1
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Regan J, DeJarnette C, Reitler P, Gihaz S, Srivastava A, Ge W, Tucker KM, Peters TL, Meibohm B, Ben Mamoun C, Fortwendel JR, Hevener KE, Palmer GE. Pantothenate kinase is an effective target for antifungal therapy. Cell Chem Biol 2025; 32:710-721.e6. [PMID: 40378822 DOI: 10.1016/j.chembiol.2025.04.007] [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: 04/22/2024] [Revised: 02/11/2025] [Accepted: 04/14/2025] [Indexed: 05/19/2025]
Abstract
Pantothenate kinase (PanK) catalyzes the first step in the conversion of pantothenate to coenzyme A (CoA), an essential cofactor in all living organisms. The findings of this study demonstrate that PanK is essential for the viability and virulence of two of the most medically significant fungi-the pathogenic yeast Candida albicans, and the infectious mold Aspergillus fumigatus-within the mammalian host. Biochemical, biophysical as well as chemical-genetic approaches were applied to identify 3,4-methylenedioxy-β-nitrostyrene (MNS) as a broad-spectrum antifungal that directly engages and inhibits PanK to block CoA production. Importantly, MNS is inactive against a mammalian PanK and demonstrates in vivo antifungal efficacy a mouse model of disseminated C. albicans infection. Thus, MNS has provided a valuable chemical probe to establish the validity of targeting PanK with small molecule inhibitors as a strategy to develop efficacious antifungal therapeutics.
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Affiliation(s)
- Jessica Regan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Christian DeJarnette
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Parker Reitler
- Department of Molecular Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Shalev Gihaz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ashish Srivastava
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Wenbo Ge
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Katie M Tucker
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Tracy L Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Bernd Meibohm
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jarrod R Fortwendel
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA.
| | - Glen E Palmer
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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2
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Daniels M, Castro J, Lee YT, Gotur D, Knockenhauer KE, Grigoriu S, Lockbaum GJ, Cheong JE, Lu C, Brennan D, Buker SM, Liu J, Yao S, Sparling BA, Sickmier EA, Ribich S, Blakemore SJ, Silver SJ, Boriack-Sjodin PA, Duncan KW, Copeland RA. Discovery of ATX968: An Orally Available Allosteric Inhibitor of DHX9. J Med Chem 2025; 68:9537-9554. [PMID: 40298172 PMCID: PMC12067447 DOI: 10.1021/acs.jmedchem.5c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 03/21/2025] [Accepted: 03/26/2025] [Indexed: 04/30/2025]
Abstract
DHX9 is an RNA/DNA helicase integral in the maintenance of genome stability that has emerged as an attractive target for oncology drug discovery. Disclosed herein is the discovery and optimization of a series of DHX9 inhibitors. Compound 1 was identified as a partial inhibitor of DHX9 ATPase activity but a full inhibitor of unwinding activity. Binding of 1 to a pocket distinct from the ATP binding site was confirmed by X-ray crystallography, enabling structure-based drug optimization. During this optimization, a sulfur-halogen bond was identified that increased on-target residence time without impacting equilibrium binding affinity. Analysis shows that cell potency more closely correlates with residence time than with equilibrium measurements of binding affinity or biochemical potency. Further optimization of potency and ADME properties led to the identification of ATX968, a potent and selective DHX9 inhibitor that is efficacious in a tumor xenograft model of microsatellite instability-high (MSI-H) colorectal cancer.
