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Artykuły w czasopismach na temat „Docking of ATP analogs”

Autor: Grafiati

Data publikacji: 29 marca 2025

Data aktualizacji: 31 lipca 2025

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1

K, Ravindrachary, Ramesh M, and Parthasarathy T. "Computational Study of Substituted 5[H] - Phenanthradin-6-Ones as Poly (ADP-Ribose) Polymerase-1 (PARP-1) Inhibitors by Analog and Structure Based Methods." INTERNATIONAL JOURNAL OF PHARMACEUTICAL AND CLINICAL RESEARCH 09, no. 07 (2017): 505–14. https://doi.org/10.25258/ijpcr.v9i7.8783.

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The poly (ADP-ribose) polymerase-1 (PARP-1) is an abundant nuclear protein involved in DNA repair and programmed cell death. Substituted 5(H) phenanthradin-6-one analogs were found to be potent PARP-1 inhibitors. Semiempirical methods were used to estimate various physicochemical parameters. The hydration energy (HE), ionization potential (IP), electrophilic index (ω) and partition coefficient ( LogP ) were resulted as independent variables for inhibitory activity of the analogs. The overall increase of HE, IP, and EI and overall decrease of LogP enhance the efficacy of inhibitory nature of th

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Choi, Kyudam, Yurim Lee, and Cheongwon Kim. "An In Silico Study for Expanding the Utility of Cannabidiol in Alzheimer’s Disease Therapeutic Development." International Journal of Molecular Sciences 24, no. 21 (2023): 16013. http://dx.doi.org/10.3390/ijms242116013.

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Cannabidiol (CBD), a major non-psychoactive component of the cannabis plant, has shown therapeutic potential in Alzheimer’s disease (AD). In this study, we identified potential CBD targets associated with AD using a drug-target binding affinity prediction model and generated CBD analogs using a genetic algorithm combined with a molecular docking system. As a result, we identified six targets associated with AD: Endothelial NOS (ENOS), Myeloperoxidase (MPO), Apolipoprotein E (APOE), Amyloid-beta precursor protein (APP), Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), an

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Elsawi, Ahmed E., Mai I. Shahin, Hager A. Elbendary, Tarfah Al-Warhi, Fatma E. Hassan, and Wagdy M. Eldehna. "1,2,4-Triazole-Tethered Indolinones as New Cancer-Fighting Small Molecules Targeting VEGFR-2: Synthesis, Biological Evaluations and Molecular Docking." Pharmaceuticals 17, no. 1 (2024): 81. http://dx.doi.org/10.3390/ph17010081.

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Targeting the VEGFR-2 signaling pathway is an inveterate approach toward combating pancreatic and hepatocellular cancers. Based on Sunitinib, the FDA-approved VEGFR-2 inhibitor, novel indolin-2-one-triazole hybrids were designed and synthesized as anti-hepatocellular and anti-pancreatic cancer agents with VEGFR-2 inhibitory activity. All the targeted compounds were assessed for their anti-cancer activity, revealing IC50 values extending from 0.17 to 4.29 µM for PANC1 and 0.58 to 4.49 µM for HepG2 cell lines. An extensive SAR study was conducted to explore the effect of different substituents a

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Wu, Yifei, Tze-chen Hsieh, Joseph M. Wu, et al. "Elucidating the Inhibitory Effect of Resveratrol and Its Structural Analogs on Selected Nucleotide-Related Enzymes." Biomolecules 10, no. 9 (2020): 1223. http://dx.doi.org/10.3390/biom10091223.

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Resveratrol, the most widely studied natural phytochemical, has been shown to interact with different target proteins. Previous studies show that resveratrol binds and inhibits DNA polymerases and some other enzymes; however, the binding and functioning mechanisms remain unknown. The elucidated knowledge of inhibitory mechanisms of resveratrol will assist us in new drug discovery. We utilized molecular docking and molecular dynamics (MD) simulation to reveal how resveratrol and structurally similar compounds bind to various nucleotide-dependent enzymes, specifically, DNA polymerases, HIV-1 rev

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5

Jayaraj, Premkumar, Chandrakala A. Narasimhulu, Andrei Maiseyeu, et al. "Methoxyphenol derivatives as reversible inhibitors of myeloperoxidase as potential antiatherosclerotic agents." Future Medicinal Chemistry 12, no. 2 (2020): 95–110. http://dx.doi.org/10.4155/fmc-2019-0080.

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Aim: To evaluate new chemical entities, based on ferulic acid scaffolds, as reversible myeloperoxidase inhibitors (MPOI). Methodology & results: In silico docking studies are performed with MPO protein as a target for several ferulic acid analogs followed by multiple in vitro assays to validate this approach. Two lead compounds 2a and 3 are identified with optimum docking and IC50 values: -7.95 kcal/mol, 0.9 μM and -8.35 kcal/mol, 8.5 μM, respectively. These MPOIs are able to inhibit oxidation of high-density lipoprotein and further promoted functionality of high-density lipoprotein. Concl

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Lande, Duc Hoàng, Abed Nasereddin, Arne Alder, et al. "Synthesis and Antiplasmodial Activity of Bisindolylcyclobutenediones." Molecules 26, no. 16 (2021): 4739. http://dx.doi.org/10.3390/molecules26164739.

