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Journal articles on the topic 'AUTODOCK4'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Valencia, Eduvan, Mauricio Galvis, Jorge Nisperuza, Vladimir Ballesteros, and Fredy Mesa. "In Silico Evaluation of Potential NDM-1 Inhibitors: An Integrated Docking and Molecular Dynamics Approach." Pharmaceuticals 17, no. 12 (2024): 1715. https://doi.org/10.3390/ph17121715.

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Background/Objectives: Non-fermenting Gram-negative bacteria are resistant to most antibiotics, due to the production of enzymes such as NDM-1. Faced with this challenge, computational methods have become essential for the design of NDM-1 carbapenemase inhibitors, optimizing both the time and cost of the development of new lead molecules. Methods: In this study, molecular docking and molecular dynamics (MD) simulations were performed in order to identify effective inhibitors against the NDM-1 enzyme. Protein preparation was carried out using UCSF Chimera and AutoDockTools 1.5.7, while ligands

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Flores, Doménica, and Carola Jerves. "Computational Comparison of the Binding Affinity of Selective and Nonselective NSAIDs to COX-2 Using Molecular Docking." Bionatura Journal 2, no. 2 (2025): 1–14. https://doi.org/10.70099/bj/2025.02.02.3.

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Cyclooxygenase-2 (COX-2) plays a key role in inflammation, making it a prime target for nonsteroidal anti-inflammatory drugs (NSAIDs). This study uses molecular docking to compare the binding affinities of four nonselective NSAIDs (aspirin, ibuprofen, diclofenac, naproxen) and three selective COX-2 inhibitors (celecoxib, rofecoxib, etoricoxib) to COX-2. Simulations with AutoDock4 and AutoDock Vina revealed distinct differences in binding profiles and selectivity. Selective COX-2 inhibitors exhibited stronger binding affinities, with etoricoxib achieving -11.22 kcal/mol (AutoDock4), driven by k

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3

Nguyen, Nguyen Thanh, Trung Hai Nguyen, T. Ngoc Han Pham, et al. "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity." Journal of Chemical Information and Modeling 60, no. 1 (2019): 204–11. http://dx.doi.org/10.1021/acs.jcim.9b00778.

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4

Casbarra, Lorenzo, and Piero Procacci. "Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges." Journal of Computer-Aided Molecular Design 35, no. 6 (2021): 721–29. http://dx.doi.org/10.1007/s10822-021-00388-4.

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AbstractWe systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

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Arcon, Juan Pablo, Carlos P. Modenutti, Demian Avendaño, et al. "AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions." Bioinformatics 35, no. 19 (2019): 3836–38. http://dx.doi.org/10.1093/bioinformatics/btz152.

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Abstract Summary The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein–ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations. Availability and implementation AutoDock Bias is distributed with MGLTools (since version 1.5.7), and

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Sarthak, Pal1 Meenu Chaudhary*2 Kanishak Kala3. "Autodock & Autodock Vina: Development, Capabilities, & Applications in Molecular Docking." International Journal of Pharmaceutical Sciences 3, no. 5 (2025): 3005–19. https://doi.org/10.5281/zenodo.15458275.

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AutoDock and AutoDock Vina are popular molecular docking technologies that are essential to structure-based drug discovery because they can predict ligand-receptor interactions. Their theoretical underpinnings, methods of application, and comparative effectiveness across several biological targets are assessed in this study. Vina's multicore support and empirical scoring are compared to AutoDock4's semi-empirical scoring function and flexible docking strategy. Furthermore, the impact of developments like AutoGridFR and GPU-accelerated versions on computational efficiency is examined. The benef

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Suwardi, Suwardi, Agus Salim, Raden Rara Fadhila Kirana Nugrahani, and Yolanda Amalia. "Molecular Docking and Dynamics Simulation for Searching Anti-Cancer Compounds of Piperlongumine Derivatives that Have Potential as an Inhibitor Against MAO-B (Monoamine Oxidase B)." Indonesian Journal of Chemistry and Environment 6, no. 1 (2023): 18–28. http://dx.doi.org/10.21831/ijoce.v6i1.61429.

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The docking of the piperlongumine molecule and its derivatives has been carried out to find molecules that have the potential as anti-cancer. A total of 18 ligands were docked to the 2v5z protein using the autodock4 and autodock vina programs. The binding energies of piperlongumine and piperlongumine derivatives [R1 = CH3 and R2 = H] were -8.6 kcal/mol and -9.3 kcal/mol, respectively. Based on molecular dynamics simulations, the hydrogen bond interaction fraction was dominated by GLN 206 residue in both the SAG (88%) and piperlongumine derivatives ((R1=CH3, R2 = H)(93%) ligand, for this reason

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8

Morris, Garrett M., Ruth Huey, William Lindstrom, et al. "AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility." Journal of Computational Chemistry 30, no. 16 (2009): 2785–91. http://dx.doi.org/10.1002/jcc.21256.

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9

Lestari, Ayu Rahmania, Irmanida Batubara, Setyanto Tri Wahyudi, and Auliya Ilmiawati. "Phenolic Compound in Garlic (Allium sativum) and Black Garlic Potency as Antigout Using Molecular Docking Approach." Jurnal Kimia Sains dan Aplikasi 25, no. 7 (2022): 253–63. http://dx.doi.org/10.14710/jksa.25.7.253-263.