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Affiliation(s)
| | - Jennifer Castro
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Young-Tae Lee
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Deepali Gotur
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Kevin E. Knockenhauer
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Simina Grigoriu
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | | | | | | | - David Brennan
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | | | - Julie Liu
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Shihua Yao
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Brian A. Sparling
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | | | | | | | - Serena J. Silver
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
| | | | - Kenneth W. Duncan
- Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States
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3
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Srinivasan B. Time-evolved metrics for safety pharmacological assessments of small molecules and biologics. Br J Pharmacol 2025. [PMID: 40289572 DOI: 10.1111/bph.70064] [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: 11/15/2024] [Revised: 01/16/2025] [Accepted: 03/21/2025] [Indexed: 04/30/2025] Open
Abstract
Safety of a small-molecule drug is oftentimes a more important criterion than efficacy in determining drug approval. Aspects of safety pharmacological and toxicological liabilities, often resulting from dose-dependent undesirable interaction with either the primary target of interest or secondary targets, have a huge role to play in determining 'first-in-human' dosage and phase I clinical trials. Given the open thermodynamic nature of the human subjects, it is mandatory that kinetics of drug-target and drug-off-target interactions govern the way selectivity margins are assessed, and dose is decided. However, lack of sufficient thrust on kinetics in guiding early drug discovery decisions has resulted in an overreliance on IC50 measure (a proxy for thermodynamic Ki) as a means of computing safety across the target of interest and potential off-targets. Moreover, based on established practises and known weight of evidence of targets with safety adverse events, the primary panel of secondary pharmacology targets are biased with greater preference for G-protein coupled receptors, transporters and ion-channels with a paucity of enzymes. This can pose unique challenges in assessing safety, especially for advancing and emergent modalities. In this perspective, the critical role kinetic margins should play in assessing safety is emphasised given the myriad assay conditions that can modulate the equilibrium thermodynamic measure as embodied in the proxy report of IC50. Further, it advocates selective and judicious expansion of primary safety panels with greater representation of enzymes and reduced redundancy in eventual read-outs based on potential for correlative output among the off-target classes assessed.
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Affiliation(s)
- Bharath Srinivasan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
- Cancer Research Horizons, Cancer Research UK, Cambridge, UK
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4
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Holmgård DSG, Zhou L, Kristensen JL, Jensen AA. The Heterogeneous Kinetic Origins of the Binding Properties of Orthosteric Ligands at Heteromeric Nicotinic Acetylcholine Receptors. J Med Chem 2025; 68:6683-6697. [PMID: 40043102 DOI: 10.1021/acs.jmedchem.5c00089] [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: 03/28/2025]
Abstract
A plethora of agonists and competitive antagonists have been developed to explore the therapeutic potential in neuronal nicotinic acetylcholine receptors (nAChRs). Based on equilibrium and kinetic [3H]epibatidine binding studies, we report that the kinetic fingerprints of [3H]epibatidine at five heteromeric αβ nAChRs and of seven classical agonists at α4β2 and α3β4 nAChRs differ substantially. While this diversity depends on both the agonist and receptor subtype, the overall pattern of kinetic determinants emerging from this profiling is complex. The dramatically different binding kinetics displayed by two alkaloids and competitive antagonists, (+)-DHβE and (+)-cocculine, at the α4β2 nAChR further exemplify how dissimilar kinetics can underlie very comparable pharmacological properties exhibited by close structural analogs. Thus, our findings elucidate the heterogeneous kinetic basis for orthosteric ligand binding to αβ nAChRs and emphasize how the binding affinities, selectivity profiles, and structure-activity relationships of these ligands are rooted in their kinetic traits at the receptors.
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Affiliation(s)
- David S G Holmgård
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Unversitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Libin Zhou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Unversitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Jesper L Kristensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Unversitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Unversitetsparken 2, DK-2100 Copenhagen Ø, Denmark
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5
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Shaihutdinova ZM, Pashirova TN, Masson P. Slow-binding inhibitors of enzymes: kinetic characteristics and pharmacological interest. BIOMEDITSINSKAIA KHIMIIA 2025; 71:81-94. [PMID: 40326015 DOI: 10.18097/pbmcr1536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2025]
Abstract
Currently, the search for new slow-binding inhibitors of enzymes (SBI) and their identification primary in vitro studies still attracts much attention in the context of their potential role as putative pharmacological agents for the treatment of various diseases. In contrast to their classical reversible analogues, SBI exhibit a slow enzyme binding kinetics, where the equilibrium steady-state is reached not in microseconds, but after longer time intervals. Such compounds could be promising drugs, because regardless of their pharmacokinetics in the bloodstream, they have such advantages as high affinity for the target enzyme, long residence time on the target, and therefore, prolonged action. These pharmacological properties ensure optimized dosage of drugs required to achieve high activity with less side effects. In this review we have considered mechanisms of SBI interaction with enzyme targets, the principles of their recognition at the level of in vitro studies and analysis of binding and kinetic parameters.
