1
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024:10.1038/s41573-024-00958-9. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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2
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Tänzel V, Jäger M, Wolf S. Learning Protein-Ligand Unbinding Pathways via Single-Parameter Community Detection. J Chem Theory Comput 2024. [PMID: 38865714 DOI: 10.1021/acs.jctc.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Understanding the dynamics of biomolecular complexes, e.g., of protein-ligand (un)binding, requires the comprehension of paths such systems take between metastable states. In MD simulations, paths are usually not observable per se, but they need to be inferred from simulation trajectories. Here, we present a novel approach to cluster trajectories based on a community detection algorithm that necessitates only the definition of a single parameter. The unbinding of the streptavidin-biotin complex is used as a benchmark system and the A2a adenosine receptor in complex with the inhibitor ZM241385 as an elaborate application. We demonstrate how such clusters of trajectories correspond to pathways and how the approach helps in the identification of reaction coordinates for a considered (un)binding process.
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Affiliation(s)
- Victor Tänzel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg 79104, Germany
| | - Miriam Jäger
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg 79104, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg 79104, Germany
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3
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Servant G, Kenakin T. A Pharmacological perspective on the temporal properties of sweeteners. Pharmacol Res 2024; 204:107211. [PMID: 38744400 DOI: 10.1016/j.phrs.2024.107211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Several non-caloric sweeteners exhibit a delay in sweetness onset and a sweetness linger after sampling. These temporal properties are thought to be the result of non-specific interactions with cell membranes and proteins in the oral cavity. Data and analysis presented in this report also support the potential involvement of receptor affinity and binding kinetics to this phenomenon. In general, affected sweeteners exhibit distinctly higher binding affinity compared to carbohydrate sweeteners, which do not have temporal issues. In addition, binding kinetic simulations illustrate much slower receptor binding association and dissociation kinetics for a set of non-caloric sweeteners presenting temporal issues, in comparison to carbohydrate sweeteners. So, the higher affinity of some non-caloric sweeteners, dictating lower use levels, and affecting binding kinetics, could contribute to their delay and linger in sweetness perception. Simple pharmacology principles could explain, at least in part, some of the temporal issues of sweeteners.
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Affiliation(s)
- Guy Servant
- dsm-firmenich, 10636 Scripps Summit Court #201, San Diego, CA 92131, USA.
| | - Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, 120 Mason Farm Rd., 4042 Genetic Medicine CB #7365, Chapel Hill, NC 27599, USA
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4
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Li C, Rounds CC, Torres VC, He Y, Xu X, Papavasiliou G, Samkoe KS, Brankov JG, Tichauer KM. Quantifying Imaging Agent Binding and Dissociation in 3-D Cancer Spheroid Tissue Culture Using Paired-Agent Principles. Ann Biomed Eng 2024; 52:1625-1637. [PMID: 38409434 PMCID: PMC10174639 DOI: 10.1007/s10439-024-03476-2] [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: 04/04/2023] [Accepted: 02/10/2024] [Indexed: 02/28/2024]
Abstract
Binding kinetics play an important role in cancer diagnosis and therapeutics. However, current methods of quantifying binding kinetics fail to consider the three-dimensional environment that drugs and imaging agents experience in biological tissue. In response, a methodology to assay agent binding and dissociation in 3-D tissue culture was developed using paired-agent molecular imaging principles. To test the methodology, the uptakes of ABY-029 (an IRDye 800CW-labeled epidermal growth factor receptor (EGFR)-targeted antibody mimetic) and IRDye-700DX carboxylate in 3-D spheroids were measured in four different human cancer cell lines throughout staining and rinsing. A compartment model (optimized for the application) was then fit to the kinetic curves of both imaging agents to estimate binding and dissociation rate constants of the EGFR-targeted ABY-029 agent. A statistically significant correlation was observed between apparent association rate constant (k3) and the receptor concentration experimentally and in simulations (r = 0.99, p < 0.05). A statistically significant difference was found between effective k3 (apparent rate constant of ABY-029 binding to EGFR) values for cell lines with varying levels of EGFR expression (p < 0.05), with no significant difference found between cell lines and controls for other fit parameters. Additionally, a similar binding affinity profile compared to a gold standard method was determined by this model. This low-cost methodology to quantify imaging agent or drug binding affinity in clinically relevant 3-D tumor spheroid models can be used to guide timing of imaging in molecular guided surgery and could have implications in drug development.
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Affiliation(s)
- Chengyue Li
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Cody C Rounds
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Veronica C Torres
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Yusheng He
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Xiaochun Xu
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Georgia Papavasiliou
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Kimberley S Samkoe
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Jovan G Brankov
- Electrical and Computer Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Kenneth M Tichauer
- Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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5
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Naskar A, Roy RK, Srivastava D, Patra N. Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson's Disease. J Phys Chem B 2024. [PMID: 38822803 DOI: 10.1021/acs.jpcb.4c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) remains a viable target for drug development since the discovery of the association of its mutations with Parkinson's disease (PD). G2019S (in the kinase domain) is the most common mutation for LRRK2-based PD. Though various types of inhibitors have been developed for the kinase domain to reduce the effect of the mutation, understanding the working of these inhibitors at the molecular level is still ongoing. This study focused on the exploration of the dissociation mechanism (pathways) of inhibitors from (WT and G2019S) LRRK2 kinase (using homology model CHK1 kinase), which is one of the crucial aspects in drug discovery. Here, two ATP-competitive type I inhibitors, PF-06447475 and MLi-2 (Comp1 and Comp2 ), and one non-ATP-competitive type II inhibitor, rebastinib (Comp3), were considered for this investigation. To study the unbinding process, random accelerated molecular dynamics simulations were performed. The binding free energies of the three inhibitors for different egression paths were determined using umbrella sampling. This work found four major egression pathways that were adopted by the inhibitors Comp1 (path1, path2, and path3), Comp2 (path1, path2 and path3), and Comp3 (path3 and path4). Also, the mechanism of unbinding for each path and key residues involved in unbinding were explored. Mutation was not observed to impact the preference of the particular egression pathways for both LRRK2-Comp1 and -Comp2 systems. However, the findings suggested that the size of the inhibitor molecules might have an effect on the preference of the egression pathways. The binding energy and residence time of the inhibitors followed a similar trend to experimental observations. The findings of this work might provide insight into designing more potent inhibitors for the G2019S LRRK2 kinase.
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Affiliation(s)
- Avigyan Naskar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Rakesh K Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Diship Srivastava
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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6
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Kosar M, Sarott RC, Sykes DA, Viray AEG, Vitale RM, Tomašević N, Li X, Ganzoni RLZ, Kicin B, Reichert L, Patej KJ, Gómez-Bouzó U, Guba W, McCormick PJ, Hua T, Gruber CW, Veprintsev DB, Frank JA, Grether U, Carreira EM. Flipping the GPCR Switch: Structure-Based Development of Selective Cannabinoid Receptor 2 Inverse Agonists. ACS CENTRAL SCIENCE 2024; 10:956-968. [PMID: 38799662 PMCID: PMC11117691 DOI: 10.1021/acscentsci.3c01461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024]
Abstract
We report a blueprint for the rational design of G protein coupled receptor (GPCR) ligands with a tailored functional response. The present study discloses the structure-based design of cannabinoid receptor type 2 (CB2R) selective inverse agonists (S)-1 and (R)-1, which were derived from privileged agonist HU-308 by introduction of a phenyl group at the gem-dimethylheptyl side chain. Epimer (R)-1 exhibits high affinity for CB2R with Kd = 39.1 nM and serves as a platform for the synthesis of a wide variety of probes. Notably, for the first time these fluorescent probes retain their inverse agonist functionality, high affinity, and selectivity for CB2R independent of linker and fluorophore substitution. Ligands (S)-1, (R)-1, and their derivatives act as inverse agonists in CB2R-mediated cAMP as well as G protein recruitment assays and do not trigger β-arrestin-receptor association. Furthermore, no receptor activation was detected in live cell ERK1/2 phosphorylation and Ca2+-release assays. Confocal fluorescence imaging experiments with (R)-7 (Alexa488) and (R)-9 (Alexa647) probes employing BV-2 microglial cells visualized CB2R expressed at endogenous levels. Finally, molecular dynamics simulations corroborate the initial docking data in which inverse agonists restrict movement of toggle switch Trp2586.48 and thereby stabilize CB2R in its inactive state.
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Affiliation(s)
- Miroslav Kosar
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Roman C. Sarott
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - David A. Sykes
- Faculty
of Medicine & Health Sciences, University
of Nottingham, Nottingham NG7 2UH, U.K.