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Phenolics, including flavonoids, are bioactive components in garlic in relatively abundant amounts and are present 2–4 times more in black garlic. Both of these compounds are reported to have biological activity, with one of them acting as an antioxidant. However, its ability as an antigout is still not widely reported. Xanthine oxidase, adenine deaminase, guanine deaminase, purine nucleoside phosphorylase, and 5-Nucleotidase II are involved during the production of uric acid and causes gout. This study predicted the potential of the phenolic and flavonoid compounds in garlic and black garlic

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10

Belhocine, Youghourta, Seyfeddine Rahali, Hamza Allal, Ibtissem Meriem Assaba, Monira Galal Ghoniem та Fatima Adam Mohamed Ali. "A Dispersion Corrected DFT Investigation of the Inclusion Complexation of Dexamethasone with β-Cyclodextrin and Molecular Docking Study of Its Potential Activity against COVID-19". Molecules 26, № 24 (2021): 7622. http://dx.doi.org/10.3390/molecules26247622.

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The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the for

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11

Scarpino, Andrea, László Petri, Damijan Knez, et al. "WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors." Journal of Computer-Aided Molecular Design 35, no. 2 (2021): 223–44. http://dx.doi.org/10.1007/s10822-020-00371-5.

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AbstractHere we present WIDOCK, a virtual screening protocol that supports the selection of diverse electrophiles as covalent inhibitors by incorporating ligand reactivity towards cysteine residues into AutoDock4. WIDOCK applies the reactive docking method (Backus et al. in Nature 534:570–574, 2016) and extends it into a virtual screening tool by introducing facile experimental or computational parametrization and a ligand focused evaluation scheme together with a retrospective and prospective validation against various therapeutically relevant targets. Parameters accounting for ligand reactiv

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Ahsana, Dina, Andika Andika, and Siti Nashihah. "Molecular Docking Study of Flavonoid Compounds in The Guava Leaves (Psidium Guajava L.) Which Has Potential as Anti-Inflammatory COX-2 Inhibitors." Lumbung Farmasi: Jurnal Ilmu Kefarmasian 2, no. 2 (2021): 67. http://dx.doi.org/10.31764/lf.v2i2.5487.

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ABSTRAKInflamasi yang bersifat progresif cenderung akan merusak dan menimbulkan beberapa permasalahan dalam tubuh. Enzim COX-2 merupakan salah satu mediator yang berkontribusi besar dalam terjadinya inflamasi progresif. Penelitian secara eksperimental daun jambu biji (Psidium guajava L.) terbukti memiliki aktivitas anti-inflamasi diduga karena banyak terkandung senyawa flavonoid, namun masih belum ada penelitian aktivitasnya terhadap penghambatan COX-2 selektif. Tujuan dari penelitian ini yaitu untuk mengetahui potensi senyawa flavonoid memiliki aktivitas anti-inflamasi penghambat COX-2 selekt

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Isaac, Arnold Emerson, Faizy Khan, Shantanu Bafna, and Tanu Gupta. "Virtual Screening of potential inhibitors from Herbs for the treatment of Breast Cancer." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (2017): 62. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.14959.

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Objectives: Cancer is a disease which results in uncontrollable abnormal cells division and destruction of body tissues. Breast cancer occurs when malignant tumors develop in the breast. Breast cancer is the second leading cause of death among women. To study the role of herbs used in the treatment for breast cancer. To investigate the anti-breast cancer activity of compounds present on most common herbs and to analyse their interaction with amino acids in the active sites. Methods: Complementary and alternative medicine is often used for curing cancer mainly the breast cancer. Also certain st

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14

Laskar, Subrata, Omar Espino, and Debasish Bandyopadhyay. "Isolation, Solid-state Structure Determination, In Silico and In Vitro Anticancer Evaluation of an Indole Amino Acid Alkaloid L-Abrine." Current Cancer Drug Targets 19, no. 9 (2019): 707–15. http://dx.doi.org/10.2174/1568009619666190111111937.

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Background: Abrus precatorius Linn. (Kunch in Bengali) is widely spread in tropical and sub-tropical regions. It is a typical plant species which is well-known simultaneously as folk medicine and for its toxicity. Objective: Phytoceutical investigation of the white variety seeds of Abrus precatorius Linn. Methods: Traditional extraction, separation, isolation, and purification processes were followed. The structure was elucidated by various spectral analyses and the solid-state structure of this indolealkaloid was determined by X-ray crystallographic analysis. Docking interactions of L-abrine

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15

Bitencourt-Ferreira, Gabriela, Amauri Duarte da Silva, and Walter Filgueira de Azevedo. "Application of Machine Learning Techniques to Predict Binding Affinity for Drug Targets: A Study of Cyclin-Dependent Kinase 2." Current Medicinal Chemistry 28, no. 2 (2020): 253–65. http://dx.doi.org/10.2174/2213275912666191102162959.