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Malaria is one of the most dangerous infectious diseases. Because the causative Plasmodium parasites have developed resistances against virtually all established antimalarial drugs, novel antiplasmodial agents are required. In order to target plasmodial kinases, novel N-unsubstituted bisindolylcyclobutenediones were designed as analogs to the kinase inhibitory bisindolylmaleimides. Molecular docking experiments produced favorable poses of the unsubstituted bisindolylcyclobutenedione in the ATP binding pocket of various plasmodial protein kinases. The synthesis of the title compounds was accomp

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7

Pislyagin, Evgeny A., Ekaterina S. Menchinskaya, Irina N. Gladkikh, et al. "Recombinant Analogs of Sea Anemone Kunitz-Type Peptides Influence P2X7 Receptor Activity in Neuro-2a Cells." Marine Drugs 21, no. 3 (2023): 192. http://dx.doi.org/10.3390/md21030192.

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Purinergic P2X7 receptors (P2X7) have now been proven to play an important role and represent an important therapeutic target in many pathological conditions including neurodegeneration. Here, we investigated the impact of peptides on purinergic signaling in Neuro-2a cells through the P2X7 subtype in in vitro models. We have found that a number of recombinant peptides, analogs of sea anemone Kunitz-type peptides, are able to influence the action of high concentrations of ATP and thereby reduce the toxic effects of ATP. The influx of calcium, as well as the fluorescent dye YO-PRO-1, was signifi

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Zhang, Xiaozhe, Shaodong Shi, Yang Su, et al. "Suramin and NF449 are IP5K inhibitors that disrupt inositol hexakisphosphate–mediated regulation of cullin–RING ligase and sensitize cancer cells to MLN4924/pevonedistat." Journal of Biological Chemistry 295, no. 30 (2020): 10281–92. http://dx.doi.org/10.1074/jbc.ra120.014375.

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Inositol hexakisphosphate (IP6) is an abundant metabolite synthesized from inositol 1,3,4,5,6-pentakisphosphate (IP5) by the single IP5 2-kinase (IP5K). Genetic and biochemical studies have shown that IP6 usually functions as a structural cofactor in protein(s) mediating mRNA export, DNA repair, necroptosis, 3D genome organization, HIV infection, and cullin–RING ligase (CRL) deneddylation. However, it remains unknown whether pharmacological perturbation of cellular IP6 levels affects any of these processes. Here, we performed screening for small molecules that regulate human IP5K activity, rev

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Reddy, K. Kumar, R. S. Rathore, P. Srujana, et al. "Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs." Mini-Reviews in Medicinal Chemistry 20, no. 12 (2020): 1179–87. http://dx.doi.org/10.2174/1389557520666200526183353.

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Background: The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values. Methods: Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values were earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibi

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Tanneeru, Karunakar, Bandi Madhusudhan Reddy, and Lalitha Guruprasad. "Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis and molecular docking of ATP-competitive triazine analogs of human mTOR inhibitors." Medicinal Chemistry Research 21, no. 7 (2011): 1207–17. http://dx.doi.org/10.1007/s00044-011-9629-x.

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Amin, Md Ruhul, Farhana Yasmin, Mohammed Anowar Hosen та ін. "Synthesis, Antimicrobial, Anticancer, PASS, Molecular Docking, Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs". Molecules 26, № 22 (2021): 7016. http://dx.doi.org/10.3390/molecules26227016.

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A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antiba

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Mayana, Ibtisam Khan, Srinivasulu Cheemanapalli, Lavanya Thopireddy, et al. "A study on design, virtual screening, and docking analysis of new ferulic acid analogs against the NF-kB therapeutic target." Current Issues in Pharmacy and Medical Sciences 38, no. 2 (2025): 101–6. https://doi.org/10.12923/cipms-2025-0016.

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The human transcription factor NF-κB has an essential role in inflammatory responses and carcinogenesis. Ferulic acid (FA) is one of the plant phenolic compounds that shows therapeutic potential for anticancer, anti-diabetes, anti-aging, anti-inflammatory activities, etc. This study aims to develop novel FA-based NF-κB inhibitors. The docking study of FA analogs has revealed that FA74 (-7.3 kcal/mol), FA75 (-7.2 kcal/mol), and FA71 (-7.1 kcal/mol) are top NF-κB binders, in comparison with their parental compound, FA (-4.0 kcal/mol). Accordingly, FA74 establishes four hydrogen bonds with Arg 24

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de Souza, Amanda Bubula, Leonardo Pereira de Araújo, Amanda Almeida Morais, et al. "In silico analysis for the proposal of new drugs against the phosphoprotein nucleocapsid of the severe acute respiratory syndrome coronavirus 2 virus." Innovative Medicines & Omics 1, no. 1 (2024): 3731. http://dx.doi.org/10.36922/imo.3731.