- Centre
of Membrane Proteins and Receptors (COMPARE), University of Birmingham
and University of Nottingham, https://www.birmingham-nottingham.ac.uk/compare
| | - Alexander E. G. Viray
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Rosa Maria Vitale
- Institute
of Biomolecular Chemistry, National Research
Council, Via Campi Flegrei
34, 80078 Pozzuoli, Italy
| | - Nataša Tomašević
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstrasse
17, 1090 Vienna, Austria
| | - Xiaoting Li
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Rudolf L. Z. Ganzoni
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Bilal Kicin
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Lisa Reichert
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Kacper J. Patej
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Uxía Gómez-Bouzó
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Wolfgang Guba
- Roche
Pharma Research & Early Development, Roche Innovation Center Basel,
F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Peter J. McCormick
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Ashton
Street, Liverpool L69 3GE, U.K.
| | - Tian Hua
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Christian W. Gruber
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstrasse
17, 1090 Vienna, Austria
| | - Dmitry B. Veprintsev
- Faculty
of Medicine & Health Sciences, University
of Nottingham, Nottingham NG7 2UH, U.K.
- Centre
of Membrane Proteins and Receptors (COMPARE), University of Birmingham
and University of Nottingham, https://www.birmingham-nottingham.ac.uk/compare
| | - James A. Frank
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
- Vollum
Institute, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Uwe Grether
- Roche
Pharma Research & Early Development, Roche Innovation Center Basel,
F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erick M. Carreira
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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7
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Kopranovic A, Meyer-Almes FJ. Rapid Determination of Kinetic Constants for Slow-Binding Inhibitors and Inactivators of Human Histone Deacetylase 8. Int J Mol Sci 2024; 25:5593. [PMID: 38891780 PMCID: PMC11171933 DOI: 10.3390/ijms25115593] [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: 04/21/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The kinetics and mechanism of drug binding to its target are critical to pharmacological efficacy. A high throughput (HTS) screen often results in hundreds of hits, of which usually only simple IC50 values are determined during reconfirmation. However, kinetic parameters such as residence time for reversible inhibitors and the kinact/KI ratio, which is the critical measure for evaluating covalent inactivators, are early predictive measures to assess the chances of success of the hits in the clinic. Using the promising cancer target human histone deacetylase 8 as an example, we present a robust method that calculates concentration-dependent apparent rate constants for the inhibition or inactivation of HDAC8 from dose-response curves recorded after different pre-incubation times. With these data, hit compounds can be classified according to their mechanism of action, and the relevant kinetic parameters can be calculated in a highly parallel fashion. HDAC8 inhibitors with known modes of action were correctly assigned to their mechanism, and the binding mechanisms of some hits from an internal HDAC8 screening campaign were newly determined. The oxonitriles SVE04 and SVE27 were classified as fast reversible HDAC8 inhibitors with moderate time-constant IC50 values of 4.2 and 2.6 µM, respectively. The hit compound TJ-19-24 and SAH03 behave like slow two-step inactivators or reversible inhibitors, with a very low reverse isomerization rate.
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Affiliation(s)
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
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8
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Eberle SA, Gustavsson M. Bilayer lipids modulate ligand binding to atypical chemokine receptor 3. Structure 2024:S0969-2126(24)00171-0. [PMID: 38776922 DOI: 10.1016/j.str.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.
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Affiliation(s)
- Stefanie Alexandra Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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9
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Spiriti J, Wong CF. Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning. J Chem Theory Comput 2024; 20:4029-4044. [PMID: 38640609 DOI: 10.1021/acs.jctc.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
We used umbrella sampling and the milestoning simulation method to study the dissociation of multiple ligands from protein kinase PYK2. The activation barriers obtained from the potential of mean force of the umbrella sampling simulations correlated well with the experimental dissociation rates. Using the zero-temperature string method, we obtained optimized paths along the free-energy surfaces for milestoning simulations of three ligands with a similar structure. The milestoning simulations gave an absolute dissociation rate within 2 orders of magnitude of the experimental value for two ligands but at least 3 orders of magnitude too high for the third. Despite the similarity in their structures, the ligands took different pathways to exit from the binding site of PYK2, making contact with different sets of residues. In addition, the protein experienced different conformational changes for dissociation of the three ligands.
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Affiliation(s)
- Justin Spiriti
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri 63121, United States
| | - Chung F Wong
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri 63121, United States
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10
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Truong DT, Ho K, Pham DQH, Chwastyk M, Nguyen-Minh T, Nguyen MT. Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics. Sci Rep 2024; 14:10475. [PMID: 38714683 PMCID: PMC11076533 DOI: 10.1038/s41598-024-59899-3] [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: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Thai Nguyen-Minh
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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11
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Khan ZR, Welsby PJ, Stasik I, Hayes JM. Discovery of Potent Multikinase Type-II Inhibitors Targeting CDK5 in the DFG-out Inactive State with Promising Potential against Glioblastoma. J Med Chem 2024. [PMID: 38686637 DOI: 10.1021/acs.jmedchem.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Kinases have proven valuable targets in successful cancer drug discovery projects, but not yet for malignant brain tumors where type-II inhibition of cyclin-dependent kinase 5 (CDK5) stabilizing the DFG-out inactive state has potential for design of selective and clinically efficient drug candidates. In the absence of crystallographic evidence for a CDK5 DFG-out inactive state protein-ligand complex, for the first time, a model was designed using metadynamics/molecular dynamics simulations. Glide docking of the ZINC15 biogenic database identified [pyrimidin-2-yl]amino-furo[3,2-b]-furyl-urea/amide hit chemical scaffolds. For four selected analogues (4, 27, 36, and 42), potent effects on glioblastoma cell viability in U87-MG, T98G, and U251-MG cell lines and patient-derived cultures were generally observed (IC50s ∼ 10-40 μM at 72 h). Selectivity profiling against 11 homologous kinases revealed multikinase inhibition (CDK2, CDK5, CDK9, and GSK-3α/β), most potent for GSK-3α in the nanomolar range (IC50s ∼ 0.23-0.98 μM). These compounds may therefore have diverse anticancer mechanisms of action and are of considerable interest for lead optimization.
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Affiliation(s)
- Zahra R Khan
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Philip J Welsby
- Education Directorate, Royal College of Physicians, Liverpool L7 3FA, United Kingdom
| | - Izabela Stasik
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Joseph M Hayes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Biomedical Evidence-Based Transdisciplinary (BEST) Health Research Institute, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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12
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Walker V. The Intricacies of Renal Phosphate Reabsorption-An Overview. Int J Mol Sci 2024; 25:4684. [PMID: 38731904 PMCID: PMC11083860 DOI: 10.3390/ijms25094684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
To maintain an optimal body content of phosphorus throughout postnatal life, variable phosphate absorption from food must be finely matched with urinary excretion. This amazing feat is accomplished through synchronised phosphate transport by myriads of ciliated cells lining the renal proximal tubules. These respond in real time to changes in phosphate and composition of the renal filtrate and to hormonal instructions. How they do this has stimulated decades of research. New analytical techniques, coupled with incredible advances in computer technology, have opened new avenues for investigation at a sub-cellular level. There has been a surge of research into different aspects of the process. These have verified long-held beliefs and are also dramatically extending our vision of the intense, integrated, intracellular activity which mediates phosphate absorption. Already, some have indicated new approaches for pharmacological intervention to regulate phosphate in common conditions, including chronic renal failure and osteoporosis, as well as rare inherited biochemical disorders. It is a rapidly evolving field. The aim here is to provide an overview of our current knowledge, to show where it is leading, and where there are uncertainties. Hopefully, this will raise questions and stimulate new ideas for further research.
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Affiliation(s)
- Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton S016 6YD, UK
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13
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Xu C, Zhang X, Zhao L, Verkhivker GM, Bai F. Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies. JACS AU 2024; 4:1632-1645. [PMID: 38665669 PMCID: PMC11040708 DOI: 10.1021/jacsau.4c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The binding kinetics of drugs to their targets are gradually being recognized as a crucial indicator of the efficacy of drugs in vivo, leading to the development of various computational methods for predicting the binding kinetics in recent years. However, compared with the prediction of binding affinity, the underlying structure and dynamic determinants of binding kinetics are more complicated. Efficient and accurate methods for predicting binding kinetics are still lacking. In this study, quantitative structure-kinetics relationship (QSKR) models were developed using 132 inhibitors targeting the ATP binding domain of heat shock protein 90α (HSP90α) to predict the dissociation rate constant (koff), enabling a direct assessment of the drug-target residence time. These models demonstrated good predictive performance, where hydrophobic and hydrogen bond interactions significantly influence the koff prediction. In subsequent applications, our models were used to assist in the discovery of new inhibitors for the N-terminal domain of HSP90α (N-HSP90α), demonstrating predictive capabilities on an experimental validation set with a new scaffold. In X-ray crystallography experiments, the loop-middle conformation of apo N-HSP90α was observed for the first time (previously, the loop-middle conformation had only been observed in holo-N-HSP90α structures). Interestingly, we observed different conformations of apo N-HSP90α simultaneously in an asymmetric unit, which was also observed in a holo-N-HSP90α structure, suggesting an equilibrium of conformations between different states in solution, which could be one of the determinants affecting the binding kinetics of the ligand. Different ligands can undergo conformational selection or alter the equilibrium of conformations, inducing conformational rearrangements and resulting in different effects on binding kinetics. We then used molecular dynamics simulations to describe conformational changes of apo N-HSP90α in different conformational states. In summary, the study of the binding kinetics and molecular mechanisms of N-HSP90α provides valuable information for the development of more targeted therapeutic approaches.
