1
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Danish M, Liaquat T, Ashraf F, Zaman S. Predictive modeling and regression analysis of diverse sulfonamide compounds employed in cancer therapy. Front Chem 2024; 12:1413850. [PMID: 38860237 PMCID: PMC11163099 DOI: 10.3389/fchem.2024.1413850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
Topological indices (TIs) have rich applications in various biological contexts, particularly in therapeutic strategies for cancer. Predicting the performance of compounds in the treatment of cancer is one such application, wherein TIs offer insights into the molecular structures and related properties of compounds. By examining, various compounds exhibit different degree-based TIs, analysts can pinpoint the treatments that are most efficient for specific types of cancer. This paper specifically delves into the topological indices (TIs) implementations in forecasting the biological and physical attributes of innovative compounds utilized in addressing cancer through therapeutic interventions. The analysis being conducted to derivatives of sulfonamides, namely, 4-[(2,4-dichlorophenylsulfonamido)methyl]cyclohexanecarboxylic acid (1), ethyl 4-[(naphthalene-2-sulfonamido)methyl]cyclohexanecarboxylate (2), ethyl 4-[(2,5-dichlorophenylsulfonamido)methyl]cyclohexanecarboxylate (3), 4-[(naphthalene-2-sulfonamido)methyl]cyclohexane-1-carboxylic acid (4) and (2S)-3-methyl-2-(naphthalene-1-sulfonamido)-butanoic acid (5), is performed by utilizing edge partitioning for the computation of degree-based graph descriptors. Subsequently, a linear regression-based model is established to forecast characteristics, like, melting point and formula weight in a quantitative structure-property relationship. The outcomes emphasize the effectiveness or capability of topological indices as a valuable asset for inventing and creating of compounds within the realm of cancer therapy.
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Affiliation(s)
- Muhammad Danish
- Department of Chemistry, University of Sialkot, Sialkot, Pakistan
| | - Tehreem Liaquat
- Department of Chemistry, University of Sialkot, Sialkot, Pakistan
| | - Farwa Ashraf
- Department of Chemistry, University of Sialkot, Sialkot, Pakistan
| | - Shahid Zaman
- Department of Mathematics, University of Sialkot, Sialkot, Pakistan
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2
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Mori S, Shionyu M, Shimamoto K, Nomura K. Bacterial Glycolipid Acting on Protein Transport Across Membranes. Chembiochem 2024; 25:e202300808. [PMID: 38400776 DOI: 10.1002/cbic.202300808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
The process of protein transport across membranes involves a variety of factors and has been extensively investigated. Traditionally, proteinaceous translocons and chaperones have been recognized as crucial factors in this process. However, recent studies have highlighted the significant roles played by lipids and a glycolipid present in biological membranes in membrane protein transport. Membrane lipids can influence transport efficiency by altering the physicochemical properties of membranes. Notably, our studies have revealed that diacylglycerol (DAG) attenuates mobility in the membrane core region, leading to a dramatic suppression of membrane protein integration. Conversely, a glycolipid in Escherichia coli inner membranes, named membrane protein integrase (MPIase), enhances integration not only through the alteration of membrane properties but also via direct interactions with membrane proteins. This review explores the mechanisms of membrane protein integration mediated by membrane lipids, specifically DAG, and MPIase. Our results, along with the employed physicochemical analysis methods such as fluorescence measurements, nuclear magnetic resonance, surface plasmon resonance, and docking simulation, are presented to elucidate these mechanisms.
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Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
- Department of Chemistry Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
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3
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Todisco M, Ding D, Szostak JW. Transient states during the annealing of mismatched and bulged oligonucleotides. Nucleic Acids Res 2024; 52:2174-2187. [PMID: 38348869 PMCID: PMC10954449 DOI: 10.1093/nar/gkae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.
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Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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4
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Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VYF. Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. eLife 2023; 12:e86258. [PMID: 36779700 PMCID: PMC9991059 DOI: 10.7554/elife.86258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023] Open
Abstract
The mammalian NF-κB p52:p52 homodimer together with its cofactor Bcl3 activates transcription of κB sites with a central G/C base pair (bp), while it is inactive toward κB sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined the crystal structures of recombinant human p52 protein in complex with a P-selectin(PSel)-κB DNA (5'-GGGGTGACCCC-3') (central bp is underlined) and variants changing the central bp to A/T or swapping the flanking bp. The structures reveal a nearly two-fold widened minor groove in the central region of the DNA as compared to all other currently available NF-κB-DNA complex structures, which have a central A/T bp. Microsecond molecular dynamics (MD) simulations of free DNAs and p52 bound complexes reveal that free DNAs exhibit distinct preferred conformations, and p52:p52 homodimer induces the least amount of DNA conformational changes when bound to the more transcriptionally active natural G/C-centric PSel-κB, but adopts closed conformation when bound to the mutant A/T and swap DNAs due to their narrowed minor grooves. Our binding assays further demonstrate that the fast kinetics favored by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for κB DNA in complex with NF-κB and pinpoint the importance of binding kinetics, dictated by DNA conformational and dynamic states, in controlling transcriptional activation for NF-κB.
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Affiliation(s)
- Wenfei Pan
- Faculty of Health Sciences, University of MacauTaipaChina
| | | | - Tianjie Li
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Yi Wang
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of MacauTaipaChina
- MoE Frontiers Science Center for Precision Oncology, University of MacauTaipaMacao
- Cancer Centre, Faculty of Health Sciences, University of MacauTaipaChina
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5
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Mori S, Nomura K, Fujikawa K, Osawa T, Shionyu M, Yoda T, Shirai T, Tsuda S, Yoshizawa-Kumagaye K, Masuda S, Nishio H, Yoshiya T, Suzuki S, Muramoto M, Nishiyama KI, Shimamoto K. Intermolecular Interactions between a Membrane Protein and a Glycolipid Essential for Membrane Protein Integration. ACS Chem Biol 2022; 17:609-618. [PMID: 35239308 DOI: 10.1021/acschembio.1c00882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inducing newly synthesized proteins to appropriate locations is an indispensable biological function in every organism. Integration of proteins into biomembranes in Escherichia coli is mediated by proteinaceous factors, such as Sec translocons and an insertase YidC. Additionally, a glycolipid named MPIase (membrane protein integrase), composed of a long sugar chain and pyrophospholipid, was proven essential for membrane protein integration. We reported that a synthesized minimal unit of MPIase possessing only one trisaccharide, mini-MPIase-3, involves an essential structure for the integration activity. Here, to elucidate integration mechanisms using MPIase, we analyzed intermolecular interactions of MPIase or its synthetic analogs with a model substrate, the Pf3 coat protein, using physicochemical methods. Surface plasmon resonance (SPR) analyses revealed the importance of a pyrophosphate for affinity to the Pf3 coat protein. Compared with mini-MPIase-3, natural MPIase showed faster association and dissociation due to its long sugar chain despite the slight difference in affinity. To focus on more detailed MPIase substructures, we performed docking simulations and saturation transfer difference-nuclear magnetic resonance. These experiments yielded that the 6-O-acetyl group on glucosamine and the phosphate of MPIase play important roles leading to interactions with the Pf3 coat protein. The high affinity of MPIase to the hydrophobic region and the basic amino acid residues of the protein was suggested by docking simulations and proven experimentally by SPR using protein mutants devoid of target regions. These results demonstrated the direct interactions of MPIase with a substrate protein and revealed detailed mechanisms of membrane protein integration.
