regimens and may be used in combinatorial treatment against VacA-positive H. pylori. Out of 110 FDA-approved antibiotics, we retrieved 92 structures, which were screened against the VacA protein. Moreover, we determined that the top eight hit antibiotics viz; cefpiramide, cefiderocol, eravacycline, doxycycline, ceftriaxone, enoxacin, tedizolid, and cefamandole show binding free energies of −9.1, −8.9, −8.1, −8.0, −7.9, −7.8, −7.8 and −7.8 Kcal/mol, respectively, with VacA protein. Finally, we performed 100 ns duplicate MD simulations on the top eight selected antibiotics showing strong VacA binding. Subsequently, five antibiotics, including cefiderocol, cefpiramide, doxycycline, enoxacin, and tedizolid show stable ligand protein distance and good binding affinity revealed by the MM-PBSA scheme. Among the five antibiotics cefiderocol act as the most potent inhibitor (-28.33 kcal/mol). Furthermore, we also identified the hotspot residue like Asn-506, Tyr-529, and Phe-483 which control the interaction. Concisely, we identified antibiotics that can be repurposed against VacA of H. pylori and explored their molecular mechanism of interaction with VacA. Communicated by Ramaswamy H. Sarma
A computational study on the mercaptopurine drug interaction with aluminum nitride nanostructures: analyzed by Marcus theory of electron-transfer
Creators: name: Kzar, Mazin Hadi
name: Al-dolaimy, F.
name: Batoo, Khalid Mujasam
name: Hussain, Sajjad
name: Ghnim, Zahraa Sabah
name: Haroon, Noor Hanoon
name: Alawadi, Ahmed Hussien
name: Alsalamy, Ali
name: Soleymanabadi, Hamed
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Hematology
subject: Plant Biology
subject: FOS: Biological sciences

description: We analyzed the mercaptopurine adsorption on AlN nanostructures consisting of zero-dimensional nanoclusters, one-dimensional nanotubes, and two-dimensional nanosheets using calculations based on density functional theory (DFT). The adsorption energy, energy band gap, fluctuations in the energy band gap, charge transfers, and types of interactions that take place after mercaptopurine is adsorbed on the AlN nanostructures have all been calculated using DFT. The results show MP adsorption energies on AlN nanoparticles are −4.22, −5.95, and −8.70 eV. In this situation, MP molecules have been drawn to the surface due to the higher adsorption energies available on the AlN nanosheet (a process known as chemisorption). The Atoms in Molecules inquiry was conducted to learn more about and better comprehend the binding properties of the investigated AlN nanostructures utilizing mercaptopurine. Our findings indicate the mercaptopurine/AlN nanosheet bonding’s electrostatic properties. Additionally, the electrical conductivity of the AlN nanostructures increases whenever mercaptopurine is adsorbed on them. This shows that the AlN nanoparticles might function as chemical sensors and offer an electrical signal in mercaptopurine. The following is the order of sensitivity: AlN nanosheet > AlN nanotube > AlN nanocluster. The outcomes indicate that the nanosheet has the most potential for mercaptopurine detection among the AlN nanostructures. Communicated by Ramaswamy H. Sarma
Derivates of 1,6-dihyadroazaazulenes as inhibitors of tyrosine kinases BCR-ABL1 wild type and mutant T315I: a molecular dynamics approach
Creators: name: de Jesus Solís-Hernández, Manuel
name: Palomares-Báez, Juan Pedro
name: Herrera-Bucio, Rafael
name: Chacón-García, Luis
name: Navarro-Santos, Pedro
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Hematology