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The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which began in late 2019, has resulted in approximately seven million deaths worldwide. This underscores the urgent need for vaccine and drug development. In silico techniques, especially molecular docking, provide promising means for discovering new treatments. This study aimed to identify novel compounds with potential activity against the nucleocapsid protein of SARS-CoV-2 using drug repositioning and bioisosterism techniques. We performed molecular docking with 20,115 co

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Abdelkrim, Yosser Zina, Emna Harigua-Souiai, Imen Bassoumi-Jamoussi, et al. "Enzymatic and Molecular Characterization of Anti-Leishmania Molecules That Differently Target Leishmania and Mammalian eIF4A Proteins, LieIF4A and eIF4AMus." Molecules 27, no. 18 (2022): 5890. http://dx.doi.org/10.3390/molecules27185890.

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Previous investigations of the Leishmania infantum eIF4A-like protein (LieIF4A) as a potential drug target delivered cholestanol derivatives inhibitors. Here, we investigated the mode of action of cholesterol derivatives as a novel scaffold structure of LieIF4A inhibitors on the RNA-dependent ATPase activity of LieIF4A and its mammalian ortholog (eIF4AI). We compared their biochemical effects on RNA-dependent ATPase activities of both proteins and investigated if rocaglamide, a known inhibitor of eIF4A, could affect LieIF4A as well. Kinetic measurements were conducted at different concentratio

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15

Lv, Han, Yongli Du, Xiehuang Sheng, Zhipei Gao, and Jingkang Shen. "Molecular modeling studies of [4-(3H-benzoimidazol-5-yl)-pyrimidin-2-yl]-amine-based CDK4 inhibitors." Future Medicinal Chemistry 13, no. 16 (2021): 1317–39. http://dx.doi.org/10.4155/fmc-2020-0393.

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Aim: CDK4 is a promising target for breast cancer therapy. This study aimed to explore the structure–activity relationship of CDK4 inhibitor abemaciclib analogs and design potent CDK4 inhibitors for breast cancer treatment. Methods & results: A faithful 3D quantitative structure–activity relationship model was established by molecular docking, comparative molecular field analysis and comparative molecular similarity index analysis based on 56 abemaciclib analogs. Molecular dynamics simulation studies revealed the key residues of the interaction between CDK4 and inhibitors. Four novel inhib

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K Singla, Rajeev, Piya Paul, Pawan G Nayak, and Varadaraj Bhat G. "Investigation of Anthramycin Analogs Induced Cell Death in MCF-7 Breast Cancer Cells." Indo Global Journal of Pharmaceutical Sciences 02, no. 04 (2012): 383–89. http://dx.doi.org/10.35652/igjps.2012.44.

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1,5-Benzodiazepines were synthesized using chalcone & o-phenylene diamine. Their structures were characterized using physical & spectral data. These molecules are analogous to anthracin, henceforth evaluated for their anti-breast cancer activity, using in vitro model MTT assay against MCF-7 cell line. Results revealed that these molecules are having potential growth inhibitory effect on the MCF-7 cell line, and certainly better than that of standard cisplatin. Docking studies revealed that these 1,5- benzodiazepine molecules may be working by inhibiting tyrosine kinase receptor, ErbB4

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Czeleń, Przemysław, та Beata Szefler. "The Oxindole Derivatives, New Promising GSK-3β Inhibitors as One of the Potential Treatments for Alzheimer’s Disease—A Molecular Dynamics Approach". Biology 10, № 4 (2021): 332. http://dx.doi.org/10.3390/biology10040332.

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The glycogen synthase kinase 3β (GSK-3β) is a protein kinase involved in regulating numerous physiological processes such as embryonic development, transcription, insulin action, cell division cycle and multiple neuronal functions. The overexpression of this enzyme is related to many diseases such as schizophrenia, Alzheimer’s disease, diabetes and cancer. One of the basic methods of treatment in these cases is the usage of ATP-competitive inhibitors. A significant group of such compounds are indirubin and its analogs, e.g., oxindole derivatives. The compounds considered in this work are 112 n

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Babu Jatavath, Mohan, Sree Kanth Sivan, Yamini Lingala та Vijjulatha Manga. "Docking and 3D QSAR Studies on p38α MAP Kinase Inhibitors". E-Journal of Chemistry 8, № 4 (2011): 1596–605. http://dx.doi.org/10.1155/2011/184863.

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The p38 signaling cascade has emerged as an attractive target for the design of novel chemotherapeutic agents for the treatment of inflammatory diseases. Three dimensional quantitative structure- activity relationship (3D- QSAR) studies were performed on a series of 25, 2-aminothiazole analogs as inhibitors of p38α mitogen activated protein (MAP) kinase. The docking results provided a reliable conformational alignment scheme for the 3D-QSAR model. The 3D-QSAR model showed very good statistical results namely q2, r2and r2predvalues for both comparative molecular field analysis (CoMFA) and compa

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Sudhana, Saddala Madhu, and Pradeepkiran Jangampalli Adi. "Synthesis, Biological Evaluation and Molecular Docking Studies of Novel Di-hydropyridine Analogs as Potent Antioxidants." Current Topics in Medicinal Chemistry 19, no. 29 (2019): 2676–86. http://dx.doi.org/10.2174/1568026619666191105100959.