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Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Tsukiho Osawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Takao Yoda
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Shugo Tsuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kumiko Yoshizawa-Kumagaye
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Shun Masuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hideki Nishio
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Sonomi Suzuki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Maki Muramoto
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Ken-ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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6
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Fujikawa K, Mori S, Nishiyama KI, Shimamoto K. A bacterial glycolipid essential for membrane protein integration. Adv Carbohydr Chem Biochem 2022; 81:95-129. [DOI: 10.1016/bs.accb.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Sadiq SK, Muñiz Chicharro A, Friedrich P, Wade RC. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations. J Chem Theory Comput 2021; 17:7912-7929. [PMID: 34739248 DOI: 10.1021/acs.jctc.1c00673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We develop an approach to characterize the effects of gating by a multiconformation protein consisting of macrostate conformations that are either accessible or inaccessible to ligand binding. We first construct a Markov state model of the apo-protein from atomistic molecular dynamics simulations from which we identify macrostates and their conformations, compute their relative macrostate populations and interchange kinetics, and structurally characterize them in terms of ligand accessibility. We insert the calculated first-order rate constants for conformational transitions into a multistate gating theory from which we derive a gating factor γ that quantifies the degree of conformational gating. Applied to HIV-1 protease, our approach yields a kinetic network of three accessible (semi-open, open, and wide-open) and two inaccessible (closed and a newly identified, "parted") macrostate conformations. The parted conformation sterically partitions the active site, suggesting a possible role in product release. We find that the binding kinetics of drugs and drug-like inhibitors to HIV-1 protease falls in the slow gating regime. However, because γ = 0.75, conformational gating only modestly slows ligand binding. Brownian dynamics simulations of the diffusional association of eight inhibitors to the protease─having a wide range of experimental association constants (∼104-1010 M-1 s-1)─yields gated rate constants in the range of ∼0.5-5.7 × 108 M-1 s-1. This indicates that, whereas the association rate of some inhibitors could be described by the model, for many inhibitors either subsequent conformational transitions or alternate binding mechanisms may be rate-limiting. For systems known to be modulated by conformational gating, the approach could be scaled computationally efficiently to screen association kinetics for a large number of ligands.
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Affiliation(s)
- S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Infection Biology Unit, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Abraham Muñiz Chicharro
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Patrick Friedrich
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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8
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Kalwarczyk T, Bielec K, Burdzy K, Holyst R. Influence of molecular rebinding on the reaction rate of complex formation. Phys Chem Chem Phys 2021; 23:19343-19351. [PMID: 34524310 DOI: 10.1039/d1cp02820k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulated Brownian diffusion and reaction-diffusion processes to study the influence of molecular rebinding on the reaction rates of bimolecular reactions. We found that the number of rebinding events, Nreb, is proportional to the target's size and inversely proportional to the diffusion coefficient D and simulation time-step Δt. We found the proportionality constant close to π-1/2. We confirmed that Nreb is defined as a ratio of the activation-limited rate constant ka to the diffusion-limited rate constant, kD. We provide the formula describing the reactivity coefficient κ, modelling the transient-native complex transition for the activation-controlled reaction rates. We show that κ is proportional to (D/Δt)1/2. Finally, we apply our rebinding-including reaction rate model to the real reactions of photoacid dissociation and protein association. Based on literature data for both types of reactions, we found the Δt time-scale. We show that for the photodissociation of a proton, the Δt is equal to 171 ± 18 fs and the average number of rebinding events is approximately equal to 40. For proteins, Δt is of the order of 100 ps with around 20 rebinding events. In both cases the timescale is similar to the timescale of fluctuation of the solvent molecules surrounding the reactants; vibrations and bending in the case of photoacid dissociation and diffusional motion for proteins.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Burdzy
- Department of Mathematics, Box 354350, University of Washington, Seattle, WA 98195, USA
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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9
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Abstract
IntroductionThe pharmacological action of a drug is linked to its affinity for a specific molecular target as quantified by in vitro equilibrium measurements. However, it is clear that for many highly effective drugs, interactions with their molecular targets do not conform to simple, equilibrium conditions in vivo and this results in a temporal discordance between pharmacokinetics and pharmacodynamics. The drug-target residence time model was developed to provide a theoretical framework with which to understand cases in which very slow dissociation of the drug-target complex in vivo results in durable PD effects even after systemic concentrations of drug have waned.Area coveredIn this article, the author provides a brief description of the drug-target residence time model and focuses on the refinements that have been made to the original model to incorporate the influences of compound rebinding in cells and pharmacokinetic properties of drug molecules.Expert opinionThere is now overwhelming evidence for the utility of the drug-target residence time model as a framework for understanding in vivo drug action. The in vitro measured residence time (τR) must be used in concert with equilibrium measures of drug-target affinity (e.g. IC50) and with in vivo measures of pharmacokinetic half-life, to afford the researcher a powerful approach to compound optimization for clinical effect. Despite the significant use and refinement of this model, continued studies are required to better understand the dynamic interplay between residence time, target pathobiology, drug distribution and drug pharmacokinetics.
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Naik A, Misra SK. Modern Sensing Approaches for Predicting Toxicological Responses of Food- and Drug-Based Bioactives on Microbiomes of Gut Origin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6396-6413. [PMID: 34081444 DOI: 10.1021/acs.jafc.1c02736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent scientific findings have correlated the gut microbes with homeostasis of human health by delineating their role in pathogen resistance, bioactive metabolization, and immune responses. Foreign materials, like xenobiotics, that induce an altering effect to the human body also influence the gut microbiome to some extent and often limit their use as a result of significant side effects. Investigating the xenobiotic effect of new therapeutic material or edible could be quite painstaking and economically non-viable. Thus, the use of predictive toxicology methods can be an innovative strategy in the food, pharma, and agriculture industries. There are reported in silico, ex vivo, in vitro, and in vivo methods to evaluate such effects but with added drawbacks, such as lower predictability, physiological dissimilarities, and high cost of associated invasive procedures. This review highlights the current and future possibilities with newer modern sensing approaches of economic and time-scale advantages for predicting toxicological responses on gut microbiomes.