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Affiliation(s)
- Chao Xu
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xianglei Zhang
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Lianghao Zhao
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Graduate Program in Computational
and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Fang Bai
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Information Science and Technology, ShanghaiTech
University, 393 Middle Huaxia Road, Shanghai 201210, China
- Shanghai
Clinical Research and Trial Center, Shanghai 201210, China
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14
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Kappel AD, Jha R, Guggilapu S, Smith WJ, Feroze AH, Dmytriw AA, Vicenty-Padilla J, Alcedo Guardia RE, Gessler FA, Patel NJ, Du R, See AP, Peruzzi PP, Aziz-Sultan MA, Bernstock JD. Endovascular Applications for the Management of High-Grade Gliomas in the Modern Era. Cancers (Basel) 2024; 16:1594. [PMID: 38672676 PMCID: PMC11049132 DOI: 10.3390/cancers16081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
High-grade gliomas (HGGs) have a poor prognosis and are difficult to treat. This review examines the evolving landscape of endovascular therapies for HGGs. Recent advances in endovascular catheter technology and delivery methods allow for super-selective intra-arterial cerebral infusion (SSIACI) with increasing precision. This treatment modality may offer the ability to deliver anti-tumoral therapies directly to tumor regions while minimizing systemic toxicity. However, challenges persist, including blood-brain barrier (BBB) penetration, hemodynamic complexities, and drug-tumor residence time. Innovative adjunct techniques, such as focused ultrasound (FUS) and hyperosmotic disruption, may facilitate BBB disruption and enhance drug penetration. However, hemodynamic factors that limit drug residence time remain a limitation. Expanding therapeutic options beyond chemotherapy, including radiotherapy and immunobiologics, may motivate future investigations. While preclinical and clinical studies demonstrate moderate efficacy, larger randomized trials are needed to validate the clinical benefits. Additionally, future directions may involve endovascular sampling for peri-tumoral surveillance; changes in drug formulations to prolong residence time; and the exploration of non-pharmaceutical therapies, like radioembolization and photodynamic therapy. Endovascular strategies hold immense potential in reshaping HGG treatment paradigms, offering targeted and minimally invasive approaches. However, overcoming technical challenges and validating clinical efficacy remain paramount for translating these advancements into clinical care.
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Affiliation(s)
- Ari D. Kappel
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Rohan Jha
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
| | - Saibaba Guggilapu
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
| | - William J. Smith
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Abdullah H. Feroze
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Adam A. Dmytriw
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Juan Vicenty-Padilla
- Neurosurgery Section, School of Medicine University of Puerto Rico, Medical Sciences Campus, San Juan P.O. Box 365067, Puerto Rico (R.E.A.G.)
| | - Rodolfo E. Alcedo Guardia
- Neurosurgery Section, School of Medicine University of Puerto Rico, Medical Sciences Campus, San Juan P.O. Box 365067, Puerto Rico (R.E.A.G.)
| | - Florian A. Gessler
- Department of Neurosurgery, Rostock University Hospital, 18057 Rostock, Germany
| | - Nirav J. Patel
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Rose Du
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Alfred P. See
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Pier Paolo Peruzzi
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Mohammad A. Aziz-Sultan
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Joshua D. Bernstock
- Harvard Medical School, Boston, MA 02115, USA; (A.D.K.); (S.G.); (R.D.); (A.P.S.)
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
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15
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Lee S, Wang D, Seeliger MA, Tiwary P. Calculating Protein-Ligand Residence Times Through State Predictive Information Bottleneck based Enhanced Sampling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589710. [PMID: 38659748 PMCID: PMC11042289 DOI: 10.1101/2024.04.16.589710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Understanding drug residence times in target proteins is key to improving drug efficacy and understanding target recognition in biochemistry. While drug residence time is just as important as binding affinity, atomic-level understanding of drug residence times through molecular dynamics (MD) simulations has been difficult primarily due to the extremely long timescales. Recent advances in rare event sampling have allowed us to reach these timescales, yet predicting protein-ligand residence times remains a significant challenge. Here we present a semi-automated protocol to calculate the ligand residence times across 12 orders of magnitudes of timescales. In our proposed framework, we integrate a deep learning-based method, the state predictive information bottleneck (SPIB), to learn an approximate reaction coordinate (RC) and use it to guide the enhanced sampling method metadynamics. We demonstrate the performance of our algorithm by applying it to six different protein-ligand complexes with available benchmark residence times, including the dissociation of the widely studied anti-cancer drug Imatinib (Gleevec) from both wild-type Abl kinase and drug-resistant mutants. We show how our protocol can recover quantitatively accurate residence times, potentially opening avenues for deeper insights into drug development possibilities and ligand recognition mechanisms.
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Affiliation(s)
- Suemin Lee
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Dedi Wang
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Pratyush Tiwary
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
- University of Maryland Institute for Health Computing, Rockville, United States
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16
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Patel D, Huma ZE, Duncan D. Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action. ACS Chem Biol 2024; 19:824-838. [PMID: 38567529 PMCID: PMC11040609 DOI: 10.1021/acschembio.3c00805] [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: 12/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Covalent inhibition has seen a resurgence in the last several years. Although long-plagued by concerns of off-target effects due to nonspecific reactions leading to covalent adducts, there has been success in developing covalent inhibitors, especially within the field of anticancer therapy. Covalent inhibitors can have an advantage over noncovalent inhibitors since the formation of a covalent adduct may serve as an additional mode of selectivity due to the intrinsic reactivity of the target protein that is absent in many other proteins. Unfortunately, many covalent inhibitors form irreversible adducts with off-target proteins, which can lead to considerable side-effects. By designing the inhibitor to form reversible covalent adducts, one can leverage competing on/off kinetics in complex formation by taking advantage of the law of mass action. Although covalent adducts do form with off-target proteins, the reversible nature of inhibition prevents accumulation of the off-target adduct, thus limiting side-effects. In this perspective, we outline important characteristics of reversible covalent inhibitors, including examples and a guide for inhibitor development.
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Affiliation(s)
| | | | - Dustin Duncan
- Department of Chemistry, Brock
University, St. Catharines, Ontario L2S 3A1, Canada
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17
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Chen X, Huang X, Ma Q, Kuzmič P, Zhou B, Zhang S, Chen J, Xu J, Liu B, Jiang H, Zhang W, Yang C, Wu S, Huang J, Li H, Long C, Zhao X, Xu H, Sheng Y, Guo Y, Niu C, Xue L, Xu Y, Liu J, Zhang T, Spencer J, Zhu Z, Deng W, Chen X, Chen SH, Zhong N, Xiong X, Yang Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol 2024; 9:1075-1088. [PMID: 38553607 PMCID: PMC10994847 DOI: 10.1038/s41564-024-01618-9] [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: 02/27/2023] [Accepted: 01/22/2024] [Indexed: 04/06/2024]
Abstract
Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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Affiliation(s)
- Xiaoxin Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xiaodong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Biao Zhou
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Sai Zhang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjie Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunguang Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiguan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Haijun Li
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Chaofeng Long
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China
| | - Hongrui Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanan Sheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaoting Guo
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
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18
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Ray D, Parrinello M. Data-driven classification of ligand unbinding pathways. Proc Natl Acad Sci U S A 2024; 121:e2313542121. [PMID: 38412121 DOI: 10.1073/pnas.2313542121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Abstract
Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics (MD) simulations, often in quantitative agreement with experiments. However, only a qualitative picture of the ligand binding/unbinding paths can be obtained through a conventional analysis of the MD trajectories. Besides, the higher degree of manual effort involved in analyzing pathways limits its applicability in large-scale drug discovery. Here, we address this limitation by introducing an automated approach for analyzing molecular transition paths with a particular focus on protein-ligand dissociation. Our method is based on the dynamic time-warping algorithm, originally designed for speech recognition. We accurately classified molecular trajectories using a very generic descriptor set of contacts or distances. Our approach outperforms manual classification by distinguishing between parallel dissociation channels, within the pathways identified by visual inspection. Most notably, we could compute exit-path-specific ligand-dissociation kinetics. The unbinding timescale along the fastest path agrees with the experimental residence time, providing a physical interpretation to our entirely data-driven protocol. In combination with appropriate enhanced sampling algorithms, this technique can be used for the initial exploration of ligand-dissociation pathways as well as for calculating path-specific thermodynamic and kinetic properties.
