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Journal articles on the topic 'Ligand design'

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Published: 4 June 2021

Last updated: 25 July 2025

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1

Apostolakist, J., and A. Caflisch. "Computational Ligand Design." Combinatorial Chemistry & High Throughput Screening 2, no. 2 (1999): 91–104. http://dx.doi.org/10.2174/1386207302666220203193501.

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Abstract: A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative st

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2

Caflisch, Amedeo, Rudolf Wälchli, and Claus Ehrhardt. "Computer-Aided Design of Thrombin Inhibitors." Physiology 13, no. 4 (1998): 182–89. http://dx.doi.org/10.1152/physiologyonline.1998.13.4.182.

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Computer-aided ligand design is an active, challenging, and multidisciplinary research field that blends knowledge of biochemistry, physics, and computer sciences. Whenever it is possible to experimentally determine or to model the three-dimensional structure of a pharmacologically relevant enzyme or receptor, computational approaches can be used to design specific high-affinity ligands. This article describes methods, applications, and perspectives of computer-assisted ligand design.

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Nash, Jessica A., Matthew D. Manning, Alexey V. Gulyuk, Aleksey E. Kuznetsov, and Yaroslava G. Yingling. "Gold nanoparticle design for RNA compaction." Biointerphases 17, no. 6 (2022): 061001. http://dx.doi.org/10.1116/6.0002043.

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RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of a

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Zhang, Bihan, Jishi Chen, Yitao Cao, Osburg Jin Huang Chai, and Jianping Xie. "Ligand Design in Ligand‐Protected Gold Nanoclusters." Small 17, no. 27 (2021): 2004381. http://dx.doi.org/10.1002/smll.202004381.

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Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sintesis Ligan Dibutilditiokarbamat (DBDTK) Sebagai Pengekstrak Logam Tanah Jarang Berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 2 (2018): 219. http://dx.doi.org/10.20961/alchemy.14.2.15006.219-235.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat ha

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Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sintesis Ligan Dibutilditiokarbamat (DBDTK) Sebagai Pengekstrak Logam Tanah Jarang Berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 1 (2018): 195. http://dx.doi.org/10.20961/alchemy.14.1.15006.195-203.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat ha

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Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sistesis Ligan Dibutilditiokarbamat (DBDTK) sebagai Pengekstrak Logam Tanah Jarang berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 1 (2018): 84. http://dx.doi.org/10.20961/alchemy.14.1.15006.84-99.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat ha

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8

Mehta, Simpi, and Seema R. Pathak. "INSILICO DRUG DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL COUMARIN DERIVATIVES AS ANTI-CANCER AGENTS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (2017): 335. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16826.

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins usi

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Date, Richard W., Eva Fernandez Iglesias, Kathryn E. Rowe, James M. Elliott, and Duncan W. Bruce. "Metallomesogens by ligand design." Dalton Trans., no. 10 (2003): 1914–31. http://dx.doi.org/10.1039/b212610a.

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10

Fryzuk, Michael D. "Ligand Design Virtual Issue." Inorganic Chemistry 54, no. 20 (2015): 9671–74. http://dx.doi.org/10.1021/acs.inorgchem.5b02191.

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11

Ishiguro, Masaji. "Modeling of receptor–ligand complex and ligand design." Japanese Journal of Pesticide Science 43, no. 1 (2018): 54–59. http://dx.doi.org/10.1584/jpestics.w18-20.

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12

Heller, Markus, and Horst Kessler. "NMR spectroscopy in drug design." Pure and Applied Chemistry 73, no. 9 (2001): 1429–36. http://dx.doi.org/10.1351/pac200173091429.

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The process of preclinical drug discovery consists of two steps: finding of initial hits (binding ligands to a medicinal relevant target, usually a protein) and lead optimization. Nuclear magnetic resonance spectroscopy is a powerful tool that can provide valuable information to every step of drug development. NMR is commonly used for characterizing the structure and molecular dynamics of target or ligand molecules. During the structure-based lead optimization, NMR provides insight into the structural and dynamical properties of the target-ligand complex. Recently, the use of NMR in the lead f

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Nin-Hill, Alba, Nicolas Pierre Friedrich Mueller, Carla Molteni, Carme Rovira, and Mercedes Alfonso-Prieto. "Photopharmacology of Ion Channels through the Light of the Computational Microscope." International Journal of Molecular Sciences 22, no. 21 (2021): 12072. http://dx.doi.org/10.3390/ijms222112072.