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Affiliation(s)
- Aishwarya Naik
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
| | - Santosh K Misra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
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11
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Kaushik S, Chang CEA. Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association. Front Mol Biosci 2021; 8:659687. [PMID: 34041265 PMCID: PMC8142692 DOI: 10.3389/fmolb.2021.659687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.
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Affiliation(s)
- Shivansh Kaushik
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
| | - Chia-En A Chang
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
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12
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Das A, Das A, Banik BK. Influence of dipole moments on the medicinal activities of diverse organic compounds. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Amangeldiuly N, Karlov D, Fedorov MV. Baseline Model for Predicting Protein–Ligand Unbinding Kinetics through Machine Learning. J Chem Inf Model 2020; 60:5946-5956. [DOI: 10.1021/acs.jcim.0c00450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nurlybek Amangeldiuly
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitry Karlov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maxim V. Fedorov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, Glasgow G4 0NG, U.K
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14
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Dogan B, Durdagi S. Drug Re-positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-target-driven In Silico Studies. Mol Inform 2020; 40:e2000012. [PMID: 33405326 DOI: 10.1002/minf.202000012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Current antiretroviral therapies against HIV involve the usage of at least two drugs that target different stages of HIV life cycle. However, potential drug interactions and side effects pose a problem. A promising concept for complex disease treatment is 'one molecule-multiple target' approach to overcome undesired effects of multiple drugs. Additionally, it is beneficial to consider drug re-purposing due to the cost of taking a drug into the market. Taking these into account, here potential anti-HIV compounds are suggested by virtually screening small approved drug molecules and clinical candidates. Initially, binary QSAR models are used to predict the therapeutic activity of around 7900 compounds against HIV and to predict the toxicity of molecules with high therapeutic activities. Selected compounds are considered for molecular docking studies against two targets, HIV-1 protease enzyme, and chemokine co-receptor CCR5. The top docking poses for all 549 molecules are then subjected to short (1 ns) individual molecular dynamics (MD) simulations and they are ranked based on their calculated relative binding free energies. Finally, 25 molecules are selected for long (200 ns) MD simulations, and 5 molecules are suggested as promising multi-target HIV agents. The results of this study may open new avenues for the designing of new dual HIV-1 inhibitor scaffolds.
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Affiliation(s)
- Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Li D, Ji B. Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2019. [DOI: 10.1016/j.medntd.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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16
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Han D, Tan J, Men J, Li C, Zhang X. Quantitative Structure Activity/Pharmacokinetics Relationship Studies of HIV-1 Protease Inhibitors Using Three Modelling Methods. Med Chem 2019; 17:396-406. [PMID: 31448716 DOI: 10.2174/1573406415666190826154505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 protease inhibitor (PIs) is a good choice for AIDS patients. Nevertheless, for PIs, there are several bugs in clinical application, like drug resistance, the large dose, the high costs and so on, among which, the poor pharmacokinetics property is one of the important reasons that leads to the failure of its clinical application. OBJECTIVE We aimed to build computational models for studying the relationship between PIs structure and its pharmacological activities. METHODS We collected experimental values of koff/Ki and structures of 50 PIs through a careful literature and database search. Quantitative structure activity/pharmacokinetics relationship (QSAR/QSPR) models were constructed by support vector machine (SVM), partial-least squares regression (PLSR) and back-propagation neural network (BPNN). RESULTS For QSAR models, SVM, PLSR and BPNN all generated reliable prediction models with the r2 of 0.688, 0.768 and 0.787, respectively, and r2pred of 0.748, 0.696 and 0.640, respectively. For QSPR models, the optimum models of SVM, PLSR and BPNN obtained the r2 of 0.952, 0.869 and 0.960, respectively, and the r2pred of 0.852, 0.628 and 0.814, respectively. CONCLUSION Among these three modelling methods, SVM showed superior ability than PLSR and BPNN both in QSAR/QSPR modelling of PIs, thus, we suspected that SVM was more suitable for predicting activities of PIs. In addition, 3D-MoRSE descriptors may have a tight relationship with the Ki values of PIs, and the GETAWAY descriptors have significant influence on both koff and Ki in PLSR equations.
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Affiliation(s)
- Dan Han
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Jingrui Men
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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17
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Abstract
The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
| | - Walter Rocchia
- CONCEPT Laboratory, Istituto Italiano di Tecnologia, I-16163 Genova, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
- Computational Sciences Domain, Istituto Italiano di Tecnologia, I-16163 Genova, Italy
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18
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Allec SI, Sun Y, Sun J, Chang CEA, Wong BM. Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems. J Chem Theory Comput 2019; 15:2807-2815. [PMID: 30916958 DOI: 10.1021/acs.jctc.8b01239] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Compared to homogeneous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing, since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. To thoroughly test and understand the performance of our heterogeneous CPU+GPU approach, we examine a variety of algorithmic implementations, benchmarks of different hardware configurations, and applications of this methodology on several large chemical and biological systems. Finally, to demonstrate the capability of our implementation, we conclude with a large-scale DFTB MD simulation of explicitly solvated HIV protease (3974 atoms total) as a proof-of-concept example of an extremely large/complex system which, to the best of our knowledge, is the first time that an entire explicitly solvated protein has been treated at a quantum-based MD level of detail.
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19
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Pourbasheer E, Azari Z, Ganjali MR. Recent Advances in Biosensors Based Nanostructure for Pharmaceutical Analysis. CURR ANAL CHEM 2019. [DOI: 10.2174/1573411014666180319152853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The development of novel nanostructures for pharmaceutical analysis has received
great attention. Biosensors are a class of analytical techniques competent in the rapid quantification
of drugs. Recently, the nanostructures have been applied for modification of biosensors.
Objective:
The goal of the present study is to review novel nanostructures for pharmaceutical analysis
by biosensors.
Method:
In this review, the application of different biosensors was extensively discussed.
Results:
Biosensors based nanostructures are a powerful alternative to conventional analytical techniques,
enabling highly sensitive, real-time, and high-frequency monitoring of drugs without extensive
sample preparation. Several examples of their application have been reported.
Conclusion:
The present paper reviews the recent advances on the pharmaceutical analysis of biosensor
based nanostructures.