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Affiliation(s)
- Dhiman Ray
- Simulations Research Line, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Michele Parrinello
- Simulations Research Line, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
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19
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Wang Y, Ngo VA, Wang X. Stereoselective recognition of morphine enantiomers by μ-opioid receptor. Natl Sci Rev 2024; 11:nwae029. [PMID: 38410825 PMCID: PMC10896590 DOI: 10.1093/nsr/nwae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 02/28/2024] Open
Abstract
Stereospecific recognition of chiral molecules plays a crucial role in biological systems. The μ-opioid receptor (MOR) exhibits binding affinity towards (-)-morphine, a well-established gold standard in pain management, while it shows minimal binding affinity for the (+)-morphine enantiomer, resulting in a lack of analgesic activity. Understanding how MOR stereoselectively recognizes morphine enantiomers has remained a puzzle in neuroscience and pharmacology for over half-a-century due to the lack of direct observation techniques. To unravel this mystery, we constructed the binding and unbinding processes of morphine enantiomers with MOR via molecular dynamics simulations to investigate the thermodynamics and kinetics governing MOR's stereoselective recognition of morphine enantiomers. Our findings reveal that the binding of (-)-morphine stabilizes MOR in its activated state, exhibiting a deep energy well and a prolonged residence time. In contrast, (+)-morphine fails to sustain the activation state of MOR. Furthermore, the results suggest that specific residues, namely D1142.50 and D1473.32, are deprotonated in the active state of MOR bound to (-)-morphine. This work highlights that the selectivity in molecular recognition goes beyond binding affinities, extending into the realm of residence time.
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Affiliation(s)
- Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Van A Ngo
- Advanced Computing for Life Sciences and Engineering Group, Science Engagement Section, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge 37831, USA
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
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20
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Huo T, Zhao X, Cheng Z, Wei J, Zhu M, Dou X, Jiao N. Late-stage modification of bioactive compounds: Improving druggability through efficient molecular editing. Acta Pharm Sin B 2024; 14:1030-1076. [PMID: 38487004 PMCID: PMC10935128 DOI: 10.1016/j.apsb.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Accepted: 11/13/2023] [Indexed: 03/17/2024] Open
Abstract
Synthetic chemistry plays an indispensable role in drug discovery, contributing to hit compounds identification, lead compounds optimization, candidate drugs preparation, and so on. As Nobel Prize laureate James Black emphasized, "the most fruitful basis for the discovery of a new drug is to start with an old drug"1. Late-stage modification or functionalization of drugs, natural products and bioactive compounds have garnered significant interest due to its ability to introduce diverse elements into bioactive compounds promptly. Such modifications alter the chemical space and physiochemical properties of these compounds, ultimately influencing their potency and druggability. To enrich a toolbox of chemical modification methods for drug discovery, this review focuses on the incorporation of halogen, oxygen, and nitrogen-the ubiquitous elements in pharmacophore components of the marketed drugs-through late-stage modification in recent two decades, and discusses the state and challenges faced in these fields. We also emphasize that increasing cooperation between chemists and pharmacists may be conducive to the rapid discovery of new activities of the functionalized molecules. Ultimately, we hope this review would serve as a valuable resource, facilitating the application of late-stage modification in the construction of novel molecules and inspiring innovative concepts for designing and building new drugs.
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Affiliation(s)
- Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zengrui Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
| | - Minghui Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, East China Normal University, Shanghai 200062, China
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21
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Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
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Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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22
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Xu J, Zhang P, Chen Y. Surface Plasmon Resonance Biosensors: A Review of Molecular Imaging with High Spatial Resolution. BIOSENSORS 2024; 14:84. [PMID: 38392003 PMCID: PMC10886473 DOI: 10.3390/bios14020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
Surface plasmon resonance (SPR) is a powerful tool for determining molecular interactions quantitatively. SPR imaging (SPRi) further improves the throughput of SPR technology and provides the spatially resolved capability for observing the molecular interaction dynamics in detail. SPRi is becoming more and more popular in biological and chemical sensing and imaging. However, SPRi suffers from low spatial resolution due to the imperfect optical components and delocalized features of propagating surface plasmonic waves along the surface. Diverse kinds of approaches have been developed to improve the spatial resolution of SPRi, which have enormously impelled the development of the methodology and further extended its possible applications. In this minireview, we introduce the mechanisms for building a high-spatial-resolution SPRi system and present its experimental schemes from prism-coupled SPRi and SPR microscopy (SPRM) to surface plasmonic scattering microscopy (SPSM); summarize its exciting applications, including molecular interaction analysis, molecular imaging and profiling, tracking of single entities, and analysis of single cells; and discuss its challenges in recent decade as well as the promising future.
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Affiliation(s)
- Jiying Xu
- National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Faculty of Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Zhang
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Chen
- National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Faculty of Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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23
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Stampelou M, Ladds G, Kolocouris A. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A 3 Receptor. J Phys Chem B 2024; 128:914-936. [PMID: 38236582 DOI: 10.1021/acs.jpcb.3c05986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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24
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Wang L, Bohmer MJ, Wang J, Nardella F, Calla J, Laureano De Souza M, Schindler KA, Montejo L, Mittal N, Rocamora F, Treat M, Charlton JT, Tumwebaze PK, Rosenthal PJ, Cooper RA, Chakrabarti R, Winzeler EA, Chakrabarti D, Gray NS. Discovery of Potent Antimalarial Type II Kinase Inhibitors with Selectivity over Human Kinases. J Med Chem 2024; 67:1460-1480. [PMID: 38214254 PMCID: PMC10950204 DOI: 10.1021/acs.jmedchem.3c02046] [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] [Indexed: 01/13/2024]
Abstract
While progress has been made in the effort to eradicate malaria, the disease remains a significant threat to global health. Acquired resistance to frontline treatments is emerging in Africa, urging a need for the development of novel antimalarial agents. Repurposing human kinase inhibitors provides a potential expedited route given the availability of a diverse array of kinase-targeting drugs that are approved or in clinical trials. Phenotypic screening of a library of type II human kinase inhibitors identified compound 1 as a lead antimalarial, which was initially developed to target human ephrin type A receptor 2 (EphA2). Here, we report a structure-activity relationship study and lead optimization of compound 1, which led to compound 33, with improved antimalarial activity and selectivity.
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Affiliation(s)
- Lushun Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Monica J Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Flore Nardella
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Lukas Montejo
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mayland Treat
- School of Public Health, University of California, Berkeley California 94704, United States
| | - Jordan T Charlton
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94110, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | - Ratna Chakrabarti
- Division of Cancer Research, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
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25
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Falkenstern L, Georgi V, Bunse S, Badock V, Husemann M, Roehn U, Stellfeld T, Fitzgerald M, Ferrara S, Stöckigt D, Stresemann C, Hartung IV, Fernández-Montalván A. A miniaturized mode-of-action profiling platform enables high throughput characterization of the molecular and cellular dynamics of EZH2 inhibition. Sci Rep 2024; 14:1739. [PMID: 38242973 PMCID: PMC10799085 DOI: 10.1038/s41598-023-50964-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024] Open
Abstract
The market approval of Tazemetostat (TAZVERIK) for the treatment of follicular lymphoma and epithelioid sarcoma has established "enhancer of zeste homolog 2" (EZH2) as therapeutic target in oncology. Despite their structural similarities and common mode of inhibition, Tazemetostat and other EZH2 inhibitors display differentiated pharmacological profiles based on their target residence time. Here we established high throughput screening methods based on time-resolved fluorescence energy transfer, scintillation proximity and high content analysis microscopy to quantify the biochemical and cellular binding of a chemically diverse collection of EZH2 inhibitors. These assays allowed to further characterize the interplay between EZH2 allosteric modulation by methylated histone tails (H3K27me3) and inhibitor binding, and to evaluate the impact of EZH2's clinically relevant mutant Y641N on drug target residence times. While all compounds in this study exhibited slower off-rates, those with clinical candidate status display significantly slower target residence times in wild type EZH2 and disease-related mutants. These inhibitors interact in a more entropy-driven fashion and show the most persistent effects in cellular washout and antiproliferative efficacy experiments. Our work provides mechanistic insights for the largest cohort of EZH2 inhibitors reported to date, demonstrating that-among several other binding parameters-target residence time is the best predictor of cellular efficacy.