description: The protein tyrosine kinase (PTK) produced by the BCR-ABL1 gene has generated significant interest in the development of inhibitors since the presence of punctual mutations causes resistance to currently approved drugs, mainly the T315I mutation has been the most difficult to address. In this work, derivatives of 1,6-dihydroazaazulenes are studied as possible inhibitors of this PTK in its wild form and the mutant T315I. The recognition of the ligands was explored through molecular docking, and the stability of the complexes and their evolution over time was studied using molecular dynamics (MD) simulations. Our results show that complexes are energetically stable and reside on the ATP binding site in all cases during the MD experiments. Interestingly, a few of our proposed ligands presented greater affinity for T315I, finding more favorable binding free energies (ΔG) than the reference drug axitinib. Furthermore, they may act as inhibitors for both isoforms. Our findings are promising because mutation of T315I does not prevent ligand recognition, as detailed in this work, which is very important to conduct further experimental research. Communicated by Ramaswamy H. Sarma
In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites
Creators: name: de Oliveira, Denilson Ferreira
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson–Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to −20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections. Communicated by Ramaswamy H. Sarma
Molecular docking, molecular dynamics and binding free energy based identification of novel potential multitarget inhibitors of Nipah virus
Creators: name: Sinha, Prashasti
name: Yadav, Anil Kumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Nipah virus (NiV) is one of the most common viral diseases affecting the brain and nervous system of the body. To date, there is no significant antiviral drug specifically designed to inhibit NiV. In the last ten years, there has been a significant increase in interest in multitarget drug development. Therefore, the reported work focuses on designing a multitarget inhibitor for NiV. Among the twelve designed compounds, five exhibited better drug-likeness and ADMET properties, hence being selected for further analysis. In a molecular docking study, these compounds possessed better binding affinity as compared to Favipiravir. The RMSD of these compounds was ≤2Å and the number of H-bonds signified the better stability of the complexes formed. The ΔGbind of C4, C6 and C7 was found to be comparatively higher than the other screened compounds, revealing their greater ability to bind efficiently with NiV-G, NiV-F and NiV-N receptors, respectively. Therefore, based on molecular docking, molecular dynamics, and MM/PBSA analysis, these compounds can act as potential inhibitors of multitargets of NiV. Communicated by Ramaswamy H. Sarma
Natural pentacyclic triterpenoid as allosteric modulators of human 5-lipoxygenase with potential anti-inflammatory activity
Creators: name: Mascayano, Carolina
name: Muñoz-Osses, Michelle
name: Navarrete, Elizabeth
name: Torres, Paulina
name: Torres-González, Simón
name: Morales, Pilar
name: Huidobro-Toro, Juan Pablo
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Hematology

description: This study explored new methods to inhibit human 5-lipoxygenase (5-hLOX) by analyzing natural terpenes that share structural similarities with acetoxyboswellic acid (AKBA). Enzymatic assays were used to evaluate the terpene’s ability to inhibit the enzyme, potentially providing anti-inflammatory benefits. Our research focused on how certain types of triterpenes can inhibit 5-hLOX allosterically via a newly discovered allosteric site identified by enzyme crystallization. To determine whether natural boswellic acid analogs mimicked the allosteric known inhibitor AKBA, we combined 5-hLOX inhibition with in silico modeling. Our research has discovered that certain amino acids, specifically Arg 138, Arg 101, Arg 68, and Gln129, located in the allosteric 5-hLOX pocket, play a critical role in stabilizing glycyrrhetinic isomers. These amino acids form hydrogen bonds and hydrophobic interactions that contribute to the inhibitory potency of boswellic acid derivatives. We have found that α and β glycyrrhetinic acid isomers, carbenoxolone, and to a minor extent, prednisolone, have a potent inhibitory effect against 5-hLOX with IC50 values of 8.64, 3.94, 52.98, and 291.20 µM, respectively. These values are in line with our calculated in silico allosteric site binding energy estimations. In contrast, other steroidal or non-steroidal anti-inflammatory agents exhibited inhibitory potencies larger than 500 μM. However, the specific pharmacodynamic mechanisms are currently unknown. We propose that AKBA analogs may lead to the future development of novel anti-inflammatory agents. Communicated by Ramaswamy H. Sarma
Structural impairment of p53 C-terminal due to the effect of phosphorylation and acetylation: a study on the interdependence of PTM
Creators: name: Ghosh, Anamika
name: Ganguly, Debabani
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Computational Biology

description: The C-terminal of tumor suppressor protein p53 is intrinsically disordered while unbound. This particular segment often shows structural plasticity when bound to other binding partners. The disordered component undergoes a disordered to ordered transition upon recognition. Post-translational modifications (PTMs), namely phosphorylation and acetylation, significantly alter the structural motifs of the segment. Among the various types of PTMs, phosphorylation, and acetylation of p53 at both N- and C- terminals lead to stabilization and activation. It has been noted experimentally that phosphorylation often regulates (enhances or reduces) the acetylation at specific sites. The phosphorylation of Thr377 and Ser378 reduces the acetylation of Lys373 and Lys382. Mutations of Thr377 and Ser378 to neutral Ala enhance and phospho mimic Asp reduce the acetylation of Lys373 and Lys382. Simulations of several single-point and pair-wise mutated systems have been generated to compare how the presence or absence of phosphorylation favors or disfavors the acetylation by thermodynamic and conformational analysis. We are using implicit solvent replica exchange molecular dynamics simulations to get 200 ns well-converged conformational ensembles of each system. Different sets of systems having both single and double PTMs are simulated. The results admit the appreciable change in the secondary structural level upon specific PTM. Also, the residual structure of the unbound p53 with single-point PTM varies significantly with pair-wise modifications. These observations further shed light on the relationship between the interdependencies of the specific PTM sites and the secondary structural levels. Communicated by Ramaswamy H. Sarma
Psalidothrips taylori Mound & Walker 1986
Creators: name: Wang, Jun
name: Mound, Laurence A.
name: Tree, Desley J.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Thysanoptera
Phlaeothripidae
Psalidothrips
Psalidothrips taylori