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Affiliation(s)
| | - T N Pashirova
- Kazan (Volga region) Federal University, Kazan, Russia; Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - P Masson
- Kazan (Volga region) Federal University, Kazan, Russia
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6
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Thinn AMM, Wang W, Chen Q. Competitive SPR chaser assay to study biomolecular interactions with very slow binding dissociation rate constant. Anal Biochem 2025; 696:115679. [PMID: 39341483 DOI: 10.1016/j.ab.2024.115679] [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: 06/05/2024] [Revised: 08/12/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
Binding kinetics of drug and its target protein is crucial for the efficacy and safety of the drug. Using surface plasmon resonance (SPR) technology, we performed a competitive SPR chaser assay, a method to study biomolecular interactions with very slow dissociation rate constants (kd < 1E-4 s-1). This report described the principle and the experimental setup of the chaser assay, which involves using a competitive probe (chaser) to detect changes in target occupancy by a test molecule over time. We demonstrated the applicability of the chaser assay for both small and large molecules and compared the results with conventional SPR kinetic analysis and other methods. We suggest that the chaser assay is a useful and robust technique to characterize very tight biomolecular interactions, and that it can also be used to study cooperativity in ternary complex formation.
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Affiliation(s)
- Aye Myat Myat Thinn
- Department of Small Molecule Therapeutic Discovery and Research Technologies, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Wei Wang
- Department of Small Molecule Therapeutic Discovery and Research Technologies, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
| | - Qing Chen
- Department of Small Molecule Therapeutic Discovery and Research Technologies, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
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7
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Du S, Wen Z, Yu J, Meng Y, Liu Y, Xia X. Breath and Beyond: Advances in Nanomedicine for Oral and Intranasal Aerosol Drug Delivery. Pharmaceuticals (Basel) 2024; 17:1742. [PMID: 39770584 PMCID: PMC11677467 DOI: 10.3390/ph17121742] [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: 11/16/2024] [Revised: 12/08/2024] [Accepted: 12/12/2024] [Indexed: 01/11/2025] Open
Abstract
Designing and standardizing drug formulations are crucial for ensuring the safety and efficacy of medications. Nanomedicine utilizes nano drug delivery systems and advanced nanodevices to address numerous critical medical challenges. Currently, oral and intranasal aerosol drug delivery (OIADD) is the primary method for treating respiratory diseases worldwide. With advancements in disease understanding and the development of aerosolized nano drug delivery systems, the application of OIADD has exceeded its traditional boundaries, demonstrating significant potential in the treatment of non-respiratory conditions as well. This study provides a comprehensive overview of the applications of oral and intranasal aerosol formulations in disease treatment. It examines the key challenges limiting the development of nanomedicines in drug delivery systems, formulation processes, and aerosol devices and explores the latest advancements in these areas. This review aims to offer valuable insights to researchers involved in the development of aerosol delivery platforms.
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Affiliation(s)
- Simeng Du
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhiyang Wen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinghan Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yingying Meng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuling Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuejun Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.D.); (Z.W.); (J.Y.); (Y.M.); (Y.L.)
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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8
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Liu H, Zhang H, IJzerman AP, Guo D. The translational value of ligand-receptor binding kinetics in drug discovery. Br J Pharmacol 2024; 181:4117-4129. [PMID: 37705429 DOI: 10.1111/bph.16241] [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: 05/19/2023] [Revised: 07/27/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
The translation of in vitro potency of a candidate drug, as determined by traditional pharmacology metrics (such as EC50/IC50 and KD/Ki values), to in vivo efficacy and safety is challenging. Residence time, which represents the duration of drug-target interaction, can be part of a more comprehensive understanding of the dynamic nature of drug-target interactions in vivo, thereby enabling better prediction of drug efficacy and safety. As a consequence, a prolonged residence time may help in achieving sustained pharmacological activity, while transient interactions with shorter residence times may be favourable for targets associated with side effects. Therefore, integration of residence time into the early stages of drug discovery and development has yielded a number of clinical candidates with promising in vivo efficacy and safety profiles. Insights from residence time research thus contribute to the translation of in vitro potency to in vivo efficacy and safety. Further research and advances in measuring and optimizing residence time will bring a much-needed addition to the drug discovery process and the development of safer and more effective drugs. In this review, we summarize recent research progress on residence time, highlighting its importance from a translational perspective.