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Affiliation(s)
- Lilia Falkenstern
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Rentschler Biopharma SE, Erwin-Rentschler-Straße 21, 88471, Laupheim, Germany
| | - Victoria Georgi
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Stefanie Bunse
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Volker Badock
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | | | - Ulrike Roehn
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Timo Stellfeld
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Mark Fitzgerald
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nested Therapeutics, 1030 Massachusetts Avenue, Suite 410, Cambridge, MA, 02138, USA
| | - Steven Ferrara
- Broad Institute, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA
| | - Detlef Stöckigt
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Carlo Stresemann
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Nuvisan Innovation Campus Berlin, Müllerstrasse 178, 13353, Berlin, Germany
| | - Ingo V Hartung
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany
- Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Amaury Fernández-Montalván
- Bayer AG, Müllerstrasse 178, 13353, Berlin, Germany.
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400, Biberach an der Riß, Germany.
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26
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Fuchs N, Zhang L, Calvo-Barreiro L, Kuncewicz K, Gabr M. Inhibitors of Immune Checkpoints: Small Molecule- and Peptide-Based Approaches. J Pers Med 2024; 14:68. [PMID: 38248769 PMCID: PMC10817355 DOI: 10.3390/jpm14010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
The revolutionary progress in cancer immunotherapy, particularly the advent of immune checkpoint inhibitors, marks a significant milestone in the fight against malignancies. However, the majority of clinically employed immune checkpoint inhibitors are monoclonal antibodies (mAbs) with several limitations, such as poor oral bioavailability and immune-related adverse effects (irAEs). Another major limitation is the restriction of the efficacy of mAbs to a subset of cancer patients, which triggered extensive research efforts to identify alternative approaches in targeting immune checkpoints aiming to overcome the restricted efficacy of mAbs. This comprehensive review aims to explore the cutting-edge developments in targeting immune checkpoints, focusing on both small molecule- and peptide-based approaches. By delving into drug discovery platforms, we provide insights into the diverse strategies employed to identify and optimize small molecules and peptides as inhibitors of immune checkpoints. In addition, we discuss recent advances in nanomaterials as drug carriers, providing a basis for the development of small molecule- and peptide-based platforms for cancer immunotherapy. Ongoing research focused on the discovery of small molecules and peptide-inspired agents targeting immune checkpoints paves the way for developing orally bioavailable agents as the next-generation cancer immunotherapies.
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Affiliation(s)
- Natalie Fuchs
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Longfei Zhang
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Laura Calvo-Barreiro
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Katarzyna Kuncewicz
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
- Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Moustafa Gabr
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
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27
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de Los Santos-Ramirez JM, Boyas-Chavez PG, Cerrillos-Ordoñez A, Mata-Gomez M, Gallo-Villanueva RC, Perez-Gonzalez VH. Trends and challenges in microfluidic methods for protein manipulation-A review. Electrophoresis 2024; 45:69-100. [PMID: 37259641 DOI: 10.1002/elps.202300056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/06/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023]
Abstract
Proteins are important molecules involved in an immensely large number of biological processes. Being capable of manipulating proteins is critical for developing reliable and affordable techniques to analyze and/or detect them. Such techniques would enable the production of therapeutic agents for the treatment of diseases or other biotechnological applications (e.g., bioreactors or biocatalysis). Microfluidic technology represents a potential solution to protein manipulation challenges because of the diverse phenomena that can be exploited to achieve micro- and nanoparticle manipulation. In this review, we discuss recent contributions made in the field of protein manipulation in microfluidic systems using different physicochemical principles and techniques, some of which are miniaturized versions of already established macro-scale techniques.
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Affiliation(s)
| | - Pablo G Boyas-Chavez
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
| | | | - Marco Mata-Gomez
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
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28
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Qu Z, Krabill AD, Zhang ZY. High-Throughput Discovery and Characterization of Covalent Inhibitors for Protein Tyrosine Phosphatases. Methods Mol Biol 2024; 2743:301-316. [PMID: 38147223 DOI: 10.1007/978-1-0716-3569-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Covalent inhibition has gained increasing interest in targeting the undruggable protein tyrosine phosphatases (PTPs). However, a systematic method for discovering and characterizing covalent PTP inhibitors has yet to be established. Here, we describe a workflow involving high-throughput screening of covalent fragment libraries and a novel biochemical assay that enables the acquisition of kinetics parameters of PTP inhibition by covalent inhibitors with higher throughput.
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Affiliation(s)
- Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA.
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA.
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29
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Powers A, Yu HH, Suriana P, Koodli RV, Lu T, Paggi JM, Dror RO. Geometric Deep Learning for Structure-Based Ligand Design. ACS CENTRAL SCIENCE 2023; 9:2257-2267. [PMID: 38161364 PMCID: PMC10755842 DOI: 10.1021/acscentsci.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024]
Abstract
A pervasive challenge in drug design is determining how to expand a ligand-a small molecule that binds to a target biomolecule-in order to improve various properties of the ligand. Adding single chemical groups, known as fragments, is important for lead optimization tasks, and adding multiple fragments is critical for fragment-based drug design. We have developed a comprehensive framework that uses machine learning and three-dimensional protein-ligand structures to address this challenge. Our method, FRAME, iteratively determines where on a ligand to add fragments, selects fragments to add, and predicts the geometry of the added fragments. On a comprehensive benchmark, FRAME consistently improves predicted affinity and selectivity relative to the initial ligand, while generating molecules with more drug-like chemical properties than docking-based methods currently in widespread use. FRAME learns to accurately describe molecular interactions despite being given no prior information on such interactions. The resulting framework for quality molecular hypothesis generation can be easily incorporated into the workflows of medicinal chemists for diverse tasks, including lead optimization, fragment-based drug discovery, and de novo drug design.
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Affiliation(s)
- Alexander
S. Powers
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Helen H. Yu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Patricia Suriana
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Rohan V. Koodli
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Biomedical
Informatics Program, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Tianyu Lu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Joseph M. Paggi
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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30
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Neto V, Victor BL, Galamba N. Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease. J Med Chem 2023; 66:16062-16074. [PMID: 37988411 DOI: 10.1021/acs.jmedchem.3c01484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Sickle cell disease is a missense genetic disorder characterized by the aggregation of deoxy-HbS into helical fibers that distort erythrocytes into a sickle-like shape. Herein, we investigate, through molecular dynamics, the effect of nine 5-mer cyclic peptides (CPs), tailor-designed to block key lateral contacts of the fibers. Our results show that the CPs bind orthogonally to the main HbS pocket involved in the latter contacts, with some revealing exceedingly long residence times. These CPs display moderate to high specificity, exhibiting molecular recognition events even at a HbS/CP (1:1) ratio. A much lower HbS-CP binding free energy, longer residence times, and higher specificity are also found relative to a previously reported CP with modest in vitro antisickling activity. These results indicate that some of these CPs have the potential to reduce the concentration of aggregation-competent deoxy-HbS, precluding or delaying the formation of lateral contact at the homogeneous nucleation stage.
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Affiliation(s)
- Vasco Neto
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Bruno Lourenço Victor
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Nuno Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
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31
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Xiang S, Wang Z, Tang R, Wang L, Wang Q, Yu Y, Deng Q, Hou T, Hao H, Sun H. Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. J Chem Inf Model 2023; 63:7529-7544. [PMID: 37983966 DOI: 10.1021/acs.jcim.3c01451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
It is well-known that the potency of a drug is heavily associated with its kinetic and thermodynamic properties with the target. Nuclear receptors (NRs), as an important target family, play important roles in regulating a variety of physiological processes in vivo. However, it is hard to understand the drug-NR interaction process because of the closed structure of the ligand-binding domain (LBD) of the NR proteins, which apparently hinders the rational design of drugs with controllable kinetic properties. Therefore, understanding the underlying mechanism of the ligand-NR interaction process seems necessary to help NR drug design. However, it is usually difficult for experimental approaches to interpret the kinetic process of drug-target interactions. Therefore, in silico methods were utilized to explore the optimal binding/dissociation pathways of the NR ligands. Specifically, farnesoid X receptor (FXR) is considered here as the target system since it has been an important target for the treatment of bile acid metabolism-associated diseases, and a series of structures cocrystallized with diverse scaffold ligands were resolved. By using random acceleration molecular dynamics (RAMD) simulation and umbrella sampling (US), 5 main dissociation pathways (pathways I-V) were identified in 11 representative FXR ligands, with most of them (9/11) preferring to go through Pathway III and the remaining two favoring escaping from Pathway I and IV. Furthermore, key residues functioning in the three main dissociation pathways were revealed by the kinetic residue energy analysis (KREA) based on the US trajectories, which may serve as road-marker residues for rapid identification of the (un)binding pathways of FXR ligands. Moreover, the preferred pathways explored by RAMD simulations are in good agreement with the minimum free energy path identified by the US simulations with the Pearson R = 0.76 between the predicted binding affinity and the experimental data, suggesting that RAMD is suitable for applying in large-scale (un)binding-pathway exploration in the case of ligands with obscure binding tunnels to the target.