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Affiliation(s)
- Eslam Pourbasheer
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| | - Zhila Azari
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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20
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Andleeb H, Khan I, Franconetti A, Tahir MN, Simpson J, Hameed S, Frontera A. Diverse structural assemblies of U-shaped hydrazinyl-sulfonamides: experimental and theoretical analysis of non-covalent interactions stabilizing solid state conformations. CrystEngComm 2019. [DOI: 10.1039/c8ce01917g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preparation and structures of five new U-shaped hydrazinyl-sulfonamides are reported.
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Affiliation(s)
- Hina Andleeb
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Imtiaz Khan
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
- School of Chemistry & Manchester Institute of Biotechnology
| | - Antonio Franconetti
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | | | - Jim Simpson
- Department of Chemistry
- University of Otago
- Dunedin
- New Zealand
| | - Shahid Hameed
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
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21
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Ganotra GK, Wade RC. Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis. ACS Med Chem Lett 2018; 9:1134-1139. [PMID: 30429958 PMCID: PMC6231175 DOI: 10.1021/acsmedchemlett.8b00397] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
![]()
A growing
consensus is emerging that optimizing the drug–target
affinity alone under equilibrium conditions does not necessarily translate
into higher potency in vivo and that instead binding kinetic parameters
should be optimized to ensure better efficacy. Therefore, in silico
methods are needed to predict the kinetic parameters and the mechanistic
determinants of drug–protein binding. Here we demonstrate the
application of COMparative BINding Energy (COMBINE) analysis to derive
quantitative structure–kinetics relationships (QSKRs) for the
dissociation rate constants (koff) of
inhibitors of heat shock protein 90 (HSP90) and HIV-1 protease. We
derived protein-specific scoring functions by correlating koff rate constants with a subset of weighted
interaction energy components determined from the energy-minimized
structures of drug–protein complexes. As the QSKRs derived
for these sets of chemically diverse compounds have good predictive
ability and provide insights into important drug–protein interactions
for optimizing koff, COMBINE analysis
offers a promising approach for binding kinetics-guided lead optimization.
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Affiliation(s)
- Gaurav K. Ganotra
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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22
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Imashimizu M, Takahashi M, Amano R, Nakamura Y. Single-round isolation of diverse RNA aptamers from a random sequence pool. Biol Methods Protoc 2018; 3:bpy004. [PMID: 32161798 PMCID: PMC6994090 DOI: 10.1093/biomethods/bpy004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/02/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
Aptamers are oligonucleotide ligands with specific binding affinity to target molecules. Generally, RNA aptamers are selected from an RNA pool with random sequences, using the technique termed SELEX, in which the target-binding RNA molecules are repeatedly isolated and exponentially amplified. Despite several advantages, SELEX often produces uncertain results during the iterative amplifications of the rare target-binding RNA molecules. Here, we develop a non-repeated, primer-less and target immobilization-free isolation method for generating RNA aptamers, which is robust to experimental noise. Uniquely, this method focuses on finding and removal of non-aptamer sequences from the RNA pool by RNase digestion leaving target-bound aptamer molecules, and thus is independent of aptamer types. The undigested RNA sequences remaining are so few in number that they must be mixed with a large excess of a known sequence for further manipulations and this sequence is then removed by restriction digestion followed by high-throughput sequencing analysis to identify aptamers. Using this method, we generated multiple RNA aptamers targeting α-thrombin and TGFβ1 proteins, independently. This method potentially generates thousands of sequences as aptamer candidates, which may enable us to predict a common average sequence or structural property of these aptamers that is different from input RNA.
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Affiliation(s)
- Masahiko Imashimizu
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Masaki Takahashi
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Ryo Amano
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshikazu Nakamura
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.,RIBOMIC Inc., Minato-ku, Tokyo, 108-0071, Japan
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23
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Miao Y, Huang YMM, Walker RC, McCammon JA, Chang CEA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry 2018; 57:1533-1541. [PMID: 29394043 PMCID: PMC5915299 DOI: 10.1021/acs.biochem.7b01248] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is important to determine the binding pathways and mechanisms of ligand molecules to target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a promising computational tool that allows us to simulate protein-drug binding at an atomistic level. However, the gap between the time scales of current simulations and those of many drug binding processes has limited the usage of conventional MD, which has been reflected in studies of the HIV protease. Here, we have applied a robust enhanced simulation method, Gaussian accelerated molecular dynamics (GaMD), to sample binding pathways of the XK263 ligand and associated protein conformational changes in the HIV protease. During two of 10 independent GaMD simulations performed over 500-2500 ns, the ligand was observed to successfully bind to the protein active site. Although GaMD-derived free energy profiles were not fully converged because of insufficient sampling of the complex system, the simulations still allowed us to identify relatively low-energy intermediate conformational states during binding of the ligand to the HIV protease. Relative to the X-ray crystal structure, the XK263 ligand reached a minimum root-mean-square deviation (RMSD) of 2.26 Å during 2.5 μs of GaMD simulation. In comparison, the ligand RMSD reached a minimum of only ∼5.73 Å during an earlier 14 μs conventional MD simulation. This work highlights the enhanced sampling power of the GaMD approach and demonstrates its wide applicability to studies of drug-receptor interactions for the HIV protease and by extension many other target proteins.
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Affiliation(s)
- Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yu-ming M. Huang
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California at San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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24
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Di Trani JM, De Cesco S, O'Leary R, Plescia J, do Nascimento CJ, Moitessier N, Mittermaier AK. Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry. Nat Commun 2018; 9:893. [PMID: 29497037 PMCID: PMC5832847 DOI: 10.1038/s41467-018-03263-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/31/2018] [Indexed: 11/23/2022] Open
Abstract
Although drug development typically focuses on binding thermodynamics, recent studies suggest that kinetic properties can strongly impact a drug candidate’s efficacy. Robust techniques for measuring inhibitor association and dissociation rates are therefore essential. To address this need, we have developed a pair of complementary isothermal titration calorimetry (ITC) techniques for measuring the kinetics of enzyme inhibition. The advantages of ITC over standard techniques include speed, generality, and versatility; ITC also measures the rate of catalysis directly, making it ideal for quantifying rapid, inhibitor-dependent changes in enzyme activity. We used our methods to study the reversible covalent and non-covalent inhibitors of prolyl oligopeptidase (POP). We extracted kinetics spanning three orders of magnitude, including those too rapid for standard methods, and measured sub-nM binding affinities below the typical ITC limit. These results shed light on the inhibition of POP and demonstrate the general utility of ITC-based enzyme inhibition kinetic measurements. There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.