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Affiliation(s)
- Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Haoran Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
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9
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Srinivasan B. Advances in binding kinetics and mechanistic PK/PD modelling. Br J Pharmacol 2024; 181:4089-4090. [PMID: 39279239 DOI: 10.1111/bph.17340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024] Open
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10
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Bálint D, Póti ÁL, Alexa A, Sok P, Albert K, Torda L, Földesi-Nagy D, Csókás D, Turczel G, Imre T, Szarka E, Fekete F, Bento I, Bojtár M, Palkó R, Szabó P, Monostory K, Pápai I, Soós T, Reményi A. Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads. Nat Commun 2024; 15:8606. [PMID: 39366946 PMCID: PMC11452492 DOI: 10.1038/s41467-024-52573-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/13/2024] [Indexed: 10/06/2024] Open
Abstract
There has been a surge of interest in covalent inhibitors for protein kinases in recent years. Despite success in oncology, the off-target reactivity of these molecules is still hampering the use of covalent warhead-based strategies. Herein, we disclose the development of precision-guided warheads to mitigate the off-target challenge. These reversible warheads have a complex and cyclic structure with optional chirality center and tailored steric and electronic properties. To validate our proof-of-concept, we modified acrylamide-based covalent inhibitors of c-Jun N-terminal kinases (JNKs). We show that the cyclic warheads have high resilience against off-target thiols. Additionally, the binding affinity, residence time, and even JNK isoform specificity can be fine-tuned by adjusting the substitution pattern or using divergent and orthogonal synthetic elaboration of the warhead. Taken together, the cyclic warheads presented in this study will be a useful tool for medicinal chemists for the deliberate design of safer and functionally fine-tuned covalent inhibitors.
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Affiliation(s)
- Dániel Bálint
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Ádám Levente Póti
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Doctoral School of Biology, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Anita Alexa
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Krisztián Albert
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Lili Torda
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Dóra Földesi-Nagy
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Dániel Csókás
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Tímea Imre
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Eszter Szarka
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Ferenc Fekete
- Metabolic Drug-interactions Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Isabel Bento
- European Molecular Biology Laboratory, EMBL, Hamburg, Germany
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Roberta Palkó
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Pál Szabó
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Katalin Monostory
- Metabolic Drug-interactions Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Imre Pápai
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Tibor Soós
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
| | - Attila Reményi
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
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11
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Zhong H, Zhang Z, Chen M, Chen Y, Yang C, Xue Y, Xu P, Liu H. Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:10477. [PMID: 39408805 PMCID: PMC11476938 DOI: 10.3390/ijms251910477] [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: 08/28/2024] [Revised: 09/25/2024] [Accepted: 09/27/2024] [Indexed: 10/19/2024] Open
Abstract
c-Src is involved in multiple signaling pathways and serves as a critical target in various cancers. Growing evidence suggests that prolonging a drug's residence time (RT) can enhance its efficacy and selectivity. Thus, the development of c-Src antagonists with longer residence time could potentially improve therapeutic outcomes. In this study, we employed molecular dynamics simulations to explore the binding modes and dissociation processes of c-Src with antagonists characterized by either long or short RTs. Our results reveal that the long RT compound DAS-DFGO-I (DFGO) occupies an allosteric site, forming hydrogen bonds with residues E310 and D404 and engaging in hydrophobic interactions with residues such as L322 and V377. These interactions significantly contribute to the long RT of DFGO. However, the hydrogen bonds between the amide group of DFGO and residues E310 and D404 are unstable. Substituting the amide group with a sulfonamide yielded a new compound, DFOGS, which exhibited more stable hydrogen bonds with E310 and D404, thereby increasing its binding stability with c-Src. These results provide theoretical guidance for the rational design of long residence time c-Src inhibitors to improve selectivity and efficacy.