description: Psalidothrips taylori Mound & Walker
(Fig. 29)
Psalidothrips taylori Mound & Walker, 1986: 76
In structure, this species is closely similar to cecryphalus described above, and shares with that species the presence of long median setae on several tergites, particularly VI–VIII. However, it lacks polygonal reticulation on the head between the eyes, the male has no fore tarsal tooth and the pore plate on sternite VIII of males is incomplete medially (Fig. 29). The two species are equally widespread across Australia, and at a few localities they have been taken together. The holotype of taylori was collected from litter on Black Mountain, Canberra, but specimens have been seen from leaf litter at various localities in eastern New South Wales, including Norfolk Island, also southeastern Queensland, South Australia including Kangaroo Island, Tasmania and southwestern Western Australia. This species has also been taken in both North and South Islands of New Zealand.
description: Published as part of Wang, Jun, Mound, Laurence A. & Tree, Desley J., 2019, Leaf-litter thrips of the genus Psalidothrips (Thysanoptera, Phlaeothripidae) from Australia, with fifteen new species, pp. 53-73 in Zootaxa 4686 (1) on page 65, DOI: 10.11646/zootaxa.4686.1.2, http://zenodo.org/record/3484342
Martinella
Creators: name: Pace, Marcelo R.
name: Marcati, Carmen R.
name: Lohmann, Lúcia G.
name: Angyalossy, Veronica
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Lamiales
Bignoniaceae
Martinella

description: III. Martinella clade
TAXONOMIC INFORMATION. — This clade contains a single genus, Martinella, with four phloem wedges in transversal section.
TOTAL NUMBER OF SPECIES IN THIS CLADE. — Five species (Kataoka & Lohmann 2021).
STUDIED SPECIES. — One species, Martinella obovata (Kunth) Bureau & K.Schum.
Regular phloem
Thin fiber bands (Fig. 8G), assemblages absent.
Variant phloem
General configuration. Non-fibrous (Fig.8H),with approximately 10 rows of sieve tubes and phloem parenchyma cells between fiber bands. The axial elements are arranged radially (Fig. 8I).
Sieve tube elements. As seen in transverse section, each sieve element is associated with one companion cell, sometimes two, one at each corner of the sieve element. Sieve tubes occur in radial multiples of 2-3 cells (Fig. 8I).
Axial parenchyma. The phloem parenchyma forms a matrix where sieve elements and fiber bands are embedded (Fig. 8I). Sometimes radial rows of phloem parenchyma are also detected between sieve elements.
Fibers. Fiber bands are present,composed by2-3rows of cells(Fig.8I).
Rays. The limiting rays are lignified only to the xylem side.
Crystals. Not observed.
Periderm
Not observed.
description: Published as part of Pace, Marcelo R., Marcati, Carmen R., Lohmann, Lúcia G. & Angyalossy, Veronica, 2023, Bark anatomy of lianescent Bignoniaceae: a generic synopsis, pp. 167-210 in Adansonia (3) (3) 45 (12) on page 182, DOI: 10.5252/adansonia2023v45a12, http://zenodo.org/record/8006364
Campsis radicans
Creators: name: Pace, Marcelo R.
name: Marcati, Carmen R.
name: Lohmann, Lúcia G.
name: Angyalossy, Veronica
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Lamiales
Bignoniaceae
Campsis
Campsis radicans

description: Campsis radicans
Non-stratified phloem (Fig. 19A), marked by scattered fibers (Fig. 19 A-C). The conducting phloem has sieve tubes solitary or in multiples of 2-4 (Fig. 19C). One companion cell lying on the corner of the sieve tube (Fig. 19C). The sieve plates are simple in transverse walls, or with 2-4 sieve areas per sieve plate in a slightly inclined wall. The axial parenchyma constitutes the background tissue (Fig. 19B, C), with parenchyma strands with 3-4 cells. Rays straight (Fig. 19A), 2-3-seriate, heterocellular, with body of procumbent cells and two square to upright marginal cells, lacking dilatation (Fig.19A). Sclerenchyma composed of scattered fibers (Fig. 19A), either solitary (Fig. 19B, C) or in multiples of two, with an angular outline (Fig. 19B). Non-storied. Nonconducting phloem marked by empty sieve elements and companion cells, collapsed. Cell expansion is the main dilatation phenomenon recorded, with no further sclerification.
description: Published as part of Pace, Marcelo R., Marcati, Carmen R., Lohmann, Lúcia G. & Angyalossy, Veronica, 2023, Bark anatomy of lianescent Bignoniaceae: a generic synopsis, pp. 167-210 in Adansonia (3) (3) 45 (12) on page 199, DOI: 10.5252/adansonia2023v45a12, http://zenodo.org/record/8006364