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Affiliation(s)
- Justin M Di Trani
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Stephane De Cesco
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Rebecca O'Leary
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Jessica Plescia
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Claudia Jorge do Nascimento
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada.,Institute of Biosciences, Federal University of the State of Rio de Janeiro, Urca, 22290-240, Rio de Janeiro, Brazil
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
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25
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Streamlined circular proximity ligation assay provides high stringency and compatibility with low-affinity antibodies. Proc Natl Acad Sci U S A 2018; 115:E925-E933. [PMID: 29339495 DOI: 10.1073/pnas.1718283115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity ligation assay (PLA) is a powerful tool for quantitative detection of protein biomarkers in biological fluids and tissues. Here, we present the circular proximity ligation assay (c-PLA), a highly specific protein detection method that outperforms traditional PLA in stringency, ease of use, and compatibility with low-affinity reagents. In c-PLA, two proximity probes bind to an analyte, providing a scaffolding that positions two free oligonucleotides such that they can be ligated into a circular DNA molecule. This assay format stabilizes antigen proximity probe complexes and enhances stringency by reducing the probability of random background ligation events. Circle formation also increases selectivity, since the uncircularized DNA can be removed enzymatically. We compare this method with traditional PLA on several biomarkers and show that the higher stringency for c-PLA improves reproducibility and enhances sensitivity in both buffer and human plasma. The limit of detection ranges from femtomolar to nanomolar concentrations for both methods. Kinetic analyses using surface plasmon resonance (SPR) and biolayer interferometry (BLI) reveal that the variation in limit of detection is due to the variation in antibody affinity and that c-PLA outperforms traditional PLA for low-affinity antibodies. The lower background signal can be used to increase proximity probe concentration while maintaining a high signal-to-noise ratio, thereby enabling the use of low-affinity reagents in a homogeneous assay format. We anticipate that the advantages of c-PLA will be useful in a variety of clinical protein detection applications where high-affinity reagents are lacking.
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26
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Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. Curr Opin Struct Biol 2017; 49:1-10. [PMID: 29132080 DOI: 10.1016/j.sbi.2017.10.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/22/2017] [Accepted: 10/01/2017] [Indexed: 02/08/2023]
Abstract
The recent and growing evidence that the efficacy of a drug can be correlated to target binding kinetics has seeded the development of a multitude of novel methods aimed at computing rate constants for receptor-ligand binding processes, as well as gaining an understanding of the binding and unbinding pathways and the determinants of structure-kinetic relationships. These new approaches include various types of enhanced sampling molecular dynamics simulations and the combination of energy-based models with chemometric analysis. We assess these approaches in the light of the varying levels of complexity of protein-ligand binding processes.
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Affiliation(s)
- Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Gaurav K Ganotra
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany.
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27
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Xia L, Burger WAC, van Veldhoven JPD, Kuiper BJ, van Duijl TT, Lenselink EB, Paasman E, Heitman LH, IJzerman AP. Structure-Affinity Relationships and Structure-Kinetics Relationships of Pyrido[2,1-f]purine-2,4-dione Derivatives as Human Adenosine A 3 Receptor Antagonists. J Med Chem 2017; 60:7555-7568. [PMID: 28806076 PMCID: PMC5601358 DOI: 10.1021/acs.jmedchem.7b00950] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
We
expanded on a series of pyrido[2,1-f]purine-2,4-dione
derivatives as human adenosine A3 receptor (hA3R) antagonists to determine their kinetic profiles and affinities.
Many compounds showed high affinities and a diverse range of kinetic
profiles. We found hA3R antagonists with very short residence
time (RT) at the receptor (2.2 min for 5) and much longer
RTs (e.g., 376 min for 27 or 391 min for 31). Two representative antagonists (5 and 27) were tested in [35S]GTPγS binding assays, and
their RTs appeared correlated to their (in)surmountable antagonism.
From a kon–koff–KD kinetic map, we divided
the antagonists into three subgroups, providing a possible direction
for the further development of hA3R antagonists. Additionally,
we performed a computational modeling study that sheds light on the
crucial receptor interactions, dictating the compounds’ binding
kinetics. Knowledge of target binding kinetics appears useful for
developing and triaging new hA3R antagonists in the early
phase of drug discovery.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Wessel A C Burger
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Jacobus P D van Veldhoven
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Boaz J Kuiper
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Tirsa T van Duijl
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Ellen Paasman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2300 RA Leiden, The Netherlands
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28
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Schuetz DA, de Witte WEA, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Heitman LH, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, Hill S, Cooke RM, De Graaf C, Leurs R, Frech M, Wade RC, de Lange ECM, IJzerman AP, Müller-Fahrnow A, Ecker GF. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time. Drug Discov Today 2017; 22:896-911. [PMID: 28412474 DOI: 10.1016/j.drudis.2017.02.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/24/2017] [Accepted: 02/17/2017] [Indexed: 01/05/2023]
Abstract
A considerable number of approved drugs show non-equilibrium binding characteristics, emphasizing the potential role of drug residence times for in vivo efficacy. Therefore, a detailed understanding of the kinetics of association and dissociation of a target-ligand complex might provide crucial insight into the molecular mechanism-of-action of a compound. This deeper understanding will help to improve decision making in drug discovery, thus leading to a better selection of interesting compounds to be profiled further. In this review, we highlight the contributions of the Kinetics for Drug Discovery (K4DD) Consortium, which targets major open questions related to binding kinetics in an industry-driven public-private partnership.
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Affiliation(s)
- Doris A Schuetz
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Yin Cheong Wong
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bernhard Knasmueller
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Reggie Bosma
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Indira Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Elena Segala
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Marta Amaral
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany; Instituto de Biologia Experimental e Tecnológica, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Dong Guo
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Dorothee Andres
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Victoria Georgi
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Leigh A Stoddart
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Steve Hill
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Robert M Cooke
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Chris De Graaf
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Rob Leurs
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Elizabeth Cunera Maria de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Anke Müller-Fahrnow
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria.
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29
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Neckles C, Eltschkner S, Cummings JE, Hirschbeck M, Daryaee F, Bommineni GR, Zhang Z, Spagnuolo L, Yu W, Davoodi S, Slayden RA, Kisker C, Tonge PJ. Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase. Biochemistry 2017; 56:1865-1878. [PMID: 28225601 DOI: 10.1021/acs.biochem.6b01048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei. Analysis of enzyme inhibition using a two-dimensional kinetic map demonstrates that the ethyl and hexyl diphenyl ethers fall into two distinct clusters. Modifications to the ethyl diphenyl ether B ring result in changes to both on and off rates, where residence times of up to ∼700 min (∼11 h) are achieved by either ground state stabilization (PT444) or transition state destabilization (slower on rate) (PT404). By contrast, modifications to the hexyl diphenyl ether B ring result in residence times of 300 min (∼5 h) through changes in only ground state stabilization (PT119). Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure-kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. Finally, we demonstrate that three compounds with residence times on bpFabI1 from 118 min (∼2 h) to 670 min (∼11 h) have in vivo efficacy in an acute B. pseudomallei murine infection model using the virulent B. pseudomallei strain Bp400.