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Background: The elucidation of the structure of cyclin-dependent kinase 2 (CDK2) made it possible to develop targeted scoring functions for virtual screening aimed to identify new inhibitors for this enzyme. CDK2 is a protein target for the development of drugs intended to modulate cellcycle progression and control. Such drugs have potential anticancer activities. Objective: Our goal here is to review recent applications of machine learning methods to predict ligand- binding affinity for protein targets. To assess the predictive performance of classical scoring functions and targeted scoring f

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16

Karlina, Lilis, and Mutista Hafshah. "Desain Turunan Kalkon Baru Sebagai Antikanker Payudara Berdasarkan Molecular Docking." Walisongo Journal of Chemistry 2, no. 2 (2019): 57. http://dx.doi.org/10.21580/wjc.v2i2.6025.

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<p>Penelitian ini dilakukan untuk menentukan senyawa turunan kalkon yang berpotensi sebagai antikanker payudara berdasarkan <em>Molecular Docking</em>. Protein yang digunakan yaitu 17β-hidroksisteroid dehydrogenase. Adapun ligan yang digunakan adalah 20 senyawa turunan kalkon yang dibandingkan dengan senyawa obat pembanding. Posisi pusat grid pada sisi aktif protein kanker payudara yang telah dilakukan pada penelitian sebelumnya yaitu pada leusin 149.X CB, serin 142.X OG, dan asparagine 152.X OD1. <em>Software</em> yang digunakan yaitu <em>hyperchem</em&g

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Rahmadani, Rizka Aulia, Elvina Astria Agustin, and Samsul Hadi. "Pengujian Pakis Kinca (Nephrolepis Cordifolia (L) C. Presl) Sebagai Inhibitor enzyim sitokrom sub time 2E1 Dengan Metode Doking." JFARM - Jurnal Farmasi 2, no. 2 (2024): 7–12. http://dx.doi.org/10.58794/jfarm.v2i2.680.

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CYP450 adalah enzim yang terlibat dalam monooksigenasi beragam senyawa asing dan endogen. Dari 57 enzim manusia, mungkin sepertiga bertanggung jawab metabolisme xenobiotik, termasuk obat-obatan. Penelitian ini menggunakan metode docking untuk melihat potensi senyawa yang terkandung dari Nephrolepis Cordifolia sebagai inhibitor CYP2E1. Doking yang dilakukan menggunkan senyawa yang terkandung dari Nephrolepis Cordifolia. Metode yang digunakan dalam docking adalah rigid docking menggunakan software autodock4. Analisis data yang digunakan adalah adanya ikatan hidrogen dan enrgy Gibbs. Hasil dari p

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Zattoni, Jacopo, Richard F. Ludueña, Maral Aminpour, and Jack A. Tuszynski. "Computational discovery of potential therapeutic agents against brain-eating amoeba (Naegleria fowleri)." PLOS One 20, no. 7 (2025): e0327621. https://doi.org/10.1371/journal.pone.0327621.

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Naegleria fowleri is a human and animal pathogen well-known for its ability to digest neurons and astrocytes of the host’s brain, causing a haemorrhagic and necrotizing inflammation called Primary Amoebic Meningoencephalitis. Although infections are rare, the mortality rate is over 97%, due to both the non-specificity of the symptoms and the absence of an effective treatment. In this work we employed bioinformatics tools to evaluate the possibility of treating the infection with tubulin-targeting compounds, which we regard as the most promising approach given the unclear view on the pathogenic

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Santos-Martins, Diogo, Stefano Forli, Maria João Ramos, and Arthur J. Olson. "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins." Journal of Chemical Information and Modeling 54, no. 8 (2014): 2371–79. http://dx.doi.org/10.1021/ci500209e.

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Collignon, Barbara, Roland Schulz, Jeremy C. Smith, and Jerome Baudry. "Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers." Journal of Computational Chemistry 32, no. 6 (2010): 1202–9. http://dx.doi.org/10.1002/jcc.21696.

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21

AlMasraf, Ghaith, and Safanah Albayati. "Lead-like compounds for inhibiting Methionine amino peptidase 2 (MetAP2)." Journal of Physics: Conference Series 2114, no. 1 (2021): 012069. http://dx.doi.org/10.1088/1742-6596/2114/1/012069.

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Abstract This research aims to find a new approach to deal with cancer, by targeting a protein that controls the growth and increases the size of the tumour. The approach uses computer-aid drug designed to find the best drug for inhibiting f Methionine Aminopeptidase (Metap2) which is an enzyme that is responsible for starting the synthesis of new protein. The inhibition of the enzyme was found to be crucial in stopping the growth of the tumour and its development. In this research, an in-silico approach was conducted to obtain compounds that are capable of inhibiting the enzyme with non-toxic

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Sirka, Lütfiye, Hacer Doğan, Mehmet Refik Bahar, et al. "(E)-1-(4-Hydroxyphenyl)-3-(substituted-phenyl) prop-2-en-1-ones: Synthesis, In Vitro Cytotoxic Activity and Molecular Docking Studies." Acta Chimica Slovenica 69, no. 2 (2022): 281–92. http://dx.doi.org/10.17344/acsi.2021.7080.