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Affiliation(s)
- Sutong Xiang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qinghua Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Yang Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qirui Deng
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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32
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Itoh Y, Zhan P, Tojo T, Jaikhan P, Ota Y, Suzuki M, Li Y, Hui Z, Moriyama Y, Takada Y, Yamashita Y, Oba M, Uchida S, Masuda M, Ito S, Sowa Y, Sakai T, Suzuki T. Discovery of Selective Histone Deacetylase 1 and 2 Inhibitors: Screening of a Focused Library Constructed by Click Chemistry, Kinetic Binding Analysis, and Biological Evaluation. J Med Chem 2023; 66:15171-15188. [PMID: 37847303 DOI: 10.1021/acs.jmedchem.3c01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Histone deacetylase 1 and 2 (HDAC1/2) inhibitors are potentially useful as tools for probing the biological functions of the isoforms and as therapeutic agents for cancer and neurodegenerative disorders. To discover potent and selective inhibitors, we screened a focused library synthesized by using click chemistry and obtained KPZ560 as an HDAC1/2-selective inhibitor. Kinetic binding analysis revealed that KPZ560 inhibits HDAC2 through a two-step slow-binding mechanism. In cellular assays, KPZ560 induced a dose- and time-dependent increase of histone acetylation and showed potent breast cancer cell growth-inhibitory activity. In addition, gene expression analyses suggested that the two-step slow-binding inhibition by KPZ560 regulated the expression of genes associated with cell proliferation and DNA damage. KPZ560 also induced neurite outgrowth of Neuro-2a cells and an increase in the spine density of granule neuron dendrites of mice. The unique two-step slow-binding character of o-aminoanilides such as KPZ560 makes them interesting candidates as therapeutic agents.
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Affiliation(s)
- Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Peng Zhan
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Toshifumi Tojo
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Pattaporn Jaikhan
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yosuke Ota
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miki Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Ying Li
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Zi Hui
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukiko Moriyama
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Shusaku Uchida
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mitsuharu Masuda
- Department of Molecular-Targeting Cancer Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshihiro Sowa
- Department of Molecular-Targeting Cancer Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Toshiyuki Sakai
- Department of Molecular-Targeting Cancer Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
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33
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Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci 2023; 14:13159-13175. [PMID: 38023523 PMCID: PMC10664576 DOI: 10.1039/d3sc04195f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Rommie Elizabeth Amaro
- Department of Molecular Biology, University of California San Diego La Jolla California 92093 USA
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34
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Mustali J, Yasuda I, Hirano Y, Yasuoka K, Gautieri A, Arai N. Unsupervised deep learning for molecular dynamics simulations: a novel analysis of protein-ligand interactions in SARS-CoV-2 M pro. RSC Adv 2023; 13:34249-34261. [PMID: 38019981 PMCID: PMC10663885 DOI: 10.1039/d3ra06375e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Molecular dynamics (MD) simulations, which are central to drug discovery, offer detailed insights into protein-ligand interactions. However, analyzing large MD datasets remains a challenge. Current machine-learning solutions are predominantly supervised and have data labelling and standardisation issues. In this study, we adopted an unsupervised deep-learning framework, previously benchmarked for rigid proteins, to study the more flexible SARS-CoV-2 main protease (Mpro). We ran MD simulations of Mpro with various ligands and refined the data by focusing on binding-site residues and time frames in stable protein conformations. The optimal descriptor chosen was the distance between the residues and the center of the binding pocket. Using this approach, a local dynamic ensemble was generated and fed into our neural network to compute Wasserstein distances across system pairs, revealing ligand-induced conformational differences in Mpro. Dimensionality reduction yielded an embedding map that correlated ligand-induced dynamics and binding affinity. Notably, the high-affinity compounds showed pronounced effects on the protein's conformations. We also identified the key residues that contributed to these differences. Our findings emphasize the potential of combining unsupervised deep learning with MD simulations to extract valuable information and accelerate drug discovery.
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Affiliation(s)
- Jessica Mustali
- Department of Electronics, Information and Bioengineering, Politecnico di Milano Italy
| | - Ikki Yasuda
- Department of Mechanical Engineering, Keio University Japan
| | | | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University Japan
| | - Alfonso Gautieri
- Department of Electronics, Information and Bioengineering, Politecnico di Milano Italy
| | - Noriyoshi Arai
- Department of Mechanical Engineering, Keio University Japan
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35
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Dodaro A, Pavan M, Menin S, Salmaso V, Sturlese M, Moro S. Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes. Front Mol Biosci 2023; 10:1294543. [PMID: 38028536 PMCID: PMC10679717 DOI: 10.3389/fmolb.2023.1294543] [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: 09/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases.
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Affiliation(s)
| | | | | | | | | | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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36
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Niazi SK. A Critical Analysis of the FDA's Omics-Driven Pharmacodynamic Biomarkers to Establish Biosimilarity. Pharmaceuticals (Basel) 2023; 16:1556. [PMID: 38004421 PMCID: PMC10675618 DOI: 10.3390/ph16111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Demonstrating biosimilarity entails comprehensive analytical assessment, clinical pharmacology profiling, and efficacy testing in patients for at least one medical indication, as required by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The efficacy testing can be waived if the drug has known pharmacodynamic (PD) markers, leaving most therapeutic proteins out of this concession. To overcome this, the FDA suggests that biosimilar developers discover PD biomarkers using omics technologies such as proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. This approach is redundant since the mode-action-action biomarkers of approved therapeutic proteins are already available, as compiled in this paper for the first time. Other potential biomarkers are receptor binding and pharmacokinetic profiling, which can be made more relevant to ensure biosimilarity without requiring biosimilar developers to conduct extensive research, for which they are rarely qualified.
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Affiliation(s)
- Sarfaraz K Niazi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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37
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Zhou J, Du T, Wang X, Yao H, Deng J, Li Y, Chen X, Sheng L, Ji M, Xu B. Discovery of Quinazoline-2,4(1 H,3 H)-dione Derivatives Containing a Piperizinone Moiety as Potent PARP-1/2 Inhibitors─Design, Synthesis, In Vivo Antitumor Activity, and X-ray Crystal Structure Analysis. J Med Chem 2023; 66:14095-14115. [PMID: 37843892 DOI: 10.1021/acs.jmedchem.3c01152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
PARP-1/2 inhibitors have become an important therapeutic strategy for the treatment of HR-deficient tumors. However, discovery of new inhibitors with an improved and distinct pharmacological file still need enormous explorations. Herein, a series of novel highly potent PARP-1/2 inhibitors bearing an N-substituted piperazinone moiety were achieved. In particular, Cpd36 was identified as a distinct PARP inhibitor, showing remarkable enzymatic activity not only toward PARP-1 (IC50 = 0.94 nM) and PARP-2 (IC50 = 0.87 nM) but also toward PARP-7 (IC50 = 0.21 nM), as well as high selectivity over other PARP isoforms. Furthermore, Cpd36 was orally bioavailable and significantly repressed the tumor growth in both breast cancer and prostate cancer xenograft model. The crystal structures of Cpd36 within PARP-1 and PARP-2 together with the predicted binding mode within PARP-7 revealed its binding features and provided insightful information for further developing highly potent and selective PARP-1 and/or PARP-7 inhibitors.
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Affiliation(s)
- Jie Zhou
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tingting Du
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiaoyu Wang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Haiping Yao
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jialing Deng
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yan Li
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Li Sheng
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ming Ji
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Bailing Xu
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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38
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Hu YX, Fei JW, Bie LH, Gao J. Simulation of the ligand-leaving process of the human heat shock protein. Phys Chem Chem Phys 2023; 25:28465-28472. [PMID: 37846475 DOI: 10.1039/d3cp03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The human heat shock protein plays a critical role in various diseases and is an important target for pharmacological modulation. Simulation of conformational changes and free energy profiles of the human heat shock protein derived by the ligand-leaving process is a challenging issue. In this work, steered molecular dynamics simulation was adopted to simulate the ligand-leaving process. Two composite systems of heat shock protein NHSP90 and small molecules 6FJ and 6G7 are selected as research objects. The free energy during the leaving of ligand small molecules is calculated using conventional molecular dynamics simulation, steered molecular dynamics simulation (SMD), and the umbrella sampling method. We found that the a slower pulling velocity (0.001 nm ns-1) will result in 2.19 kcal mol-1, and the umbrella sampling method gives a value of 3.26 kcal mol-1 for the free energy difference for the two systems, which reasonably agrees with experimental results. A faster-pulling velocity (0.01 nm ns-1) leads to a large overestimation of free energy. At the same time, the conformational analysis indicated that the faster pulling velocity may lead to the conformational change of NHSP90, which was proved to be false by the slower pulling velocity and the umbrella sampling method.