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Aims: The aim of this study is to synthesize, characterize and biological evaluation of 3-ethyl 5- methyl2-(2-aminoethoxy)-4-(2-chlorophenyl)-1,4-dihydropyridine-3,5-dicarboxylate derivatives. Background: An efficient synthesis of two series of novel carbamate and sulfonamide derivatives of amlodipine, 3-ethyl 5-methyl 2-(2-aminoethoxy)-4-(2-chlorophenyl)-1,4-dihydropyridine-3,5-dicarboxylate (amlodipine) 1 were chemical synthesized process. Materials & Methods: In this process, various chloroformates 2(a-e) and sulfonyl chlorides 4(a-e) on reaction with 1 in the presence of N,N–dimethylpi

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Luthra, Amit, Naduni Paranagama, William Swinehart, et al. "Conformational communication mediates the reset step in t6A biosynthesis." Nucleic Acids Research 47, no. 12 (2019): 6551–67. http://dx.doi.org/10.1093/nar/gkz439.

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Abstract The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-

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Roster, Colm P., Danielle LaVigne, Jillian E. Milanes, et al. "Enolase Inhibitors as Early Lead Therapeutics against Trypanosoma brucei." Pathogens 12, no. 11 (2023): 1290. http://dx.doi.org/10.3390/pathogens12111290.

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Glucose metabolism is critical for the African trypanosome, Trypanosoma brucei, serving as the lone source of ATP production for the bloodstream form (BSF) parasite in the glucose-rich environment of the host blood. Recently, phosphonate inhibitors of human enolase (ENO), the enzyme responsible for the interconversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP) in glycolysis or PEP to 2-PG in gluconeogenesis, have been developed for the treatment of glioblastoma multiforme (GBM). Here, we have tested these agents against T. brucei ENO (TbENO) and found the compounds to be potent

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Zaki, Waheed A., Selwan M. El-Sayed, Mohamed Alswah, et al. "Design, Synthesis, In Vitro, and In Silico Studies of New N5-Substituted-pyrazolo[3,4-d]pyrimidinone Derivatives as Anticancer CDK2 Inhibitors." Pharmaceuticals 16, no. 11 (2023): 1593. http://dx.doi.org/10.3390/ph16111593.

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CDK2 is a key player in cell cycle processes. It has a crucial role in the progression of various cancers. Hepatocellular carcinoma (HCC) and colorectal cancer (CRC) are two common cancers that affect humans worldwide. The available therapeutic options suffer from many drawbacks including high toxicity and decreased specificity. Therefore, there is a need for more effective and safer therapeutic agents. A series of new pyrazolo[3,4-d]pyrimidine analogs was designed, synthesized, and evaluated as anticancer agents against the CRC and HCC cells, HCT116, and HepG2, respectively. Pyrazolo[3,4-d]py

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RAJALAKSHMI, RAMARAJAN, RAJAVEL SANTHI, and THANGARAJ ELAKKIYA. "Synthesis, Characterization, Biological Evaluation and Molecular Docking Studies of Some Oxazinyl-Thiazolidinone Derivatives." Asian Journal of Chemistry 32, no. 9 (2020): 2125–29. http://dx.doi.org/10.14233/ajchem.2020.22710.

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A series of new 4-thiazolidinone derivatives of 2-(4-chlorophenyl)-3-(6-(thiophen-2-yl)-4-p-tolyl-4H-1,3-oxazin-2-yl)- thiazolidin-4-one (7h-m) are synthesized because of its wide range of biological activities.1H & 13C NMR, IR studies were applied for the elucidation of all the synthesized compounds. All the synthesized compounds have been tested for antidiabetic and antioxidant activity in vitro method against standard. The analogs 7h-m was evaluated for α-amylase and α-glucosidase inhibitory potential. The structures of all the compounds have been screened for antioxidant activity using

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Kapoor, Neha, Tanushree Banerjee, Ponnusamy Babu, Koustav Maity, Namita Surolia, and Avadhesha Surolia. "Design, development, synthesis, and docking analysis of 2â²-substituted triclosan analogs as inhibitors forPlasmodium falciparumEnoyl-ACP reductase." IUBMB Life 61, no. 11 (2009): 1083–91. http://dx.doi.org/10.1002/iub.258.

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Janežič, Matej, Katja Valjavec, Kaja Bergant Loboda та ін. "Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα". International Journal of Molecular Sciences 22, № 24 (2021): 13474. http://dx.doi.org/10.3390/ijms222413474.

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In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibit

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Marciniec, Krzysztof, Zuzanna Rzepka, Elwira Chrobak, et al. "Design, Synthesis and Biological Evaluation of Quinoline-8-Sulfonamides as Inhibitors of the Tumor Cell-Specific M2 Isoform of Pyruvate Kinase: Preliminary Study." Molecules 28, no. 6 (2023): 2509. http://dx.doi.org/10.3390/molecules28062509.

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Cancer cells need to carefully regulate their metabolism to keep them growing and dividing under the influence of different nutrients and oxygen levels. Muscle isoform 2 of pyruvate kinase (PKM2) is a key glycolytic enzyme involved in the generation of ATP and is critical for cancer metabolism. PKM2 is expressed in many human tumors and is regulated by complex mechanisms that promote tumor growth and proliferation. Therefore, it is considered an attractive therapeutic target for modulating tumor metabolism. Various modulators regulate PKM2, shifting it between highly active and less active sta

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Liu, Yong-Xuan, Shuang Gao, Tong Ye, Jia-Zhong Li, Fei Ye, and Ying Fu. "Combined 3D-quantitative structure–activity relationships and topomer technology-based molecular design of human 4-hydroxyphenylpyruvate dioxygenase inhibitors." Future Medicinal Chemistry 12, no. 9 (2020): 795–811. http://dx.doi.org/10.4155/fmc-2019-0349.