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The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch desi

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Solo, Peter, Sangdintuile Zeliang, Muluvelu Lohe, Avünü Neikha, and Akumsunep Jamir. "Structure-based Drug Design, ADME and Molecular Docking analyses of anti-viral agents against SARS-CoV-2 virus, Zika virus and Hepatitis C virus." Journal of Drug Delivery and Therapeutics 13, no. 7 (2023): 65–74. http://dx.doi.org/10.22270/jddt.v13i7.5909.

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Computer-aided drug design has been taking an increasing role in the field of modern drug discovery. These in silico computational methods are cost-effective, reduce the use of animal models in pharmacological research, and can be used to study pathogenic organisms without the need for any facilities. Based on the structure of known anti-viral agents, a total of 812 ligands have been designed. All ligands were screened for drug-likeness based on Lipinski rule of five. A database of ligands was constructed and in silico docking analyses were performed using MOE 2015.10 program against three sel

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15

Shcherbakov, K. A., and A. V. Veselovsky. "A Way for Finding Ligands for New Binding Sites." Biomedical Chemistry: Research and Methods 6, no. 3 (2023): e00200. http://dx.doi.org/10.18097/bmcrm00200.

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Analysis of protein structures shows that most of them have potential binding sites that may be considered as applicable for new ligand design. The lack of known ligands interacting with such binding sites seriously complicated potential ligands selection. We have developed an approach that can increase the effectiveness of virtual screening for such ligands. It integrates methods of de novo ligand design, pharmacophore modeling, molecular docking, molecular dynamics, calculation of binding energies by MM- GBSA. This approach starts by the de novo design of virtual library of potential compoun

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Chen, Xinyue, Wafaa W. Qoutah, Paul Free, Jonathan Hobley, David G. Fernig, and David Paramelle. "Features of Thiolated Ligands Promoting Resistance to Ligand Exchange in Self-Assembled Monolayers on Gold Nanoparticles." Australian Journal of Chemistry 65, no. 3 (2012): 266. http://dx.doi.org/10.1071/ch11432.

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An important feature necessary for biological stability of gold nanoparticles is resistance to ligand exchange. Here, we design and synthesize self-assembled monolayers of mixtures of small ligands on gold nanoparticles promoting high resistance to ligand exchange. We use as ligands short thiolated peptidols, e.g. H-CVVVT-ol, and ethylene glycol terminated alkane thiols (HS-C11-EG4). We present a straightforward method to evaluate the relative stability of each ligand shell against ligand exchange with small thiolated molecules. The results show that a ligand with a ‘thin’ stem, such as HS-C11

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17

Yang, Qi, Dongmeng Chen, Wenjing Fang, and Bing Liu. "The Regulation of Photoelectronic Property and Energy State of FAPbI₃ Surface Via Ligand Dipole Design." E3S Web of Conferences 580 (2024): 01004. http://dx.doi.org/10.1051/e3sconf/202458001004.

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Although the adding multifunction ligand can regulate the perovskite property, the effect of the enhancement depends on the ligand structure. In this paper, the polarity of aromatic ligand is regulated by design strategy — introducing fluorine (F) atom and alkyl chain (R-NH3). Those ligands affect the structure, photoelectric properties and energy state of formamidinium (FAPbI3) perovskite surface. The ligand polarity increases with more F atoms and R-NH3 length, which increases fermi energy and then decreasing band gap and increasing work function (WF). The CF3-PEA/BEA obtains the higher pola

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Payne, Philippa R., Jason A. Bexrud, David C. Leitch, and Laurel L. Schafer. "Asymmetric hydroamination catalyzed by in situ generated chiral amidate and ureate complexes of zirconium — Probing the role of the tether in ligand design." Canadian Journal of Chemistry 89, no. 10 (2011): 1222–29. http://dx.doi.org/10.1139/v11-091.