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Affiliation(s)
- Yi-Xiao Hu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jun-Wen Fei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Li-Hua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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39
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Rao M, McDuffie E, Sachs C. Artificial Intelligence/Machine Learning-Driven Small Molecule Repurposing via Off-Target Prediction and Transcriptomics. TOXICS 2023; 11:875. [PMID: 37888725 PMCID: PMC10611213 DOI: 10.3390/toxics11100875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
The process of discovering small molecule drugs involves screening numerous compounds and optimizing the most promising ones, both in vitro and in vivo. However, approximately 90% of these optimized candidates fail during trials due to unexpected toxicity or insufficient efficacy. Current concepts with respect to drug-protein interactions suggest that each small molecule interacts with an average of 6-11 targets. This implies that approved drugs and even discontinued compounds could be repurposed by leveraging their interactions with unintended targets. Therefore, we developed a computational repurposing framework for small molecules, which combines artificial intelligence/machine learning (AI/ML)-based and chemical similarity-based target prediction methods with cross-species transcriptomics information. This repurposing methodology incorporates eight distinct target prediction methods, including three machine learning methods. By using multiple orthogonal methods for a "dataset" composed of 2766 FDA-approved drugs targeting multiple therapeutic target classes, we identified 27,371 off-target interactions involving 2013 protein targets (i.e., an average of around 10 interactions per drug). Relative to the drugs in the dataset, we identified 150,620 structurally similar compounds. The highest number of predicted interactions were for drugs targeting G protein-coupled receptors (GPCRs), enzymes, and kinases with 10,648, 4081, and 3678 interactions, respectively. Notably, 17,283 (63%) of the off-target interactions have been confirmed in vitro. Approximately 4000 interactions had an IC50 of <100 nM for 1105 FDA-approved drugs and 1661 interactions had an IC50 of <10 nM for 696 FDA-approved drugs. Together, the confirmation of numerous predicted interactions and the exploration of tissue-specific expression patterns in human and animal tissues offer insights into potential drug repurposing for new therapeutic applications.
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Affiliation(s)
- Mohan Rao
- Neurocrine Biosciences, Inc., Nonclinical Toxicology, San Diego, CA 92130, USA; (E.M.); (C.S.)
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40
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Crawford MC, Tripu DR, Barritt SA, Jing Y, Gallimore D, Kales SC, Bhanu NV, Xiong Y, Fang Y, Butler KAT, LeClair CA, Coussens NP, Simeonov A, Garcia BA, Dibble CC, Meier JL. Comparative Analysis of Drug-like EP300/CREBBP Acetyltransferase Inhibitors. ACS Chem Biol 2023; 18:2249-2258. [PMID: 37737090 PMCID: PMC11059198 DOI: 10.1021/acschembio.3c00293] [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] [Indexed: 09/23/2023]
Abstract
The human acetyltransferase paralogues EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potencies of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize the binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of the relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.
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Affiliation(s)
- McKenna C Crawford
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Deepika R Tripu
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yihang Jing
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Diamond Gallimore
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kamaria A T Butler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jordan L Meier
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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41
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309149. [PMID: 38529044 PMCID: PMC10962547 DOI: 10.1002/ange.202309149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 03/27/2024]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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42
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. Angew Chem Int Ed Engl 2023; 62:e202309149. [PMID: 37607127 PMCID: PMC10962598 DOI: 10.1002/anie.202309149] [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: 06/29/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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43
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Kasahara K, Masayama R, Okita K, Matubayasi N. Elucidating protein-ligand binding kinetics based on returning probability theory. J Chem Phys 2023; 159:134103. [PMID: 37787130 DOI: 10.1063/5.0165692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023] Open
Abstract
The returning probability (RP) theory, a rigorous diffusion-influenced reaction theory, enables us to analyze the binding process systematically in terms of thermodynamics and kinetics using molecular dynamics (MD) simulations. Recently, the theory was extended to atomistically describe binding processes by adopting the host-guest interaction energy as the reaction coordinate. The binding rate constants can be estimated by computing the thermodynamic and kinetic properties of the reactive state existing in the binding processes. Here, we propose a methodology based on the RP theory in conjunction with the energy representation theory of solution, applicable to complex binding phenomena, such as protein-ligand binding. The derived scheme of calculating the equilibrium constant between the reactive and dissociate states, required in the RP theory, can be used for arbitrary types of reactive states. We apply the present method to the bindings of small fragment molecules [4-hydroxy-2-butanone (BUT) and methyl methylthiomethyl sulphoxide (DSS)] to FK506 binding protein (FKBP) in an aqueous solution. Estimated binding rate constants are consistent with those obtained from long-timescale MD simulations. Furthermore, by decomposing the rate constants to the thermodynamic and kinetic contributions, we clarify that the higher thermodynamic stability of the reactive state for DSS causes the faster binding kinetics compared with BUT.
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Affiliation(s)
- Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ren Masayama
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazuya Okita
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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44
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Xu J, Huang C, Li L, Zhao Y, Guo Z, Chen Y, Zhang P. Label-free analysis of membrane protein binding kinetics and cell adhesions using evanescent scattering microscopy. Analyst 2023; 148:5084-5093. [PMID: 37671903 DOI: 10.1039/d3an00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Measuring ligand interactions with membrane proteins in single live cells is critical for understanding many cellular processes and screening drugs. However, developing such a capability has been a difficult challenge. Here, we employ evanescent scattering microscopy (ESM) to show that ligand binding to membrane proteins can change the cell adhesion properties, which are intrinsic cell properties and independent of random cell micromotions and ligand mass, thus allowing the kinetics analyses of both proteins and small molecules binding to membrane proteins in both single fixed and live cells. In addition, utilizing the high spatiotemporal resolution of ESM, the positions of cell adhesion sites can be tracked in real-time to analyze the cell deformations and migrations, thus providing a potential approach for understanding the cell activity during the ligand binding process in detail. The presented method may pave the road for developing a versatile and easy-to-use label-free detection strategy for in situ analysis of molecular interaction dynamics in living biosystems with single-cell resolution.
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Affiliation(s)
- Jiying Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100049, China
| | - Caixin Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Liangju Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Ying Zhao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
- Xinxiang Key Laboratory of Clinical psychopharmacology, Xinxiang 453003, China
| | - Zhenpeng Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100049, China
- National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Huaiyin Institute of Technology, Huaian 223003, China
| | - Pengfei Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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45
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Janezic EM, Doan A, Mai E, Bravo DD, Wang J, Kim HS, Spiess C, Bewley K, ElSohly A, Liang WC, Koerber JT, Richalet P, Vanhove M, Comps-Agrar L. A novel, label-free, pre-equilibrium assay to determine the association and dissociation rate constants of therapeutic antibodies on living cells. Br J Pharmacol 2023. [PMID: 37783572 DOI: 10.1111/bph.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Monoclonal antibodies (Ab) represent the fastest growing drug class. Knowledge of the biophysical parameters (kon , koff and KD ) that dictate Ab:receptor interaction is critical during the drug discovery process. However, with the increasing complexity of Ab formats and their targets, it became apparent that existing technologies present limitations and are not always suitable to determine these parameters. Therefore, novel affinity determination methods represent an unmet assay need. EXPERIMENTAL APPROACH We developed a pre-equilibrium kinetic exclusion assay using recent mathematical advances to determine the kon , koff and KD of monoclonal Ab:receptor interactions on living cells. The assay is amenable to all human IgG1 and rabbit Abs. KEY RESULTS Using our novel assay, we demonstrated for several monoclonal Ab:receptor pairs that the calculated kinetic rate constants were comparable with orthogonal methods that were lower throughput or more resource consuming. We ran simulations to predict the critical conditions to improve the performance of the assays. We further showed that this method could successfully be applied to both suspension and adherent cells. Finally, we demonstrated that kon and koff , but not KD , correlate with in vitro potency for a panel of monoclonal Abs. CONCLUSIONS AND IMPLICATIONS Our novel assay has the potential to systematically probe binding kinetics of monoclonal Abs to cells and can be incorporated in a screening cascade to identify new therapeutic candidates. Wide-spread adoption of pre-equilibrium assays using physiologically relevant systems will lead to a more holistic understanding of how Ab binding kinetics influence their potency.