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Affiliation(s)
- Haiyang Zhong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhengshuo Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Mengdan Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Yue Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Can Yang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Yunsheng Xue
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Pei Xu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, China
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12
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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. J Chem Theory Comput 2024; 20:6341-6349. [PMID: 38991145 PMCID: PMC11990086 DOI: 10.1021/acs.jctc.4c00503] [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: 07/13/2024]
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 time scales. Recent advances in rare event sampling have allowed us to reach these time scales, 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 magnitude of time scales. 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 anticancer 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, Bethesda, Maryland 20852, USA
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13
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Maruyama Y, Ohsawa Y, Suzuki T, Yamauchi Y, Ohno K, Inoue H, Yamamoto A, Hayashi M, Okuhara Y, Muramatsu W, Namiki K, Hagiwara N, Miyauchi M, Miyao T, Ishikawa T, Horie K, Hayama M, Akiyama N, Hirokawa T, Akiyama T. Pseudoirreversible inhibition elicits persistent efficacy of a sphingosine 1-phosphate receptor 1 antagonist. Nat Commun 2024; 15:5743. [PMID: 39030171 PMCID: PMC11271513 DOI: 10.1038/s41467-024-49893-8] [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: 04/18/2023] [Accepted: 06/19/2024] [Indexed: 07/21/2024] Open
Abstract
Sphingosine 1-phosphate receptor 1 (S1PR1), a G protein-coupled receptor, is required for lymphocyte trafficking, and is a promising therapeutic target in inflammatory diseases. Here, we synthesize a competitive S1PR1 antagonist, KSI-6666, that effectively suppresses pathogenic inflammation. Metadynamics simulations suggest that the interaction of KSI-6666 with a methionine residue Met124 in the ligand-binding pocket of S1PR1 may inhibit the dissociation of KSI-6666 from S1PR1. Consistently, in vitro functional and mutational analyses reveal that KSI-6666 causes pseudoirreversible inhibition of S1PR1, dependent on the Met124 of the protein and substituents on the distal benzene ring of KSI-6666. Moreover, in vivo study suggests that this pseudoirreversible inhibition is responsible for the persistent activity of KSI-6666.
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Affiliation(s)
- Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Yusuke Ohsawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Takayuki Suzuki
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Yuko Yamauchi
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Kohsuke Ohno
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Hitoshi Inoue
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Akitoshi Yamamoto
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Morimichi Hayashi
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Yuji Okuhara
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotaka-Kashiwabara, Azumino, Nagano, 399-8304, Japan
| | - Wataru Muramatsu
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Kano Namiki
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Takahisa Miyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan.
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14
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Zhao Y, Hadavi D, Dijkgraaf I, Honing M. Coupling of surface plasmon resonance and mass spectrometry for molecular interaction studies in drug discovery. Drug Discov Today 2024; 29:104027. [PMID: 38762085 DOI: 10.1016/j.drudis.2024.104027] [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: 03/11/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Various analytical technologies have been developed for the study of target-ligand interactions. The combination of these technologies gives pivotal information on the binding mechanism, kinetics, affinity, residence time, and changes in molecular structures. Mass spectrometry (MS) offers structural information, enabling the identification and quantification of target-ligand interactions. Surface plasmon resonance (SPR) provides kinetic information on target-ligand interaction in real time. The coupling of MS and SPR complements each other in the studies of target-ligand interactions. Over the last two decades, the capabilities and added values of SPR-MS have been reported. This review summarizes and highlights the benefits, applications, and potential for further research of the SPR-MS approach.
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Affiliation(s)
- Yuandi Zhao
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands
| | - Darya Hadavi
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands.