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Affiliation(s)
- Carla Neckles
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Sandra Eltschkner
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Jason E Cummings
- Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States
| | - Maria Hirschbeck
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Fereidoon Daryaee
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Gopal R Bommineni
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Zhuo Zhang
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lauren Spagnuolo
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Weixuan Yu
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Shabnam Davoodi
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Richard A Slayden
- Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Peter J Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
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30
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Huang YMM, Raymundo MAV, Chen W, Chang CEA. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease. Biochemistry 2017; 56:1311-1323. [PMID: 28060481 DOI: 10.1021/acs.biochem.6b01112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Equilibrium constants, together with kinetic rate constants of binding, are key factors in the efficacy and safety of drug compounds, informing drug design. However, the association pathways of protein-ligand binding, which contribute to their kinetic behaviors, are little understood. In this work, we used unbiased all-atom molecular dynamics (MD) simulations with an explicit solvent model to study the association processes of protein-ligand binding. Using the HIV protease (HIVp)-xk263 and HIVp-ritonavir protein-ligand systems as cases, we observed that ligand association is a multistep process involving diffusion, localization, and conformational rearrangements of the protein, ligand, and water molecules. Moreover, these two ligands preferred different routes of binding, which reflect two well-known binding mechanisms: induced-fit and conformation selection models. Our study shows that xk263 has a stronger capacity for desolvating surrounding water molecules, thereby inducing a semiopen conformation of the HIVp flaps (induced-fit model). In contrast, the slow dehydration characteristic of ritonavir allows for gradual association with the binding pocket of HIVp when the protein's flap conformation is fully open (conformation selection model). By studying the mechanism of ligand association and understanding the role of solvent molecules during the binding event, we can obtain a different perspective on the mechanism of macromolecule recognition, providing insights into drug discovery.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Mark Anthony V Raymundo
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Wei Chen
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States.,ChemConsulting LLC , Frederick, Maryland 21704, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
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31
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Qu S, Huang S, Pan X, Yang L, Mei H. Constructing Interconsistent, Reasonable, and Predictive Models for Both the Kinetic and Thermodynamic Properties of HIV-1 Protease Inhibitors. J Chem Inf Model 2016; 56:2061-2068. [PMID: 27624663 DOI: 10.1021/acs.jcim.6b00326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Accumulated evidence suggests that the in vivo biological potency of a ligand is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of the protein-ligand interaction (PLI). However, the existing experimental and computational techniques are largely insufficient and limited in large-scale measurements or accurate predictions of the kinetic properties of PLI. In this work, elaborate efforts have been made to develop interconsistent, reasonable, and predictive models of the association rate constant (kon), dissociation rate constant (koff), and equilibrium dissociation constant (KD) of a series of HIV protease inhibitors with different structural skeletons. The results showed that nine Volsurf descriptors derived from water (OH2) and hydrophobic (DRY) probes are key molecular determinants for the kinetic and thermodynamic properties of HIV-1 protease inhibitors. To the best of our knowledge, this is the first time that interconsistent and reasonable models with strong prediction power have been established for both the kinetic and thermodynamic properties of HIV protease inhibitors.
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Affiliation(s)
- Sujun Qu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University , Chongqing 400044, China
| | - Shuheng Huang
- College of Bioengineering, Chongqing University , Chongqing 400044, China
| | - Xianchao Pan
- College of Bioengineering, Chongqing University , Chongqing 400044, China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University , Chongqing 400044, China.,College of Bioengineering, Chongqing University , Chongqing 400044, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University , Chongqing 400044, China.,College of Bioengineering, Chongqing University , Chongqing 400044, China
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32
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Ferruz N, De Fabritiis G. Binding Kinetics in Drug Discovery. Mol Inform 2016; 35:216-26. [PMID: 27492236 DOI: 10.1002/minf.201501018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/20/2016] [Indexed: 12/19/2022]
Abstract
Over the last years, researchers have increasingly become interested in measuring and understanding drugs' binding kinetics, namely the time in which drug and its target associate and dissociate. Historically, drug discovery programs focused on the optimization of target affinity as a proxy of in-vivo efficacy. However, often the efficacy of a ligand is not appropriately described by the in-vitro measured drug-receptor affinity, but rather depends on the lifetime of the in-vivo drug-receptor interaction. In this review we review recent works that highlight the importance of binding kinetics, molecular determinants for rational optimization and the recent emergence of computational methods as powerful tools in measuring and understanding binding kinetics.
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Affiliation(s)
- Noelia Ferruz
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain.,Acellera, Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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33
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Chiu SH, Xie L. Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics. J Chem Inf Model 2016; 56:1164-74. [PMID: 27159844 DOI: 10.1021/acs.jcim.5b00632] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of protein-ligand interactions (PLIs). However, existing experimental and computational techniques are insufficient in studying the molecular details of kinetics processes of PLIs on a large scale. Consequently, we not only have limited mechanistic understanding of the kinetic processes but also lack a practical platform for high-throughput screening and optimization of drug leads on the basis of their kinetic properties. For the first time, we address this unmet need by integrating coarse-grained normal mode analysis with multitarget machine learning (MTML). To test our method, HIV-1 protease is used as a model system. We find that computational models based on the residue normal mode directionality displacement of PLIs can not only recapitulate the results from all-atom molecular dynamics simulations but also predict protein-ligand binding/unbinding kinetics accurately. When this is combined with energetic features, the accuracy of combined kon and koff prediction reaches 74.35%. Furthermore, our integrated model provides us with new insights into the molecular determinants of the kinetics of PLIs. We propose that the coherent coupling of conformational dynamics and thermodynamic interactions between the receptor and the ligand may play a critical role in determining the kinetic rate constants of PLIs. In conclusion, we demonstrate that residue normal mode directionality displacement can serve as a kinetic fingerprint to capture long-time-scale conformational dynamics of the binding/unbinding kinetics. When this is coupled with MTML, it is possible to screen and optimize compounds on the basis of their binding/unbinding kinetics in a high-throughput fashion. The further development of such computational tools will bridge one of the critical missing links between in vitro compound screening and in vivo drug activity.