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Simple chiral proligands have been synthesized from inexpensive chiral starting materials. These amidate and ureate ligands support zirconium complexes that successfully catalyze intramolecular hydroamination with up to 26% ee. Several elements necessary for successful ligand design are highlighted and discussed. In particular, the strict control of metal geometry through multidentate tethered ligands is determined to be an essential aspect of future ligand development.

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Rother, Kristian, Mathias Dunkel, Elke Michalsky, et al. "A structural keystone for drug design." Journal of Integrative Bioinformatics 3, no. 1 (2006): 21–31. http://dx.doi.org/10.1515/jib-2006-19.

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Abstract 3D-structures of proteins and potential ligands are the cornerstones of rational drug design. The first brick to build upon is selecting a protein target and finding out whether biologically active compounds are known. Both tasks require more information than the structures themselves provide. For this purpose we have built a web resource bridging protein and ligand databases. It consists of three parts: i) A data warehouse on annotation of protein structures that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others. ii) A conformational library of structur

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Hasegawa, Tokio, Mayo Osaka, Yusaku Miyamae та ін. "Two Types of PPARγ Ligands Identified in the Extract of Artemisia campestris". Chemistry 3, № 2 (2021): 647–57. http://dx.doi.org/10.3390/chemistry3020045.

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The 70% ethanol extract of Artemisia campestris was screened to find PPARγ ligands using the PPARγ ligand-responsive chimera luciferase reporter system. Capillartemisin B was identified as a PPARγ ligand that stimulated lipid accumulation in 3T3-L1 cells. By further purification of PPARγ ligands from a large-scale preparation of the methanol extract of Artemisia campestris, we isolated and identified eupatilin and santaflavone as PPARγ ligands. Weak PPARγ ligand activity of eupatilin or santaflavone in reporter assay was enhanced by a PPARγ antagonist, GW9662, suggesting that santaflavone or e

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21

Amitesh, Chakraborty Tushar Adhikari*. "The Basic Journey of A Molecule From Pharmacophore To Successful Drug Candidate By Computer Aided Drug Design – A Detailed Review." International Journal of Pharmaceutical Sciences 2, no. 7 (2024): 781–98. https://doi.org/10.5281/zenodo.12736660.

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Computer Aided Drug Design aims at developing <em>in – silico </em>or computer software-based techniques and methods to design and develop a drug molecule which have Pharmacological activity when binds to the desired target and have minimum side effect. For a drug to show desired biological effect, the drug target should be chosen with special emphasis such that normal body functioning does not get hampered. The bioactive conformer of the ligand molecule is chosen which have highest docking score and shows three point attachment to the receptor’s active site. Drug designing can be

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Bremner, J., R. Griffith, and B. Coban. "Ligand Design for Alpha1 Adrenoceptors." Current Medicinal Chemistry 8, no. 6 (2001): 607–20. http://dx.doi.org/10.2174/0929867013373110.

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23

Stalke, D. "Charge density based ligand design." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C69. http://dx.doi.org/10.1107/s010876730809778x.

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Zabłocka, Maria, Alain Igau, Victorio Cadierno, Marek Koprowski та Jean-Pierre Majoral. "α-Phosphino-Imine Ligand Design". Phosphorus, Sulfur, and Silicon and the Related Elements 177, № 8-9 (2002): 1965. http://dx.doi.org/10.1080/10426500213421.

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Funk, Michael A. "Learning from diminutive ligand design." Science 362, no. 6411 (2018): 195.5–196. http://dx.doi.org/10.1126/science.362.6411.195-e.

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Chan, Ting-Fung, and X. F. Steven Zheng. "De novo chemical ligand design ▾." Drug Discovery Today 7, no. 15 (2002): 802–3. http://dx.doi.org/10.1016/s1359-6446(02)02363-2.

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Love, Jason. "Reactions facilitated by ligand design." Dalton Transactions 45, no. 40 (2016): 15700–15701. http://dx.doi.org/10.1039/c6dt90177h.

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Giri, Nabin, and Jianlin Cheng. "Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge." Biomolecules 13, no. 1 (2023): 132. http://dx.doi.org/10.3390/biom13010132.