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A series of chalcone compounds (2–11) were designed and synthesized to determine their cytotoxic effects. The structures of 2–11 were fully characterized by their physical and spectral data. The in vitro cytotoxic effects of 2–11 were evaluated against human ovarian cancer (A2780), breast cancer (MCF-7) and prostate cancer (PC-3 and LNCaP) cell lines. The activity potentials of compounds were further evaluated through molecular docking studies with AutoDock4 and Vina softwares. All the compounds (except compound 5) showed significant cytotoxic effects at high doses in all cancer cell lines. Am

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Tripathi, Parul, Saad Sabir Siddiqui, Anju Sharma, Parul Johri, and Aditi Singh. "MOLECULAR DOCKING STUDIES OF CURCUMA LONGA AND ALOE VERA FOR THEIR POTENTIAL ANTICANCER EFFECTS." Asian Journal of Pharmaceutical and Clinical Research 11, no. 4 (2018): 314. http://dx.doi.org/10.22159/ajpcr.2018.v11i4.23995.

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Objective: In this paper, docking study is presented to use these phytocompounds for their prospective role in various types of cancers.Methods: A group of the different set of phytocompounds (aloesin, barbaloin, curcumin, and emodin) were taken and docked into the active sites of Topoisomerase I, a 91-kDa monomer (having 765 amino acids), is encoded by a single copy gene (Top 1) located on chromosome 20q12–13.2 using Autodock4 Software. The docking studies of the selected proteins were also docked to study the anticancerous property of the selected phytocompounds.Result: These studies were ba

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S., Sinha,, Kumari, S., and Mishra, K. "Molecular Docking Study of Crocetin with Interleukin–18 for the Treatment of Atrial Fibrillation." CARDIOMETRY, no. 24 (November 30, 2022): 379–84. http://dx.doi.org/10.18137/cardiometry.2022.24.379384.

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The most frequent arrhythmias are atrial fibrillation. Although the mechanisms underlying are not fully understood, they encompass postoperative and intraoperative phenomena like cardiac ischemia sympathetic activation and inflammation that ends up causing atrial fibrillation. Atrial fibrillation is frequently associated with the presence of pre-existing factors, making the atria susceptible to atrial fibrillation. There are various treatments have been used to manage the condition. However, they are sometimes ineffective, costly, and have side effects stressing the need to explore alternative

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Çayli, Mert, Enis Güzel, Mustafa Macit, and Metin Yavuz. "Organometalik Bakır Kompleksinin Spektroskopik Analizi, Kuantum Kimyasal Hesaplamaları ve Moleküler Kenetleme Çalışmaları." Karadeniz Fen Bilimleri Dergisi 14, no. 4 (2024): 1782–806. https://doi.org/10.31466/kfbd.1480163.

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Bu araştırmada, yeni bir bileşik olan Bis{(E)-2-((3-bromofenilimino)metil)-4,6-di-tert-bütilfenolato-N,O-}bakır(II) (PMTB)2Cu sentezlendi. (PMTB)2Cu bileşiği FT-IR, UV-Vis, X-ışını kırınım spektroskopisi, DFT ve Hirshfeld yüzey analiz yöntemleriyle karakterize edildi. Ayrıca elde edilen sonuçlar arasındaki uyumluluk ve farklılıklar değerlendirilerek teorik ve deneysel veriler karşılaştırılmıştır. (PMTB)2Cu bileşiği için biyolojik aktivitesi, fizikokimyasal, lipofilik, suda çözünürlük, farmakokinetiği ve ilaca benzerliği çevrimiçi bir SwissADME programı ile araştırıldı. Bileşiğin moleküler kene

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Ramadhan, Dwi syah fitra, Ratnasari Dewi, Ismail Ibrahim, et al. "Studi Molecular Docking Senyawa Ircinianin Terhadap Reseptor Sodium-Glukose Co-Transporter 2 (SGLT-2)." FASKES : Jurnal Farmasi, Kesehatan, dan Sains 2, no. 2 (2024): 1–7. https://doi.org/10.32665/faskes.v2i2.3514.

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Latar Belakang: Sodium-glucose cotransporter 2 (SGLT-2) merupakan target potensial dalam pengobatan diabetes tipe 2, dengan inhibitor SGLT-2 yang bekerja menghambat reabsorpsi glukosa di ginjal. Penelitian ini bertujuan untuk mengevaluasi potensi ircinianin, senyawa alami yang diisolasi dari spons Ircinia sp., sebagai inhibitor SGLT-2 menggunakan pendekatan molecular docking. Tujuan: Penelitian ini bertujuan untuk menganalisis interaksi antara ircinianin dan protein SGLT-2 serta mengevaluasi potensi penghambatan ircinianin terhadap reseptor SGLT-2. Metode: Metode yang digunakan adalah molecula

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Bashir, Imtiaz, Maheen Zahid, Aymen Mumtaz, et al. "FENUGREEK TREATMENT OF POLYCYSTIC OVARIAN SYNDROME: AN IN-SILICO EVALUATION TO EXPLORE THE THERAPEUTIC EFFICACY OF QUERCETIN." Journal of Akhtar Saeed Medical & Dental College 04, no. 03 (2022): 116–21. https://doi.org/10.51127/jamdcv4i3oa03.