| | - Ingrid Dijkgraaf
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Department of Radiology and Nuclear Medicine, MUMC+, The Netherlands
| | - Maarten Honing
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands
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15
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Wang X, DeFilippis RA, Yan W, Shah NP, Li HY. Overcoming Secondary Mutations of Type II Kinase Inhibitors. J Med Chem 2024; 67:9776-9788. [PMID: 38837951 PMCID: PMC11586107 DOI: 10.1021/acs.jmedchem.3c01629] [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: 06/07/2024]
Abstract
Type II kinase inhibitors bind in the "DFG-out" kinase conformation and are generally considered to be more potent and selective than type I inhibitors, which target a DFG-in conformation. Nine type II inhibitors are currently clinically approved, with more undergoing clinical development. Resistance-conferring secondary mutations emerged with the first series of type II inhibitors, most commonly at residues within the kinase activation loop and at the "gatekeeper" position. Recently, new inhibitors have been developed to overcome such mutations; however, mutations activating other pathways (and/or other targets) have subsequently emerged on occasion. Here, we systematically summarize the secondary mutations that confer resistance to type II inhibitors, the structural basis for resistance, newer inhibitors designed to overcome resistance, as well as the challenges and opportunities for the development of new inhibitors to overcome secondary kinase domain mutations.
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Affiliation(s)
- Xiuqi Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rosa Anna DeFilippis
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
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16
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Sharrouf K, Schlosser C, Mildenberger S, Fluhrer R, Hoeppner S. In vitro cleavage of tumor necrosis factor α (TNFα) by Signal-Peptide-Peptidase-like 2b (SPPL2b) resembles mechanistic principles observed in the cellular context. Chem Biol Interact 2024; 395:111006. [PMID: 38636792 DOI: 10.1016/j.cbi.2024.111006] [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: 12/22/2023] [Revised: 03/27/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Members of the Signal Peptide-Peptidase (SPP) and Signal Peptide-Peptidase-like (SPPL) family are intramembrane aspartyl-proteases like their well-studied homologs, the presenilins, which comprise the catalytically active subunit within the γ-secretase complex. The lack of in vitro cleavage assays for SPPL proteases limited their biochemical characterization as well as substrate identification and validation. So far, SPPL proteases have been analyzed exclusively in intact cells or membranes, restricting mechanistic analysis to co-expression of enzyme and substrate variants colocalizing in the same subcellular compartments. We describe the details of developing an in vitro cleavage assay for SPPL2b and its model substrate TNFα and analyzed the influence of phospholipids, detergent supplements, and cholesterol on the SPPL2b in vitro activity. SPPL2b in vitro activity resembles mechanistic principles that have been observed in a cellular context, such as cleavage sites and consecutive turnover of the TNFα transmembrane domain. The novel in vitro cleavage assay is functional with separately isolated protease and substrate and amenable to a high throughput plate-based readout overcoming previous limitations and providing the basis for studying enzyme kinetics, catalytic activity, substrate recognition, and the characteristics of small molecule inhibitors. As a proof of concept, we present the first biochemical in vitro characterization of the SPPL2a and SPPL2b specific small molecule inhibitor SPL-707.
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Affiliation(s)
- Kinda Sharrouf
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätsstrasse 2, D-86159, Augsburg, Germany
| | - Christine Schlosser
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätsstrasse 2, D-86159, Augsburg, Germany
| | - Sandra Mildenberger
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätsstrasse 2, D-86159, Augsburg, Germany; Institut für Entwicklungsbiologie und Neurobiologie, Johannes Gutenberg-Universität Mainz, Hanns-Dieter-Hüsch-Weg 15, 55099, Mainz, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätsstrasse 2, D-86159, Augsburg, Germany; University of Augsburg, Center for Interdisciplinary Health Research, 86135, Augsburg, Germany
| | - Sabine Hoeppner
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätsstrasse 2, D-86159, Augsburg, Germany.