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Affiliation(s)
- See Hong Chiu
- Department of Computer Science, The Graduate Center, The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Lei Xie
- Department of Computer Science, The Graduate Center, The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States.,Department of Computer Science, Hunter College, The City University of New York , 695 Park Avenue, New York, New York 10065, United States
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34
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Abstract
The drug-target residence time model was first introduced in 2006 and has been broadly adopted across the chemical biology, biotechnology and pharmaceutical communities. While traditional in vitro methods view drug-target interactions exclusively in terms of equilibrium affinity, the residence time model takes into account the conformational dynamics of target macromolecules that affect drug binding and dissociation. The key tenet of this model is that the lifetime (or residence time) of the binary drug-target complex, and not the binding affinity per se, dictates much of the in vivo pharmacological activity. Here, this model is revisited and key applications of it over the past 10 years are highlighted.
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35
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Zhan P, Pannecouque C, De Clercq E, Liu X. Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends. J Med Chem 2015; 59:2849-78. [PMID: 26509831 DOI: 10.1021/acs.jmedchem.5b00497] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The early effectiveness of combinatorial antiretroviral therapy (cART) in the treatment of HIV infection has been compromised to some extent by rapid development of multidrug-resistant HIV strains, poor bioavailability, and cumulative toxicities, and so there is a need for alternative strategies of antiretroviral drug discovery and additional therapeutic agents with novel action modes or targets. From this perspective, we first review current strategies of antiretroviral drug discovery and optimization, with the aid of selected examples from the recent literature. We highlight the development of phosphate ester-based prodrugs as a means to improve the aqueous solubility of HIV inhibitors, and the introduction of the substrate envelope hypothesis as a new approach for overcoming HIV drug resistance. Finally, we discuss future directions for research, including opportunities for exploitation of novel antiretroviral targets, and the strategy of activation of latent HIV reservoirs as a means to eradicate the virus.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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36
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Schoop A, Dey F. On-rate based optimization of structure-kinetic relationship--surfing the kinetic map. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 17:9-15. [PMID: 26724331 DOI: 10.1016/j.ddtec.2015.08.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/24/2015] [Indexed: 05/16/2023]
Abstract
In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed.
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Affiliation(s)
- Andreas Schoop
- Proteros biostructures GmbH, Bunsenstrasse 7a, 82152 Martinsried, Germany.
| | - Fabian Dey
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
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37
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Schneider CS, Bhargav AG, Perez JG, Wadajkar AS, Winkles JA, Woodworth GF, Kim AJ. Surface plasmon resonance as a high throughput method to evaluate specific and non-specific binding of nanotherapeutics. J Control Release 2015; 219:331-344. [PMID: 26415854 DOI: 10.1016/j.jconrel.2015.09.048] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 12/18/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful analytical technique used to quantitatively examine the interactions between various biomolecules, such as proteins and nucleic acids. The technique has been particularly useful in screening and evaluating binding affinity of novel small molecule and biomolecule-derived therapeutics for various diseases and applications including lupus medications, thrombin inhibitors, HIV protease inhibitors, DNA gyrase inhibitors and many others. Recently, there has been increasing interest in nanotherapeutics (nanoRx), due to their unique properties and potential for controlled release of encapsulated drugs and structure-specific targeting to diseased tissues. NanoRx offer the potential to solve many drug delivery challenges by enabling, specific interactions between molecules on the surface of the nanoparticle and molecules in the diseased tissue, while minimizing off-target interactions toward non-diseased tissues. These properties are largely dependent upon careful control and balance of nanoRx interactions and binding properties with tissues in vivo. Given the great promise of nanoRx with regard to engineering specific molecular interactions, SPR can rapidly quantify small aliquots of nanoRx formulations for desired and undesired molecular interactions. Moving forward, we believe that utilization of SPR in the screening and design of nanoRx has the potential to greatly improve the development of targeted nanoRx formulations and eventually lead to improved therapeutic efficacy. In this review, we discuss (1) the fundamental principles of SPR and basic quantitative analysis of SPR data, (2) previous applications of SPR in the study of non-particulate therapeutics and nanoRx, and (3) future opportunities for the use of SPR in the evaluation of nanoRx.
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Affiliation(s)
- Craig S Schneider
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adip G Bhargav
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jimena G Perez
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Aniket S Wadajkar
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jeffrey A Winkles
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Graeme F Woodworth
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Anthony J Kim
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA; Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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38
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Yu Z, van Veldhoven JPD, Louvel J, ’t Hart IME, Rook MB, van der Heyden MAG, Heitman LH, IJzerman AP. Structure–Affinity Relationships (SARs) and Structure–Kinetics Relationships (SKRs) of Kv11.1 Blockers. J Med Chem 2015; 58:5916-29. [DOI: 10.1021/acs.jmedchem.5b00518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhiyi Yu
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jacobus P. D. van Veldhoven
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Julien Louvel
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Ingrid M. E. ’t Hart
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Martin B. Rook
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Marcel A. G. van der Heyden
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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39
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Design strategies to address kinetics of drug binding and residence time. Bioorg Med Chem Lett 2015; 25:2019-27. [DOI: 10.1016/j.bmcl.2015.02.027] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 02/06/2023]
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40
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Huang YMM, Kang M, Chang CEA. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J Mol Recognit 2015; 27:537-48. [PMID: 25042708 DOI: 10.1002/jmr.2377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/05/2022]
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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41
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Olaru A, Bala C, Jaffrezic-Renault N, Aboul-Enein HY. Surface Plasmon Resonance (SPR) Biosensors in Pharmaceutical Analysis. Crit Rev Anal Chem 2015; 45:97-105. [DOI: 10.1080/10408347.2014.881250] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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42
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Bondza S, Stenberg J, Nestor M, Andersson K, Björkelund H. Conjugation Effects on Antibody–Drug Conjugates: Evaluation of Interaction Kinetics in Real Time on Living Cells. Mol Pharm 2014; 11:4154-63. [DOI: 10.1021/mp500379d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sina Bondza
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
| | - Jonas Stenberg
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Marika Nestor
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Section
of Otolaryngology and Head and Neck Surgery, Department of Surgical
Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Karl Andersson
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Hanna Björkelund
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
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43
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Abstract
UNLABELLED HIV-1 assembles at the plasma membrane of virus-producing cells as an immature, noninfectious particle. Processing of the Gag and Gag-Pol polyproteins by the viral protease (PR) activates the viral enzymes and results in dramatic structural rearrangements within the virion--termed maturation--that are a prerequisite for infectivity. Despite its fundamental importance for viral replication, little is currently known about the regulation of proteolysis and about the dynamics and structural intermediates of maturation. This is due mainly to the fact that HIV-1 release and maturation occur asynchronously both at the level of individual cells and at the level of particle release from a single cell. Here, we report a method to synchronize HIV-1 proteolysis in vitro based on protease inhibitor (PI) washout from purified immature virions, thereby temporally uncoupling virus assembly and maturation. Drug washout resulted in the induction of proteolysis with cleavage efficiencies correlating with the off-rate of the respective PR-PI complex. Proteolysis of Gag was nearly complete and yielded the correct products with an optimal half-life (t(1/2)) of ~5 h, but viral infectivity was not recovered. Failure to gain infectivity following PI washout may be explained by the observed formation of aberrant viral capsids and/or by pronounced defects in processing of the reverse transcriptase (RT) heterodimer associated with a lack of RT activity. Based on our results, we hypothesize that both the polyprotein processing dynamics and the tight temporal coupling of immature particle assembly and PR activation are essential for correct polyprotein processing and morphological maturation and thus for HIV-1 infectivity. IMPORTANCE Cleavage of the Gag and Gag-Pol HIV-1 polyproteins into their functional subunits by the viral protease activates the viral enzymes and causes major structural rearrangements essential for HIV-1 infectivity. This proteolytic maturation occurs concomitant with virus release, and investigation of its dynamics is hampered by the fact that virus populations in tissue culture contain particles at all stages of assembly and maturation. Here, we developed an inhibitor washout strategy to synchronize activation of protease in wild-type virus. We demonstrated that nearly complete Gag processing and resolution of the immature virus architecture are accomplished under optimized conditions. Nevertheless, most of the resulting particles displayed irregular morphologies, Gag-Pol processing was not faithfully reconstituted, and infectivity was not recovered. These data show that HIV-1 maturation is sensitive to the dynamics of processing and also that a tight temporal link between virus assembly and PR activation is required for correct polyprotein processing.