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Background:Polycystic ovarian syndrome(PCOS)is a fairly common condition that affects both endocrine and metabolic systems. It affects women of reproductive age of all ethnicity and race. Only a small number of females are diagnosed with it.There is a good percentage of people who are still not diagnosed because of a lack of good diagnostic criteria and varying symptoms among different individuals.Fenugreek is an herb that contains many constituents including Quercetin. It helps in the regulation of steroidogenesis.Material and Methods: Molecular docking of Quercetin with insulin receptor subs

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Djajadisastra, Joshita, Hamka Decky Purnama, and Arry Yanuar. "IN SILICO BINDING INTERACTION STUDY OF MEFENAMIC ACID AND PIROXICAM ON HUMAN ALBUMIN." International Journal of Applied Pharmaceutics 9 (October 30, 2017): 102. http://dx.doi.org/10.22159/ijap.2017.v9s1.56_62.

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Objective: A drug can replace other drugs in the same binding position in protein plasma, increasing pharmacological response due to the increasedfree drug concentration. Drug shifting is critical when a compound is tightly bound to a protein. For example, a binding fraction change, from 98% to94%, may increase the free fraction 3 times, from 2% to 6%. Knowing that there is an interaction between mefenamic acid and piroxicam on plasmaprotein, more specifically on human albumin, this study aimed to visualize the interaction between both drugs and human albumin in silico.Methods: This study used

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S., Sahoo,, Sinha, S. та Singh, A. "Molecular Docking Study Reveals α-Santalol from Santalum album Linn. as Promising Inhibitor of CD36 for Atherosclerosis". CARDIOMETRY, № 24 (30 листопада 2022): 353–59. http://dx.doi.org/10.18137/cardiometry.2022.24.353359.

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Atherosclerosis is an inflammatory vascular disease defined by the increasing buildup of cholesterol in the walls of the arteries, and it is a primary contributor to cardiovascular diseases (CVDs). Issues concerning the adverse effects of synthetic treatments have recently resulted in a lack of patient consultations, drug misuse, and, as a result, a disturbance in meticulous disease control. As a result, a new understanding of traditional medicines has recently developed, and much research has been undertaken on such botanicals in an attempt to produce newer naturally based drugs. Santalum alb

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Rasyid, Herlina, Riska Mardiyanti, Ihsanul Arief, and Wahyu Dita Saputri. "An Insight of Cryptocarya Secondary Metabolites as Anticancer P388: Study of Molecular Docking and ADMET Properties." Molekul 18, no. 1 (2023): 89. http://dx.doi.org/10.20884/1.jm.2023.18.1.6364.

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Secondary metabolites isolated from Cryptocarya was known to have various activity especially their cytotoxicity in P388 cell. There were two species of Cryptocarya studied in this research that were Cryptocarya konishii and Cryptocarya lucida. In both species, 8 isolate compounds had bioactivity as anticancer in P388 cells. This study aimed to know the binding affinity and ADMET properties of each isolated compound through P-glycoprotein substrate since this protein was reported to be responsible for the inhibition of P388 cells. Molecular docking was performed using AutoDock4 and AutoDockToo

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Dongre, S., N. Shah, and T. Sharma. "In silico Study to Investigate Targeting Ability of Genistein against Fatty acid binding protein 4 (FABP4) in Peripheral Artery Disease." CARDIOMETRY, no. 26 (March 1, 2023): 329–34. http://dx.doi.org/10.18137/cardiometry.2023.26.329334.

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“Peripheral artery disease” or PAD, is considered as a most prevalent condition, and it commonly coexists with vascular diseases in other body parts. The epidemiology of PAD is well known and connected to age and, particularly, the predisposing factors of smoking and diabetes mellitus. Diagnosis on early basis is important for enhancing the quality of life (QOL) in addition to the reducing risk for the development of significant subsequent vascular events such as “acute myocardial infarction (AMI)” or “stroke”. There are a variety of treatments used to manage and treat the disease. However, th

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Riswana, I. Kadek Rizki, Ni Luh Ari Krisma Anjani, Ni Made Pitri Susanti, and Ni Made Linda Laksmiani. "The activity of of vitexicarpin and artemetin in inhibiting hyperpigmentation: an in silico study." Pharmacy Reports 3, no. 1 (2023): 57. http://dx.doi.org/10.51511/pr.57.

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Hyperpigmentation, characterized by increased skin darkening, is primarily attributed to augmented melanin production, often exacerbated by UV ray exposure. Inhibiting melanogenesis enzymes, such as tyrosinase, tyrosinase-related protein 1, and d-dopachrome tautomerase, is a recognized strategy for managing hyperpigmentation. Flavonoid compounds, namely vitexicarpin and artemetin, have emerged as potential antihyperpigmentation agents. This study explores the inhibitory capabilities of vitexicarpin and artemetin on melanogenesis enzymes through in silico molecular docking. The process involved

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Paturel, Vivien, Stéphanie Baud, Christophe Schneider та Sylvie Brassart-Pasco. "In Silico Prediction of Tetrastatin-Derived Peptide Interactions with αvβ3 and α5β1 Integrins". Pharmaceuticals 18, № 7 (2025): 940. https://doi.org/10.3390/ph18070940.

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Background/Objectives: Tetrastatin, the globular non collagenous (NC1) domain of the α4 chain of collagen IV, was previously demonstrated to inhibit melanoma progression. We identified the minimal active sequence (QKISRCQVCVKYS: QS-13) that reproduced the anti-tumor effects of whole Tetrastatin and demonstrated its anti-angiogenic activity mediated through αvβ3 and α5β1 binding. As QS-13 peptide was not fully soluble in aqueous solution, we designed new peptides with better water solubility. The present work aimed to investigate the interactions of ten QS-13-derived peptides, exhibiting improv

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Jović, Ozren, and Tomislav Šmuc. "Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides." Molecules 25, no. 9 (2020): 2198. http://dx.doi.org/10.3390/molecules25092198.