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Aim: 4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted increasing attention as an important target against tyrosinemia type I. This paper aimed to explore the structure–activity relationship of HPPD inhibitors with pyrazole scaffolds and to design novel HPPD inhibitors. Methodology & results: The best 3D-quantitative structure–activity relationships model was established by two different strategies based on 40 pyrazole scaffold-based analogs. Screening of molecular fragments by topomer technology, combined with molecular docking, 14 structures were identified for potential human HPP

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Betari, Nibal, Kristoffer Sahlholm, Yuta Ishizuka, Knut Teigen, and Jan Haavik. "Discovery and biological characterization of a novel scaffold for potent inhibitors of peripheral serotonin synthesis." Future Medicinal Chemistry 12, no. 16 (2020): 1461–74. http://dx.doi.org/10.4155/fmc-2020-0127.

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Aim: Tryptophan hydroxylase 1 (TPH1) catalyzes serotonin synthesis in peripheral tissues. Selective TPH1 inhibitors may be useful for treating disorders related to serotonin dysregulation. Results & methodology: Screening using a thermal shift assay for TPH1 binders yielded Compound 1 (2-(4-methylphenyl)-1,2-benzisothiazol-3(2 H)-one), which showed high potency (50% inhibition at 98 ± 30 nM) and selectivity for inhibiting TPH over related aromatic amino acid hydroxylases in enzyme activity assays. Structure–activity relationships studies revealed several analogs of 1 showing comparable pot

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Narasimha, M., B. Revanth, D. Mahender, and P. Sarita Rajender. "Synthesis and Molecular Docking Studies of Triazole Conjugated Novel 2,4-Disubstituted Thiazole Derivatives as CDK2 Inhibitors." Asian Journal of Chemistry 33, no. 8 (2021): 1849–54. http://dx.doi.org/10.14233/ajchem.2021.23257.

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A series of triazole conjugated novel 2,4-disubstituted thiazole derivatives (9a-l) were synthesized from salicylaldehyde. These new chemical entities were characterized by their IR, 1H & 13C NMR, mass spectral data and their molecular docking studies were performed to identify potential inhibitors of CDK2 protein. The synthesized analogs 9a-l were docked with CDK2 protein (PDB: 1GIJ). Among these 9h, 9j and 9k showed better Glide score, Prime MM-GBSA and ADME properties as compared to seliciclib and dinaciclib cancer inhibiting drugs of CDK2 protein. The amino acid Val83 of CDK2 protein w

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Tammanna, R. Sahrawat, and Taneja Sanya. "Investigation of Mutant GFAP Protein Associated with Alexander Disease and Its Therapeutic Intervention: Structure Based Drug Design Approach." Journal of Progressive Research in Biology 3, no. 2 (2016): 184–91. https://doi.org/10.5281/zenodo.3970414.

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Systems Biology approach involves integration of experimental and computational research to understand complex biological systems. Alexander's Disease (AxD) was first described by W. S. Alexander in 1949, and is a rare, but often fatal neurological disorder that has been divided into three subtypes based on the age of onset: the infantile, juvenile and adult forms that are shown to be caused by mutations in the gfap gene. The infantile form, with onset between birth and about two years of age, is currently the most common form of the disease. The characteristic neuropathological feature of

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Gao, Kai, Wenjia Wang, Thales Kronenberger, Carsten Wrenger, and Matthew R. Groves. "The Crystal Structure of the Plasmodium falciparum PdxK Provides an Experimental Model for Pro-Drug Activation." Crystals 9, no. 10 (2019): 534. http://dx.doi.org/10.3390/cryst9100534.

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Pyridoxine/pyridoxal kinase (PdxK), belongs to the ribokinase family and is involved in the vitamin B6 salvage pathway by phosphorylating 5-pyridoxal (PL) into an active form. In the human malaria parasite, Plasmodium falciparum, PfPdxK functions to salvage vitamin B6 from both itself and its host. Here, we report the crystal structure of PfPdxK from P. falciparum in complex with a non-hydrolyzable ATP analog (AMP-PNP) and PL. As expected, the fold is retained and both AMP-PNP and PL occupy the same binding sites when compared to the human ortholog. However, our model allows us to identify a F

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32

Alagöz, Mehmet Abdullah. "New molecule design with in-silico methods for Covid-19 treatment." Bioorganic and Medicinal Chemistry Reports 3, no. 2 (2020): 32–40. http://dx.doi.org/10.25135/acg.bmcr.23.20.08.1773.