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Boufas W, Dupont N, Berredjem M, Berrezag K, Becheker I, Berredjem H, Aouf NE. Synthesis and antibacterial activity of sulfonamides. SAR and DFT studies. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.05.066] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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45
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Synthesis and structure of potentially biologically active N-(silylmethyl)tetrahydropyrimidin-2-ones. Russ Chem Bull 2014. [DOI: 10.1007/s11172-014-0705-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Gonçalves AM, Pedro AQ, Santos FM, Martins LM, Maia CJ, Queiroz JA, Passarinha LA. Trends in protein-based biosensor assemblies for drug screening and pharmaceutical kinetic studies. Molecules 2014; 19:12461-85. [PMID: 25153865 PMCID: PMC6270898 DOI: 10.3390/molecules190812461] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/02/2014] [Accepted: 08/05/2014] [Indexed: 12/20/2022] Open
Abstract
The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.
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Affiliation(s)
- Ana M Gonçalves
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Augusto Q Pedro
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Fátima M Santos
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Luís M Martins
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Cláudio J Maia
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - João A Queiroz
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Luís A Passarinha
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
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Simard JR, Rauh D. FLiK: a direct-binding assay for the identification and kinetic characterization of stabilizers of inactive kinase conformations. Methods Enzymol 2014; 548:147-71. [PMID: 25399645 DOI: 10.1016/b978-0-12-397918-6.00006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the hundreds of kinase inhibitors currently in discovery and preclinical phases, the number of FDA-approved kinase inhibitors remains very low by comparison, a discrepancy which reflects the challenges which accompanies kinase inhibitor development. Targeting protein kinases with ATP-competitive inhibitors has been the classical approach to inhibit kinase activity, but the highly conserved nature of the ATP-binding site often contributes to the poor inhibitor selectivity. To address this problem, we developed a high-throughput screening technology that can discriminate for inhibitors, which stabilize inactive kinase conformations by binding within allosteric pockets in the kinase domain. Here, we describe how to use the Fluorescence Labels in Kinases approach to measure the K(d) of ligands as well as how to kinetically characterize the binding and dissociation of ligands to the kinase. We also describe how this technology can be used to rapidly screen small molecule libraries in high throughput.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany; Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany.
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48
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Manvar A, Shah A. Subtle Mitsunobu couplings under super-heating: the role of high-throughput continuous flow and microwave strategies. Org Biomol Chem 2014; 12:8112-24. [DOI: 10.1039/c4ob01432d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fragile Mitsunobu reaction can efficiently be performed under super-heating.
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Affiliation(s)
- Atul Manvar
- Department of Pharmaceutical and Medicinal Chemistry
- Royal College of Surgeons in Ireland
- Dublin, Ireland
| | - Anamik Shah
- National Facility for Drug Discovery
- Centre of Excellence
- Saurashtra University
- Rajkot-360005, India
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49
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Spillane W, Malaubier JB. Sulfamic Acid and Its N- and O-Substituted Derivatives. Chem Rev 2013; 114:2507-86. [DOI: 10.1021/cr400230c] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- William Spillane
- School
of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Jean-Baptiste Malaubier
- Manufacturing Science
and
Technology, Roche Ireland Limited, Clarecastle, Co. Clare, Ireland
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50
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Xu B, Varasteh Z, Orlova A, Andersson K, Larhammar D, Björkelund H. Detecting ligand interactions with G protein-coupled receptors in real-time on living cells. Biochem Biophys Res Commun 2013; 441:820-4. [PMID: 24211197 DOI: 10.1016/j.bbrc.2013.10.149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 10/28/2013] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large group of receptors of great biological and clinical relevance. Despite this, the tools for a detailed analysis of ligand-GPCR interactions are limited. The aim of this paper was to demonstrate how ligand binding to GPCRs can be followed in real-time on living cells. This was conducted using two model systems, the radiolabeled porcine peptide YY (pPYY) interacting with transfected human Y2 receptor (hY2R) and the bombesin antagonist RM26 binding to the naturally expressed gastrin-releasing peptide receptor (GRPR). By following the interaction over time, the affinity and kinetic properties such as association and dissociation rate were obtained. Additionally, data were analyzed using the Interaction Map method, which can evaluate a real-time binding curve and present the number of parallel interactions contributing to the curve. It was found that pPYY binds very slowly with an estimated time to equilibrium of approximately 12h. This may be problematic in standard end-point assays where equilibrium is required. The RM26 binding showed signs of heterogeneity, observed as two parallel interactions with unique kinetic properties. In conclusion, measuring binding in real-time using living cells opens up for a better understanding of ligand interactions with GPCRs.
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Affiliation(s)
- Bo Xu
- Department of Neuroscience, Unit of Pharmacology, Uppsala University, Husargatan 2, 751 24 Uppsala, Sweden.
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