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Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density ma

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Mikhailov, Oleg V. "Template Synthesis (Self-Assembly) of Macrocycles: Theory and Practice." Molecules 27, no. 15 (2022): 4829. http://dx.doi.org/10.3390/molecules27154829.

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For more than 60 years, in coordination chemistry (and since the beginning of the 21st century, in molecular nanotechnology, too), there has been very significant interest in template synthesis reactions, in which the design of coordination compounds (metal complexes) with complex ligands is carried out not according to the classical scheme [metal ion + ligand → complex], but according to scheme [metal ion + “building blocks” of the future ligand (the so-called ligand synthons or ligsons) → complex] [...]

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Jiang, Xiaolin, Jiahui Zhang, Dongmei Zhao, and Yuehui Li. "Aldehyde effect and ligand discovery in Ru-catalyzed dehydrogenative cross-coupling of alcohols to esters." Chemical Communications 55, no. 19 (2019): 2797–800. http://dx.doi.org/10.1039/c8cc10315a.

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31

Zheng, Fang, and Chang-Guo Zhan. "Computational Modeling of Solvent Effects on Protein-Ligand Interactions Using Fully Polarizable Continuum Model and Rational Drug Design." Communications in Computational Physics 13, no. 1 (2013): 31–60. http://dx.doi.org/10.4208/cicp.130911.121011s.

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AbstractThis is a brief review of the computational modeling of protein-ligand interactions using a recently developed fully polarizable continuum model (FPCM) and rational drug design. Computational modeling has become a powerful tool in understanding detailed protein-ligand interactions at molecular level and in rational drug design. To study the binding of a protein with multiple molecular species of a ligand, one must accurately determine both the relative free energies of all of the molecular species in solution and the corresponding microscopic binding free energies for all of the molecu

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Kühl, Olaf. "The natural bite angle — Seen from a ligand's point of view." Canadian Journal of Chemistry 85, no. 3 (2007): 230–38. http://dx.doi.org/10.1139/v07-023.

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The natural bite angle concept is examined using N,N′-bisphosphino urea ligands as rigid scaffolds. The ligand has an upper limit of about 95° for the observed bite angle in chelate complexes, but prefers a much lower one. The ligand can be described as possessing downward flexibility. The dependence of the bite angle on the P—P distance within the ligand and the M—P bond length is illustrated. The metal tries to force the ligand into its own preferred structure, whereas the ligand wants to achieve a short P—P distance. A truly rigid ligand such as the N,N′-bisphosphino urea family is thus see

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Wang, Weibo, Gerald B. Hammond, and Bo Xu. "Ligand Effects and Ligand Design in Homogeneous Gold(I) Catalysis." Journal of the American Chemical Society 134, no. 12 (2012): 5697–705. http://dx.doi.org/10.1021/ja3011397.

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Dugal-Tessier, Julien, Gregory R Dake, and Derek P Gates. "Chiral Ligand Design: A Bidentate Ligand Incorporating an Acyclic Phosphaalkene." Angewandte Chemie International Edition 47, no. 42 (2008): 8064–67. http://dx.doi.org/10.1002/anie.200802949.

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Dugal-Tessier, Julien, Gregory R Dake, and Derek P Gates. "Chiral Ligand Design: A Bidentate Ligand Incorporating an Acyclic Phosphaalkene." Angewandte Chemie 120, no. 42 (2008): 8184–87. http://dx.doi.org/10.1002/ange.200802949.

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Khorn, P. A., A. P. Luginina, V. A. Pospelov, et al. "Rational drug design targeting g-protein-coupled receptors: a structural biology perspective." Biohimiâ 89, no. 4 (2024): 705–25. http://dx.doi.org/10.31857/s0320972524040124.

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G protein-coupled Receptors (G protein-coupled Receptors, GPCRs) play a key role in the transmission of extracellular signals and regulation of many biological processes, which makes these membrane proteins one of the most important classes of targets for pharmacological agents. The significant increase in the number of atomic structures of GPCRs recently has paved the way for Structure Based Drug Design (SBDD). SBDD uses information on the structure of the receptor-ligand complex to search for affinity and selective ligands without the need for high-throughput experimental ligand screening an

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Piromchom, Jureepan, Jintana Othong, Jaursup Boonmak, Ilpo Mutikainen та Sujittra Youngme. "A novel one-dimensional metal–organic framework with a μ-cyanido-argentate group:catena-poly[[(5,5′-dimethyl-2,2′-bipyridyl-κ2N,N′)silver(I)]-μ-cyanido-κ2N:C]". Acta Crystallographica Section C Structural Chemistry 71, № 12 (2015): 1057–61. http://dx.doi.org/10.1107/s2053229615020288.