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17
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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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18
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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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19
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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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20
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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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21
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Sangkanu S, Pitakbut T, Phoopha S, Khanansuk J, Chandarajoti K, Dej-adisai S. A Comparative Study of Chemical Profiling and Bioactivities between Thai and Foreign Hemp Seed Species ( Cannabis sativa L.) Plus an In-Silico Investigation. Foods 2023; 13:55. [PMID: 38201083 PMCID: PMC10778124 DOI: 10.3390/foods13010055] [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: 11/19/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Hemp (Cannabis sativa L.) is a plant widely used by humans for textiles, food, and medicine. Thus, this study aimed to characterize the chemical profiling of 12 hemp seed extracts from Thai (HS-TH) and foreign (HS-FS) samples using gas chromatography-mass spectrometry (GC-MS). Their antibacterial activity and α-glucosidase inhibitory activity were assayed. Linoleic acid (17.63-86.53%) was a major component presented in Thai hemp seed extracts, while α,β-gluco-octonic acid lactone (30.39%), clionasterol (13.42-29.07%), and glyceryl-linoleate (15.12%) were detected as the main metabolites found in foreign hemp seed extracts. Furthermore, eight extracts from both Thai and foreign hemp seed exhibited antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis, Methicillin-resistant Staphylococcus aureus, and Cutibacterium acnes, with MIC values ranging from 128 to 2048 µg/mL. Interestingly, the ethanol extract of Thai hemp seed (HS-TH-2-M-E) showed superior α-glucosidase inhibition (IC50 value of 33.27 ug/mL) over foreign species. The combination between Thai hemp species (HS-TH-2-M-E) and acarbose showed a synergistic effect against α-glucosidase. Furthermore, the docking investigation revealed that fatty acids had a greater impact on α-glucosidase than fatty acid esters and cannabinoids. The computational simulation predicts a potential allosteric binding pocket of guanosine on glucosidase and is the first description of gluco-octonic acid's anti-glucosidase activity in silico. The findings concluded that Thai hemp seed could be used as a resource for supplemental drugs or dietary therapy for diabetes mellitus.
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Affiliation(s)
- Suthinee Sangkanu
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (S.S.); (J.K.)
| | - Thanet Pitakbut
- Pharmaceutical Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany;
- Computational Structural Biology Unit, RIKEN-Center for Computational Science, Chuo, Kobe 650-0047, Japan
| | - Sathianpong Phoopha
- Traditional Thai Medical Research and Innovation Center, Faculty of Traditional Thai Medicine, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand;
| | - Jiraporn Khanansuk
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (S.S.); (J.K.)
| | - Kasemsiri Chandarajoti
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand;
| | - Sukanya Dej-adisai
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (S.S.); (J.K.)
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22
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Abhishek S, Deeksha W, Nethravathi KR, Davari MD, Rajakumara E. Allosteric crosstalk in modular proteins: Function fine-tuning and drug design. Comput Struct Biotechnol J 2023; 21:5003-5015. [PMID: 37867971 PMCID: PMC10589753 DOI: 10.1016/j.csbj.2023.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
Modular proteins are regulatory proteins that carry out more than one function. These proteins upregulate or downregulate a biochemical cascade to establish homeostasis in cells. To switch the function or alter the efficiency (based on cellular needs), these proteins require different facilitators that bind to a site different from the catalytic (active/orthosteric) site, aka 'allosteric site', and fine-tune their function. These facilitators (or effectors) are allosteric modulators. In this Review, we have discussed the allostery, characterized them based on their mechanisms, and discussed how allostery plays an important role in the activity modulation and function fine-tuning of proteins. Recently there is an emergence in the discovery of allosteric drugs. We have also emphasized the role, significance, and future of allostery in therapeutic applications.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | - Waghela Deeksha
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | | | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Eerappa Rajakumara
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
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23
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [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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24
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Mokrov GV. Multitargeting in cardioprotection: An example of biaromatic compounds. Arch Pharm (Weinheim) 2023; 356:e2300196. [PMID: 37345968 DOI: 10.1002/ardp.202300196] [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: 04/05/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
A multitarget drug design approach is actively developing in modern medicinal chemistry and pharmacology, especially with regard to multifactorial diseases such as cardiovascular diseases, cancer, and neurodegenerative diseases. A detailed study of many well-known drugs developed within the single-target approach also often reveals additional mechanisms of their real pharmacological action. One of the multitarget drug design approaches can be the identification of the basic pharmacophore models corresponding to a wide range of the required target ligands. Among such models in the group of cardioprotectors is the linked biaromatic system. This review develops the concept of a "basic pharmacophore" using the biaromatic pharmacophore of cardioprotectors as an example. It presents an analysis of possible biological targets for compounds corresponding to the biaromatic pharmacophore and an analysis of the spectrum of biological targets for the five most known and most studied cardioprotective drugs corresponding to this model, and their involvement in the biological effects of these drugs.
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