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Intensive studies are being conducted to develop effective prevention and treatment strategies for the Covid-19 pandemic. During a pandemic, it is vital to act quickly to develop a defense strategy. It usually takes a long time to develop a preventive vaccine, and immediate drug development is needed to reduce the impact of the rapidly increasing Covid-19 pandemic. This study aimed to design an effective and potent drug by selecting remdesivir, a nucleotide analog prodrug that inhibits viral RNA polymerases and is known to be active against Covid-19. Remdesivir is metabolized into active nucle

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Shirasawa, Hiroshi. "Novel Chiral Chalcone Analogs that Induce M Phase Arrest and Apoptosis in HeLa Cells." Medicinal Chemistry 9, no. 6 (2019): 9. https://doi.org/10.5281/zenodo.10669775.

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We identified two chiral chalcone analogs CCL360 and CCL361 from the Chiba Chemical Library, which exhibit antiproliferative effects on human cancer cells. Flow cytometry analyses revealed that HeLa and Vero cells treated with CCL360 and CCL361 had higher populations of cells in the G2 /M phase than untreated cells. Docking studies suggested that the R-isomer of CCL361 binds to the taxol binding domain (TBD) of β-tubulin, and the S-isomers of CCL360 and CCL361 bind to β-tubulin at the colchicine binding domain and the TBD. Further investigations using a fluorescent ubiquitination-bas

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34

Kassem, Asmaa F., Eman M. H. Abbas, Dina S. El-Kady, Hanem M. Awad, and Wael A. El-Sayed. "Design, Synthesis and Anticancer Activity of New Thiazole-Tetrazole or Triazole Hybrid Glycosides Targeting CDK-2 via Structure-Based Virtual Screening." Mini-Reviews in Medicinal Chemistry 19, no. 11 (2019): 933–48. http://dx.doi.org/10.2174/1389557519666181231121217.

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Background & Objective: The target tetrazole glycosides were synthesized by construction of ring system by cycloaddition reaction of benzothiazole-linked nitrile derivative and sodium azide followed by N-glycosylation process and deprotection. Methods: The triazole glycosides were prepared by applying click approach involving dipolar cycloaddition of benzothiazole possessing alkyne functionality and different glycosyl azides. The products incorporating acyclic analogs of sugar moieties were synthesized through alkylation using acyclic oxygenated halides. Results: The anticancer activity wa

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35

Qiao, Shigang, Wen-jie Zhao, Huan-qiu Li, et al. "Necrostatin-1 Analog DIMO Exerts Cardioprotective Effect against Ischemia Reperfusion Injury by Suppressing Necroptosis via Autophagic Pathway in Rats." Pharmacology 106, no. 3-4 (2021): 189–201. http://dx.doi.org/10.1159/000510864.

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Aim: It has been reported that necrostatin-1 (Nec-1) is a specific necroptosis inhibitor that could attenuate programmed cell death induced by myocardial ischemia/reperfusion (I/R) injury. This study aimed to observe the effect and mechanism of novel Nec-1 analog (Z)-5-(3,5-dimethoxybenzyl)-2-imine-1-methylimidazolin-4-1 (DIMO) on myocardial I/R injury. Methods: Male SD rats underwent I/R injury with or without different doses of DIMO (1, 2, or 4 mg/kg) treatment. Isolated neonatal rat cardiomyocytes were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) treatment with or without D

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36

Khan, Shah Alam, S. Monawwar Imam, Aftab Ahmad, Syed Hussain Basha, and Asif Husain. "Synthesis, molecular docking with COX 1& II enzyme, ADMET screening and in vivo anti-inflammatory activity of oxadiazole, thiadiazole and triazole analogs of felbinac." Journal of Saudi Chemical Society 22, no. 4 (2018): 469–84. http://dx.doi.org/10.1016/j.jscs.2017.05.006.

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Li, Yue, Zheng-Mei Shi, Yong He, et al. "Inosine, AMP, and Vidarabine: Network Pharmacology and LC-MS Reveal Key Bioactive Compounds in Periplaneta americana for Ulcerative Colitis Management." International Journal of Molecular Sciences 26, no. 12 (2025): 5446. https://doi.org/10.3390/ijms26125446.

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Ulcerative colitis (UC) is a chronic inflammatory bowel disease with unmet therapeutic needs. This study investigates the therapeutic potential of Periplaneta americana L. extract (PAE) and its molecular mechanisms, integrating network pharmacology and experimental validation. Liquid chromatography–mass spectrometry identified 1355 compounds in PAE. Network pharmacology analysis revealed that inosine, vidarabine, and adenosine 5′-monophosphate (AMP) were core components and the core components synergistically regulated key targets and acted on inflammation-related pathways, thereby establishin

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38

Pei, ShanShan, Monica L. Guzman, Shama Nasim, Lei Shi, Peter A. Crooks, and Craig T. Jordan. "Analysis of the Anti-Leukemia Mechanism of Parthenolide." Blood 114, no. 22 (2009): 2734. http://dx.doi.org/10.1182/blood.v114.22.2734.2734.