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The design and synthesis of metal coordination and supramolecular frameworks containingN-donor ligands and dicyanidoargentate units is of interest due to their potential applications in the fields of molecular magnetism, catalysis, nonlinear optics and luminescence. In the design and synthesis of extended frameworks, supramolecular interactions, such as hydrogen bonding, π–π stacking and van der Waals interactions, have been exploited for molecular recognition associated with biological activity and for the engineering of molecular solids.The title compound, [Ag(CN)(C12H12N2)]n, crystallizes w

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Whitesides, George M., and Vijay M. Krishnamurthy. "Designing ligands to bind proteins." Quarterly Reviews of Biophysics 38, no. 4 (2005): 385–95. http://dx.doi.org/10.1017/s0033583506004240.

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The ability to design drugs (so-called ‘rational drug design’) has been one of the long-term objectives of chemistry for 50 years. It is an exceptionally difficult problem, and many of its parts lie outside the expertise of chemistry. The much more limited problem – how to design tight-binding ligands (rational ligand design) – would seem to be one that chemistry could solve, but has also proved remarkably recalcitrant. The question is ‘Why is it so difficult?’ and the answer is ‘We still don't entirely know’. This perspective discusses some of the technical issues – potential functions, prote

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Üngör, Ökten, Dilyara Igimbayeva, Alina Dragulescu-Andrasi, et al. "Pyridyl-Thioethers as Capping Ligands for the Design of Heteroleptic Fe(II) Complexes with Spin-Crossover Behavior." Magnetochemistry 7, no. 10 (2021): 134. http://dx.doi.org/10.3390/magnetochemistry7100134.

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Mononuclear heteroleptic complexes [Fe(tpma)(bimz)](ClO4)2 (1a), [Fe(tpma)(bimz)](BF4)2 (1b), [Fe(bpte)(bimz)](ClO4)2 (2a), and [Fe(bpte)(bimz)](BF4)2 (2b) (tpma = tris(2-pyridylmethyl)amine, bpte = S,S′-bis(2-pyridylmethyl)-1,2-thioethane, bimz = 2,2′-biimidazoline) were prepared by reacting the corresponding Fe(II) salts with stoichiometric amounts of the ligands. All complexes exhibit temperature-induced spin crossover (SCO), but the SCO temperature is substantially lower for complexes 1a and 1b as compared to 2a and 2b, indicating the stronger ligand field afforded by the N2S2-coordinating

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Yuan, Xiaojing, and Yechun Xu. "Recent Trends and Applications of Molecular Modeling in GPCR–Ligand Recognition and Structure-Based Drug Design." International Journal of Molecular Sciences 19, no. 7 (2018): 2105. http://dx.doi.org/10.3390/ijms19072105.

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G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the rece

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Davis, Carol A., Jeong Kim, Leonard F. Lindoy, Seong-Hwa Lee, and Anthony J. Leong. "Macrocyclic Ligand Design. Structure - Function Relationships Underlying the Interaction of Zinc(II), Cadmium(II), Silver(I) and Lead(II) with Mixed-Donor Macrocyclic Ligands." Australian Journal of Chemistry 51, no. 3 (1998): 189. http://dx.doi.org/10.1071/c97188.

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An investigation of the interaction of zinc(II), cadmium(II), silver(I) and lead(II) with a series of mixed-donor dibenzo-substituted macrocyclic ligands, incorporating O2N3-, O2N4-, O3N2-, O3N3-, O4N2- and O2N3S-donor sets, has been carried out. The log K values for the respective complexes in 95% methanol (I = 0·1; Et4NClO4, 25°C) have been determined potentiometrically. All ligands form 1 : 1 (metal/ligand) complexes with the above metal ions although in isolated cases species of type MLH2+ were also observed. An investigation of the effect of variation of ligand structure on the respective

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Komiyama, Yusuke, Masaki Banno, Kokoro Ueki, Gul Saad, and Kentaro Shimizu. "Automatic generation of bioinformatics tools for predicting protein–ligand binding sites." Bioinformatics 32, no. 6 (2015): 901–7. http://dx.doi.org/10.1093/bioinformatics/btv593.