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Novel machine learning and molecular modelling filtering procedures for drug repurposing have been carried out for the recognition of the novel fungicide targets of Cyp51 and Erg2. Classification and regression approaches on molecular descriptors have been performed using stepwise multilinear regression (FS-MLR), uninformative-variable elimination partial-least square regression, and a non-linear method called Forward Stepwise Limited Correlation Random Forest (FS-LM-RF). Altogether, 112 prediction models from two different approaches have been built for the descriptor recognition of fungicide

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Sunani, Sunani, Maya Andani, Asilla Mauri Ramdini Kamaludin, et al. "In Silico Study of Compounds in Bawang Dayak (Eleutherine palmifolia (L) Merr.) Bulbs on Alpha Estrogen Receptors." Indonesian Journal of Cancer Chemoprevention 13, no. 2 (2022): 83. http://dx.doi.org/10.14499/indonesianjcanchemoprev13iss2pp83-93.

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Breast cancer is an uncontrolled malignancy of the breast that originates from glandular cells, gland ducts, and the supporting tissues of the breast. The development of herbal-based anticancer drugs is progressing, one of which is derived from the natural ingredients of Eleutherine palmifolia tubers. The aim of this study was to determine the activity of compounds derived from Eleutherine palmifolia tubers on the alpha-estrogen receptor (ERα) using an in silico study. The crystal structure of the enzyme used was 3ERT which was obtained from the Protein Data Bank (PDB). The applications used i

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MA, RUIXIN, XIUJUAN XU, LEI ZHAO, REN CAO, and QIANG FANG. "MUTUAL ARTIFICIAL BEE COLONY ALGORITHM FOR MOLECULAR DOCKING." International Journal of Biomathematics 06, no. 06 (2013): 1350038. http://dx.doi.org/10.1142/s1793524513500381.

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Molecular docking method plays an important role on the quest of potential drug candidates, which has been proven to be a valuable tool for virtual screening. Molecular docking is commonly referred to as a parameter optimization problem. During the last decade, some optimization algorithms have been introduced, such as Lamarckian genetic algorithm (LGA) and SODOCK embedded in the AutoDock program. On the basis of the latest docking software AutoDock4.2, we present a novel docking program ABCDock, which incorporates mutual artificial bee colony (MutualABC) into AutoDock. Computer simulation res

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Sharifi, Hoda, Ahmad Ebadi, and Meysam Soleimani. "Biological Evaluation and Molecular Modeling of 3,4-dihydropyrimidine- 2(1H)-one Derivatives as Cytotoxic Agents on Breast Cancer In Vitro." Letters in Drug Design & Discovery 17, no. 8 (2020): 983–92. http://dx.doi.org/10.2174/1570180817666200203125010.

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Background: Kinesins and tubulin inhibitors have attracted researchers’ attention as hopeful targets for achieving effective anticancer agents. Dihydropyrimidine-2-ones (DHPMs) inhibit motor proteins Eg5 in the polymerization process of tubulin, also scaffold bearing benzothiazole heterocycle can block tubulin polymerization/depolymerization. Objective: In this study, the cytotoxic effects and molecular modeling of newly synthesized derivatives of DHPM that were designed by the Scaffold-hopping approach were investigated as potential dual-inhibitors of Eg5 and tubulin. Methods: We investigated

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Hermawan, Faris, Jumina Jumina, Harno Dwi Pranowo, Eti Nurwening Sholikhah, and Muthia Rahayu Iresha. "Computational Design of Thioxanthone Derivatives as Potential Antimalarial Agents through <i>Plasmodium falciparum</i> Protein Inhibition." Indonesian Journal of Chemistry 22, no. 1 (2021): 263. http://dx.doi.org/10.22146/ijc.69448.

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Plasmodium falciparum (P. falciparum) is the most fatal among the other Plasmodium parasites that infect humans with the malaria disease. Currently, the resistance of P. falciparum against some antifolate drugs has become a severe problem. On the other hand, xanthone and thioxanthone derivatives have been reported to have remarkable antimalarial activity. However, molecular docking studies have not evaluated thioxanthone derivative compounds as antimalarial agents. Accordingly, this research investigated the binding pose and inhibition mechanism of several thioxanthone derivatives against P. f

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Muchtaridi, Muchtaridi, Muhammmad Jajuli, and Muhammad Yusuf. "Antagonistic Mechanism of Chalcone Derivatives Against Human Estrogen Alpha of Breast Cancer Using Molecular Dynamic Simulation." Oriental Journal of Chemistry 34, no. 6 (2018): 2735–41. http://dx.doi.org/10.13005/ojc/340607.