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Abstract Abstract 2734 Poster Board II-710 We have previously demonstrated that parthenolide (PTL), a naturally occurring small molecule found in feverfew Chrysanthemum parthenium, induces apoptosis in primary acute myeloid leukemia (AML) cells, including the stem and progenitor cell compartment. Based on these preclinical findings, a PTL derivative (dimethylamino parthenolide) is currently being evaluated in a phase I clinical trial. However, despite the promising activity of PTL, its underlying mechanism of action remains poorly understood. Thus, we have undertaken biochemical studies to bet

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39

Choudhary, Dhiraj Kumar, Navaneet Chaturvedi, Amit Singh, and Abha Mishra. "Investigation of hypoglycemic effects, oxidative stress potential and xanthine-oxidase activity of polyphenols (gallic acid, catechin) derived from faba bean on 3T3-L1 cell line: insights into molecular docking and simulation study." Toxicology Research 9, no. 3 (2020): 308–22. http://dx.doi.org/10.1093/toxres/tfaa025.

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Abstract Hypoglycemic potential and xanthine-oxidase (XO) activity of polyphenols from faba bean were evaluated in the 3T3-L1 cell line, and an interaction study in silico with XO was performed with considerable bioactive components of acetone extract of faba beans. The protonated and fragmented behavior of acetone seed extract revealed the presence of gallic acid (MS/MS, m/z 169) and catechin (MSn, m/z 288.3). Flow cytometry study explained the effect of hydrogen peroxide (H2O2) on cell line as cell death was increased from 9.72 to 41.66% as compared to the control (without H2O2). The atomic

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Pradhan, Joohee, and Sunita Panchawat. "Molecular Docking Studies and Pharmacophore Modeling of Some Insulin Mimetic Agents from Herbal Sources: A Rational Approach towards Designing of Orally Active Insulin Mimetic Agents." Current Traditional Medicine 6, no. 2 (2020): 121–33. http://dx.doi.org/10.2174/2215083805666191001220342.

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Background:: Many herbal drugs have been found to possess oral insulin mimetic property as evidenced from the literature. Although, to date there is no efficient, synthetic orally active insulin-mimetic drug available clinically. Computer-Aided Drug Design (CADD) may help in the development of such agents through Pharmacophore modeling. Objective:: The present work is aimed at the In-silico designing of Pharmacophore that defines the structural requirements of a molecule to possess oral insulin-mimetic properties. Methods:: A set of 16 orally active insulin-mimetic natural compounds available

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41

Dandamudi, Akhila, William Seibel, Huzoor Akbar, and Yi Zheng. "Structure-Activity Relationship Analysis of Analogs of Rhosin, a RhoA Inhibitor, Reveals a New Generation of Improved Antiplatelet Agents." Blood 138, Supplement 1 (2021): 3989. http://dx.doi.org/10.1182/blood-2021-153108.

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Abstract Platelet activation and aggregation play a key role in mediating hemostasis and thrombosis. The antiplatelet therapies currently available in the market are associated with a high risk of hemorrhage and are mostly irreversible in suppressing platelet activity; hence, there is a need to develop better therapeutic agents. Previous genetic and pharmacological studies have implicated the small GTPase RhoA in multiple platelet signaling pathways. We devised a lead RhoA activity-specific inhibitor, Rhosin/G04, based on the structure-function relationship of RhoA interaction with its activat

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42

Liu, Ming, Lei Wang, Xiao Li Liu, and Wen Xiang Hu. "Study of Molecular Docking of Mu Opioid Receptor Agonist - Fentanyl and its Analogs Based on Docking." Advanced Materials Research 655-657 (January 2013): 1931–34. http://dx.doi.org/10.4028/www.scientific.net/amr.655-657.1931.

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The interaction mechanism of a series of fentanyl analogs are examined using molecular docking to the mu-opioid receptor based on Surflex-Docking. Fully automatic flexible molecular docking (Surflex-Docking) was performed by using the possible active conformations of 70 fentanyl analogs and optimized 3D structure of mu-opioid receptor. The site mainly consist of residues ILE 109, ASP 112, TYR113, MET116, HIS262, TYR291. All these residues take part in interaction between fentanyl and mu-opioid receptor. Meanwhile, the results provide new insight to design of experiments aimed at understanding

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Wang, Zhiguo, Robert J. Sheaff, and Syed R. Hussaini. "Chloroquine-Based Mitochondrial ATP Inhibitors." Molecules 28, no. 3 (2023): 1161. http://dx.doi.org/10.3390/molecules28031161.

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Mitochondria is an important drug target for ailments ranging from neoplastic to neurodegenerative diseases and metabolic diseases. Here, we describe the synthesis of chloroquine analogs and show the results of mitochondrial ATP inhibition testing. The 2,4-dinitrobenzene-based analogs showed concentration-dependent mitochondrial (mito.) ATP inhibition. The most potent mito. ATP inhibitor was found to be N-(4-((2,4-Dinitrophenyl)amino)pentyl)-N-ethylacetamide (17).

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Choudary, Jayant, Suvarna G. Kini, Sreedhara Ranganath Pai Karkala, and Muhammad Mubeen. "Docking Studies and Biological Activity of Fosinopril Analogs." International Journal of Medicinal Chemistry 2014 (July 6, 2014): 1–5. http://dx.doi.org/10.1155/2014/721834.