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Abstract Motivation: Predictive tools that model protein–ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein–ligand binding predictive tools would be useful. Results: We developed a system for automatically generating protein–ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web

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Binder, Patrick, Nikolas D. Schnellbächer, Thomas Höfer, Nils B. Becker, and Ulrich S. Schwarz. "Optimal ligand discrimination by asymmetric dimerization and turnover of interferon receptors." Proceedings of the National Academy of Sciences 118, no. 37 (2021): e2103939118. http://dx.doi.org/10.1073/pnas.2103939118.

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In multicellular organisms, antiviral defense mechanisms evoke a reliable collective immune response despite the noisy nature of biochemical communication between tissue cells. A molecular hub of this response, the interferon I receptor (IFNAR), discriminates between ligand types by their affinity regardless of concentration. To understand how ligand type can be decoded robustly by a single receptor, we frame ligand discrimination as an information-theoretic problem and systematically compare the major classes of receptor architectures: allosteric, homodimerizing, and heterodimerizing. We demo

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Raingeval, Claire, and Isabelle Krimm. "NMR investigation of protein–ligand interactions for G-protein coupled receptors." Future Medicinal Chemistry 11, no. 14 (2019): 1811–25. http://dx.doi.org/10.4155/fmc-2018-0312.

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In this review, we report NMR studies of ligand–GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a

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Hendlich, Manfred. "Databases for Protein–Ligand Complexes." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (1998): 1178–82. http://dx.doi.org/10.1107/s0907444998007124.

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Recent advances in experimental techniques have led to an enormous explosion of available data about protein–ligand complexes. To exploit the information that is hidden in these large data, collection tools for managing and accessing huge data collections are needed. This paper discusses databases for protein–ligand data which are accessibleviathe World Wide Web. A strong focus is placed on the ReLiBase database system which is a new three-dimensional database for storing and analysing structures of protein–ligand complexes currently deposited in the Brookhaven Protein Data Bank (PDB). ReLiBas

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Данилкович, А. В., and A. V. Danilkovich. "Application of Taguchi Method for Optimization of the Peptide Ligand Structure." Mathematical Biology and Bioinformatics 11, no. 2 (2016): 385–93. http://dx.doi.org/10.17537/2016.11.385.

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Taguchi method was used to optimize peptide ligand structure using the H-2/TCR complex (PDB ID 2Z31). This approach greatly reduces the number of experiments that are required to analyze the contribution of various amino acid residues for each position into ligand molecule. Taguchi matrix was used to design a set of peptide ligands for molecular docking and molecular mechanics energy minimization. This approach allowed creating a new peptide structure with lower molecular mechanics energy than native peptide and demonstrates the applicability of the Taguchi method for peptide ligand optimizati

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Borisov, D. V., and A. V. Veselovsky. "Ligand-receptor binding kinetics in drug design." Biomeditsinskaya Khimiya 66, no. 1 (2020): 42–53. http://dx.doi.org/10.18097/pbmc20206601042.

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Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured in vitro at steady concentrations of the receptor and ligand, which are differed from in vivo environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of dr

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MATSUI, Masakazu. "Ligand design for ion size recognition." Bunseki kagaku 45, no. 3 (1996): 209–23. http://dx.doi.org/10.2116/bunsekikagaku.45.209.

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De Benedetti, Pier, and Francesca Fanelli. "Ligand-Receptor Communication and Drug Design." Current Protein & Peptide Science 10, no. 2 (2009): 186–93. http://dx.doi.org/10.2174/138920309787847581.

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Riccardi, Laura, Vito Genna, and Marco De Vivo. "Metal–ligand interactions in drug design." Nature Reviews Chemistry 2, no. 7 (2018): 100–112. http://dx.doi.org/10.1038/s41570-018-0018-6.

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