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2’,4’-dihydroxy-6-methoxy-3,5-dimethylchalcone (ChalcEA) that isolated from Eugenia aquea Burm f. leaves has a potential anticancer activity against human breast adenocarcinoma cell lines (MCF-7). The objective of this study was to modify ChalcEA to increase its activity as an antagonist of breast cancer with computational simulation approach. A molecular docking simulation was done against the modification structure of ChalcEA with Autodock4 to determine binding interaction between ChalcEA and hERα receptor agonists (PDB ID 1g50). Subsequently, the structure with the smallest bond energy valu

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P., Siyana Saleem, Anoopa Satheesan, Suresh N. Nair, et al. "Phytochemical Identification of Methanolic Extract of Leaves Hernandia peltata Meisn and Evaluation of Anti-Inflammatory Activity In silico." Asian Journal of Research in Biochemistry 14, no. 5 (2024): 122–33. http://dx.doi.org/10.9734/ajrb/2024/v14i5318.

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Aim: To identify the phytochemicals present in the methanolic extract of Hernandia peltata Meisn and to assess their potential anti-inflammatory activity using in silico methods. Place and Duration of Study: Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, between February 2024 and March 2024. Methodology: The chemical profiling of the methanolic leaf extract of Hernandia peltata Meisn. was performed using GC-MS analysis. In silico molecular docking studies were carried out using AutoDock4 to evaluate the binding affinities of

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Khanal, Pukar, B. M. Patil, Jagdish Chand, and Yasmin Naaz. "Anthraquinone Derivatives as an Immune Booster and their Therapeutic Option Against COVID-19." Natural Products and Bioprospecting 10, no. 5 (2020): 325–35. http://dx.doi.org/10.1007/s13659-020-00260-2.

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Abstract Anthraquinone derivatives are identified for their immune-boosting, anti-inflammatory, and anti-viral efficacy. Hence, the present study aimed to investigate the reported anthraquinone derivatives as immune booster molecules in COVID-19 infection and evaluate their binding affinity with three reported targets of novel coronavirus i.e. 3C-like protease, papain-like protease, and spike protein. The reported anthraquinone derivatives were retrieved from an open-source database and filtered based on a positive druglikeness score. Compounds with positive druglikeness scores were predicted

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Parhan Naja, Akhmad, Andika, and Mi’rajunnisa. "STUDI IN SILICO SENYAWAhMETABOLIThSEKUNDER DAUN SIRIH HIJAU (Piper betle L) SEBAGAI INHIBITOR ENZIM MAINhPROTEASE (Mpro) PADA SARS-CoV-2." Medical Sains : Jurnal Ilmiah Kefarmasian 7, no. 2 (2022): 189–202. http://dx.doi.org/10.37874/ms.v7i2.337.

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Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) adalah virus penyebab COVID-19. Salah satu target potensial untuk pengobatan SARS-CoV-2 ialah Main protease (Mpro). Daun sirih hijau (Piper betle L.) adalah tanaman yang terbukti secara ilmiah mempunyai efek sebagai antibakteri dan antivirus. Bagian dari tanaman sirih (Piper betle L.) seperti akar, biji, dan daun bermanfaat untuk pengobatan, tetapi yang paling umum digunakan adalah bagian daun. Tujuan penelitian ini ialah untuk mengetahui potensi dan interaksi senyawa metabolit sekunder daun sirih hijau sebagai antivirus penghambat M

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Naufal, Muhammad, Ika Wiani Hidayat, Elvira Hermawati, Yana Maolana Syah, and Jamaludin Al-Anshori. "Benzalhydantoin Derivative-Based Inhibitors of Eight Receptor Tyrosine Kinases: Synthesis, in-vitro, and in-silico Study." Sains Malaysiana 54, no. 1 (2025): 3661–72. https://doi.org/10.17576/jsm-2025-5401-16.

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Some hydantoin derivatives have been explored for their potential as anticancer agents by inhibiting receptor tyrosine kinases (RTKs). Benzalhydantoin derivatives were obtained from a two-step reaction: condensation and alkylation reaction. The benzalhydantoin activities were obtained from the enzymatic assay, while the molecular interaction was simulated with molecular docking. Five known compounds (5-9) and two new benzalhydantoin derivatives 10-11 have been synthesized from the appropriate precursors with 4-71% yields. The structures of the compounds were determined mainly by NMR and mass s

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Blanco Capurro, Juan I., Matias Di Paola, Marcelo Daniel Gamarra, Marcelo A. Martí, and Carlos P. Modenutti. "An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein–monosaccharide complexes." Glycobiology 29, no. 2 (2018): 124–36. http://dx.doi.org/10.1093/glycob/cwy102.

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Abstract Unraveling the structure of lectin–carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conform

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Ketut Yuantarisa Kartika Putri and Ni Putu Linda Laksmiani. "Potensi Galangin Pada Rimpang Lengkuas sebagai Anti-Photoaging dengan Metode Molecular Docking." Prosiding Workshop dan Seminar Nasional Farmasi 1 (January 16, 2023): 553–65. http://dx.doi.org/10.24843/wsnf.2022.v01.i01.p44.