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Affiliation(s)
| | | | - Elaine Mai
- Genentech, Inc, South San Francisco, California, USA
| | | | - Jianyong Wang
- Genentech, Inc, South San Francisco, California, USA
| | - Hok Seon Kim
- Genentech, Inc, South San Francisco, California, USA
| | | | | | - Adel ElSohly
- Genentech, Inc, South San Francisco, California, USA
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46
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Yoon HJ, Kundu S, Wu S. Molecular Dynamics Simulation Study of the Selective Inhibition of Coagulation Factor IXa over Factor Xa. Molecules 2023; 28:6909. [PMID: 37836752 PMCID: PMC10574344 DOI: 10.3390/molecules28196909] [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: 08/04/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Thromboembolic disorders, arising from abnormal coagulation, pose a significant risk to human life in the modern world. The FDA has recently approved several anticoagulant drugs targeting factor Xa (FXa) to manage these disorders. However, these drugs have potential side effects, leading to bleeding complications in patients. To mitigate these risks, coagulation factor IXa (FIXa) has emerged as a promising target due to its selective regulation of the intrinsic pathway. Due to the high structural and functional similarities of these coagulation factors and their inhibitor binding modes, designing a selective inhibitor specifically targeting FIXa remains a challenging task. The dynamic behavior of protein-ligand interactions and their impact on selectivity were analyzed using molecular dynamics simulation, considering the availability of potent and selective compounds for both coagulation factors and the co-crystal structures of protein-ligand complexes. Throughout the simulations, we examined ligand movements in the binding site, as well as the contact frequencies and interaction fingerprints, to gain insights into selectivity. Interaction fingerprint (IFP) analysis clearly highlights the crucial role of strong H-bond formation between the ligand and D189 and A190 in the S1 subsite for FIXa selectivity, consistent with our previous study. This dynamic analysis also reveals additional FIXa-specific interactions. Additionally, the absence of polar interactions contributes to the selectivity for FXa, as observed from the dynamic profile of interactions. A contact frequency analysis of the protein-ligand complexes provides further confirmation of the selectivity criteria for FIXa and FXa, as well as criteria for binding and activity. Moreover, a ligand movement analysis reveals key interaction dynamics that highlight the tighter binding of selective ligands to the proteins compared to non-selective and inactive ligands.
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Affiliation(s)
- Hyun Jung Yoon
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea;
| | - Sibsankar Kundu
- R&D Center, PharmCADD Co., Ltd., Busan 48792, Republic of Korea;
| | - Sangwook Wu
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea;
- R&D Center, PharmCADD Co., Ltd., Busan 48792, Republic of Korea;
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47
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Guzzetti S, Morentin Gutierrez P. An integrated modelling approach for targeted degradation: insights on optimization, data requirements and PKPD predictions from semi- or fully-mechanistic models and exact steady state solutions. J Pharmacokinet Pharmacodyn 2023; 50:327-349. [PMID: 37120680 PMCID: PMC10460745 DOI: 10.1007/s10928-023-09857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/28/2023] [Indexed: 05/01/2023]
Abstract
The value of an integrated mathematical modelling approach for protein degraders which combines the benefits of traditional turnover models and fully mechanistic models is presented. Firstly, we show how exact solutions of the mechanistic models of monovalent and bivalent degraders can provide insight on the role of each system parameter in driving the pharmacological response. We show how on/off binding rates and degradation rates are related to potency and maximal effect of monovalent degraders, and how such relationship can be used to suggest a compound optimization strategy. Even convoluted exact steady state solutions for bivalent degraders provide insight on the type of observations required to ensure the predictive capacity of a mechanistic approach. Specifically for PROTACs, the structure of the exact steady state solution suggests that the total remaining target at steady state, which is easily accessible experimentally, is insufficient to reconstruct the state of the whole system at equilibrium and observations on different species (such as binary/ternary complexes) are necessary. Secondly, global sensitivity analysis of fully mechanistic models for PROTACs suggests that both target and ligase baselines (actually, their ratio) are the major sources of variability in the response of non-cooperative systems, which speaks to the importance of characterizing their distribution in the target patient population. Finally, we propose a pragmatic modelling approach which incorporates the insights generated with fully mechanistic models into simpler turnover models to improve their predictive ability, hence enabling acceleration of drug discovery programs and increased probability of success in the clinic.
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Affiliation(s)
- Sofia Guzzetti
- DMPK, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
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48
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Conflitti P, Raniolo S, Limongelli V. Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness. J Chem Theory Comput 2023; 19:6047-6061. [PMID: 37656199 PMCID: PMC10536999 DOI: 10.1021/acs.jctc.3c00641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/02/2023]
Abstract
Computational techniques applied to drug discovery have gained considerable popularity for their ability to filter potentially active drugs from inactive ones, reducing the time scale and costs of preclinical investigations. The main focus of these studies has historically been the search for compounds endowed with high affinity for a specific molecular target to ensure the formation of stable and long-lasting complexes. Recent evidence has also correlated the in vivo drug efficacy with its binding kinetics, thus opening new fascinating scenarios for ligand/protein binding kinetic simulations in drug discovery. The present article examines the state of the art in the field, providing a brief summary of the most popular and advanced ligand/protein binding kinetics techniques and evaluating their current limitations and the potential solutions to reach more accurate kinetic models. Particular emphasis is put on the need for a paradigm change in the present methodologies toward ligand and protein parametrization, the force field problem, characterization of the transition states, the sampling issue, and algorithms' performance, user-friendliness, and data openness.
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Affiliation(s)
- Paolo Conflitti
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
| | - Stefano Raniolo
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
| | - Vittorio Limongelli
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
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49
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Sharma S, Joshi S, Kalidindi T, Digwal CS, Panchal P, Lee SG, Zanzonico P, Pillarsetty N, Chiosis G. Unraveling the Mechanism of Epichaperome Modulation by Zelavespib: Biochemical Insights on Target Occupancy and Extended Residence Time at the Site of Action. Biomedicines 2023; 11:2599. [PMID: 37892973 PMCID: PMC10604720 DOI: 10.3390/biomedicines11102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drugs with a long residence time at their target sites are often more efficacious in disease treatment. The mechanism, however, behind prolonged retention at the site of action is often difficult to understand for non-covalent agents. In this context, we focus on epichaperome agents, such as zelavespib and icapamespib, which maintain target binding for days despite rapid plasma clearance, minimal retention in non-diseased tissues, and rapid metabolism. They have shown significant therapeutic value in cancer and neurodegenerative diseases by disassembling epichaperomes, which are assemblies of tightly bound chaperones and other factors that serve as scaffolding platforms to pathologically rewire protein-protein interactions. To investigate their impact on epichaperomes in vivo, we conducted pharmacokinetic and target occupancy measurements for zelavespib and monitored epichaperome assemblies biochemically in a mouse model. Our findings provide evidence of the intricate mechanism through which zelavespib modulates epichaperomes in vivo. Initially, zelavespib becomes trapped when epichaperomes bound, a mechanism that results in epichaperome disassembly, with no change in the expression level of epichaperome constituents. We propose that the initial trapping stage of epichaperomes is a main contributing factor to the extended on-target residence time observed for this agent in clinical settings. Zelavespib's residence time in tumors seems to be dictated by target disassembly kinetics rather than by frank drug-target unbinding kinetics. The off-rate of zelavespib from epichaperomes is, therefore, much slower than anticipated from the recorded tumor pharmacokinetic profile or as determined in vitro using diluted systems. This research sheds light on the underlying processes that make epichaperome agents effective in the treatment of certain diseases.
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Affiliation(s)
- Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Teja Kalidindi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Chander S. Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Sang-Gyu Lee
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Pat Zanzonico
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Nagavarakishore Pillarsetty
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
- Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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50
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Mukherjee A, Zamani F, Suzuki T. Evolution of Slow-Binding Inhibitors Targeting Histone Deacetylase Isoforms. J Med Chem 2023; 66:11672-11700. [PMID: 37651268 DOI: 10.1021/acs.jmedchem.3c01160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Because the overexpression of histone deacetylase enzymes (HDACs) has been linked to numerous diseases, including various cancers and neurodegenerative disorders, HDAC inhibitors have emerged as promising therapeutic agents. However, most HDAC inhibitors lack both subclass and isoform selectivity, which leads to potential toxicity. Unlike classical hydroxamate HDAC inhibitors, slow-binding HDAC inhibitors form tight and prolonged bonds with HDAC enzymes. This distinct mechanism of action improves both selectivity and toxicity profiles, which makes slow-binding HDAC inhibitors a promising class of therapeutic agents for various diseases. Therefore, the development of slow-binding HDAC inhibitors that can effectively target a wide range of HDAC isoforms is crucial. This Perspective provides valuable insights into the potential and progress of slow-binding HDAC inhibitors as promising drug candidates for the treatment of various diseases.
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Affiliation(s)
| | - Farzad Zamani
- SANKEN, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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