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The purpose of the present study was to determine the angiotensin-I converting enzyme inhibitory activity of few novel Fosinopril derivatives which were predicted to possess better ACE inhibitory activity and lesser side effects than the existing drug molecule. In vitro study was carried out to determine ACE inhibitory activity of six different Fosinopril analogs by spectrophotometric assay procedure. Analog A2 showed the highest activity compared to other analogs and as well as Fosinopril itself. Docking studies of the compounds were done with the help of VLife MDS 3.0 software using GRIP bat

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45

Arsianti, Ade, Fadilah Fadilah, Linda Erlina, and Rafika Indah Paramita. "MOLECULAR DOCKING OF ANTIMYCIN A3 ANALOGS AND ITS AROMATIC SEGMENTS AS INHIBITORS OF APOPTOSIS PROTEIN MARKER BCL-XL AND MCL-1." Asian Journal of Pharmaceutical and Clinical Research 10, no. 8 (2017): 317. http://dx.doi.org/10.22159/ajpcr.2017.v10i8.18165.

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Objective: Apoptosis is an important cellular process that causes the death of damaged cells. Its malfunction can lead to cancer development and poor response to conventional chemotherapy. Cellular proteins from the B-cell lymphoma 2 (BCL-2) family are crucial for apoptosis. Breast cancer is the most commonly diagnosed cancer among women worldwide. The aim of this work was to design using in silico docking antimycin A3, antimycin analogs, and its aromatic segments as inhibitors of Bcl-xl and Mcl-1.Methods: In silico molecular docking approach has been utilized to find the potential anticancer

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Joseph, Sheldon M., Matthew A. Pifer, Ronald J. Przybylski, and George R. Dubyak. "Methylene ATP analogs as modulators of extracellular ATP metabolism and accumulation." British Journal of Pharmacology 142, no. 6 (2004): 1002–14. http://dx.doi.org/10.1038/sj.bjp.0705865.

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Martins, Lucas Sousa, Reinaldo W. A. Gonçalves, Joana J. S. Moraes, Cláudio Nahum Alves, and José Rogério A. Silva. "Computational Analysis of Triazole-Based Kojic Acid Analogs as Tyrosinase Inhibitors by Molecular Dynamics and Free Energy Calculations." Molecules 27, no. 23 (2022): 8141. http://dx.doi.org/10.3390/molecules27238141.

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Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key metalloenzyme of the melanogenesis process. Initially, molecular docking calculations satisfactorily predicted the binding mode of evaluated KA analogs, where the KA part overlays the crystal conformation of the KA inhibitor into the catalytic site of TYR. The MD simulations were followed by the LIE method, which reproduced the experimental bindin

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Ibrahim, Mahmoud A. A., Doaa G. M. Mahmoud, Alaa H. M. Abdelrahman, et al. "Benzothiazinone analogs as Anti-Mycobacterium tuberculosis DprE1 irreversible inhibitors: Covalent docking, validation, and molecular dynamics simulations." PLOS ONE 19, no. 11 (2024): e0314422. http://dx.doi.org/10.1371/journal.pone.0314422.

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Mycobacterium tuberculosis is a lethal human pathogen, with the key flavoenzyme for catalyzing bacterial cell-wall biosynthesis, decaprenylphosphoryl-D-ribose oxidase (DprE1), considered an Achilles heal for tuberculosis (TB) progression. Inhibition of DprE1 blocks cell wall biosynthesis and is a highly promising antitubercular target. Macozinone (PBTZ169, a benzothiazinone (BTZ) derivative) is an irreversible DprE1 inhibitor that has attracted considerable attention because it exhibits an additive activity when combined with other anti-TB drugs. Herein, 754 BTZ analogs were assembled in a vir

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Nuñez, María, Yaowei Wang, Eugenia Russinova, et al. "Synthesis, Biological Activity, and Molecular-Docking Studies of New Brassinosteroid Analogs." International Journal of Molecular Sciences 25, no. 18 (2024): 10158. http://dx.doi.org/10.3390/ijms251810158.

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Much work has been dedicated to the quest to determine the structure–activity relationship in synthetic brassinosteroid (BR) analogs. Recently, it has been reported that analogs with phenyl or benzoate groups in the alkyl chain present activities comparable to those shown by natural BRs, depending on the nature of the substituent in the aromatic ring. However, as it is well known that the activity depends on the structure of the whole molecule, in this work, we have synthesized a series of compounds with the same substituted benzoate in the alkyl chain and a hydroxyl group at C3. The main goal

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Astuti, Endang, Tri Joko Raharjo, Putra Boang Manalu, Ilham Satria Putra, Stephanus Satria Waskitha, and Junita Solin. "Synthesis, Molecular Docking, and Evaluation of Some New Curcumin Analogs as Antimalarial Agents." Indonesian Journal of Chemistry 21, no. 2 (2021): 452. http://dx.doi.org/10.22146/ijc.57646.

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This research involves the synthesis, antimalarial evaluation, and molecular docking of several curcumin analogs. A total of six curcumin analog compounds were synthesized using aldol condensation using hydrochloric acid and sodium hydroxide catalysts. The synthesized compounds were elucidated using FTIR, 1H-NMR, 13C-NMR, and LC-MS/MS. Subsequently, all curcumin analogs were tested as an antimalarial agent against Plasmodium falciparum 3D7 strain, and their mechanism of action was evaluated through a molecular docking study. Six curcumin analogs, i.e. 2,6-bis(2-hydroxybenzylidene)cyclohexanone

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