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Photoaging adalah penuaan pada kulit yang disebabkan oleh paparan sinar ultraviolet. Indonesia merupakan negara tropis yang mendapatkan paparan sinar matahari sepanjang tahun. Kondisi tersebut mengakibatkan masyarakatnya rentan untuk mengalami photoaging. Degradasi kulit disebabkan oleh protein MMP-1 (matrix metalloproteinase-1), sehingga untuk mengatasi photoaging diperlukan agen penghambat MMP-1. Salah satu penghambat MMP-1 yang digunakan secara luas di masyarakat adalah vitamin C. Rimpang lengkuas diketahui sebagai bahan alami yang memiliki aktivitas antioksidan dengan galangin sebagai biom

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Sundari, Khadijah, Aras Syazili, Lia Hapsari, and Abdu Mas'ud. "In Silico Docking to Explore the Coronavirus-2 ACE2 Inhibitor Potential in Brown Seaweed Padina sp. from Morotai Island, North Maluku, Indonesia." International Journal on Advanced Science, Engineering and Information Technology 13, no. 6 (2023): 2081–87. http://dx.doi.org/10.18517/ijaseit.13.6.19110.

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Efforts to explore new sources of antivirals for coronavirus-2 from abundant marine natural materials are highly encouraged. The study aimed to explore the potential compounds of brown seaweed Padina sp. from Morotai Island extracted using three solvents, i.e., n-hexane, ethyl acetate, and acetone, as an antiviral against coronavirus-2 through an entry inhibitor mechanism using bioinformatics tools. The target protein was Angiotensin-Converting Enzyme-related carboxypeptidase (ACE2) receptor. Protein structure was downloaded from PDB and prepared using Chimera. The interaction of compounds to

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Sundari, Khadijah, Aras Syazili, Lia Hapsari, and Abdu Mas'ud. "In Silico Docking to Explore the Coronavirus-2 ACE2 Inhibitor Potential in Brown Seaweed Padina sp. from Morotai Island, North Maluku, Indonesia." International Journal on Advanced Science, Engineering and Information Technology 13, no. 6 (2023): 2081–87. http://dx.doi.org/10.18517/ijaseit.v13i6.19110.

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Efforts to explore new sources of antivirals for coronavirus-2 from abundant marine natural materials are highly encouraged. The study aimed to explore the potential compounds of brown seaweed Padina sp. from Morotai Island extracted using three solvents, i.e., n-hexane, ethyl acetate, and acetone, as an antiviral against coronavirus-2 through an entry inhibitor mechanism using bioinformatics tools. The target protein was Angiotensin-Converting Enzyme-related carboxypeptidase (ACE2) receptor. Protein structure was downloaded from PDB and prepared using Chimera. The interaction of compounds to

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Macedo, Eduardo Hernany Pantoja de, Fernando Loza Guariero, Cristian Lucas Oliveira Paiva, Lucas Marques da Cunha, and Fernando Berton Zanchi. "eAutoDock - Aplicação WEB para cálculo de energia de ligação entre ligante e proteína." OBSERVATÓRIO DE LA ECONOMÍA LATINOAMERICANA 22, no. 10 (2024): e7051. http://dx.doi.org/10.55905/oelv22n10-049.

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Um dos ensaios in silico mais utilizados na prospecção de fármacos é o Virtual Screening por docking molecular. Nesta abordagem, os candidatos a fármacos são encaixados em regiões especificas da macromolécula, normalmente num sítio ativo ou de ligação de uma proteína. Independente do receptor ou das moléculas selecionadas, é necessário estabelecer uma métrica para dizer se a molécula será ou não uma candidata a fármaco. A métrica mais robusta é a energia de ligação, medida em kcal/mol ou kJ/mol, de um ligante muito bem encaixado no sítio de ligação. Esta energia é o limite para se selecionar n

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Tan, Boyang, Tao Tao, Dongyang Lin, Qingyuan Yu, Fengling Sun, and Zhenhua Li. "Exploration of the potential mechanism of Yiyi Tongfeng Formula in the treatment of acute gouty arthritis based on network pharmacology and molecular docking: A review." Medicine 103, no. 37 (2024): e39609. http://dx.doi.org/10.1097/md.0000000000039609.

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The global prevalence of gout is on the rise. Yiyi Tongfeng Formula (YTF), a traditional herbal compound, has gained recognition for its efficacy in managing acute gouty arthritis (AGA). Despite its widespread use, the underlying mechanisms of YTF in AGA treatment remain largely undefined. This study employed network pharmacology and molecular docking to elucidate these mechanisms. We utilized the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, SymMap database, and various literature sources to identify active components and corresponding targets of YTF. Relev

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Rasyid, Herlina, Teni Ernawati, and Indah Muthmainnah Monoarfa. "2-Cinnamamido-4-Methylpentanamide and N-(2-Hydroxypropanoyl)Cinnamamide: Synthesis, Characterization, and Molecular Docking Studies Through PBP2a Protein." Molekul 19, no. 2 (2024): 262. http://dx.doi.org/10.20884/1.jm.2024.19.2.10154.

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ABSTRACT. Cinnamic acid has been found in several types of plants and has a diverse spectrum of bioactivity. Derivatization of cinnamic acid related to the improving bioactivity of a compound. Cinnamic acid can be found as an acid or in conjugated form with amides, esters, aldehydes. This research focus on the synthesis of amide derivatives of cinnamic acid to improve the bioactivity. Two compounds namely 2-cinnamamido-4-methylpentanamide (1a) and N-(2-hydroxypropanoyl)cinnamamide (1b) were carried out through amidation reaction using carbodiimide coupling reagent for 24 hours. The synthesized

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