1
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Domin H, Burnat G. mGlu4R, mGlu7R, and mGlu8R allosteric modulation for treating acute and chronic neurodegenerative disorders. Pharmacol Rep 2024:10.1007/s43440-024-00657-7. [PMID: 39348087 DOI: 10.1007/s43440-024-00657-7] [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: 07/19/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 10/01/2024]
Abstract
Neuroprotection, defined as safeguarding neurons from damage and death by inhibiting diverse pathological mechanisms, continues to be a promising approach for managing a range of central nervous system (CNS) disorders, including acute conditions such as ischemic stroke and traumatic brain injury (TBI) and chronic neurodegenerative diseases like Parkinson's disease (PD), Alzheimer's disease (AD), and multiple sclerosis (MS). These pathophysiological conditions involve excessive glutamatergic (Glu) transmission activity, which can lead to excitotoxicity. Inhibiting this excessive Glu transmission has been proposed as a potential therapeutic strategy for treating the CNS disorders mentioned. In particular, ligands of G protein-coupled receptors (GPCRs), including metabotropic glutamatergic receptors (mGluRs), have been recognized as promising options for inhibiting excessive Glu transmission. This review discusses the complex interactions of mGlu receptors with their subtypes, including the formation of homo- and heterodimers, which may vary in function and pharmacology depending on their protomer composition. Understanding these intricate details of mGlu receptor structure and function enhances researchers' ability to develop targeted pharmacological interventions, potentially offering new therapeutic avenues for neurological and psychiatric disorders. This review also summarizes the current knowledge of the neuroprotective potential of ligands targeting group III mGluRs in preclinical cellular (in vitro) and animal (in vivo) models of ischemic stroke, TBI, PD, AD, and MS. In recent years, experiments have shown that compounds, especially those activating mGlu4 or mGlu7 receptors, exhibit protective effects in experimental ischemia models. The discovery of allosteric ligands for specific mGluR subtypes has led to reports suggesting that group III mGluRs may be promising targets for neuroprotective therapy in PD (mGlu4R), TBI (mGlu7R), and MS (mGlu8R).
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Affiliation(s)
- Helena Domin
- Maj Institute of Pharmacology, Department of Neurobiology, Polish Academy of Sciences, Smętna 12, Kraków, 31-343, Poland.
| | - Grzegorz Burnat
- Maj Institute of Pharmacology, Department of Neurobiology, Polish Academy of Sciences, Smętna 12, Kraków, 31-343, Poland
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2
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Blanco MJ, Buskes MJ, Govindaraj RG, Ipsaro JJ, Prescott-Roy JE, Padyana AK. Allostery Illuminated: Harnessing AI and Machine Learning for Drug Discovery. ACS Med Chem Lett 2024; 15:1449-1455. [PMID: 39291033 PMCID: PMC11403745 DOI: 10.1021/acsmedchemlett.4c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
In the past several years there has been rapid adoption of artificial intelligence (AI) and machine learning (ML) tools for drug discovery. In this Microperspective, we comment on recent AI/ML applications to the discovery of allosteric modulators, focusing on breakthroughs with AlphaFold, structure-based drug discovery (SBDD), and medicinal chemistry applications. We discuss how these technologies are facilitating drug discovery and the remaining challenges to identify allosteric binding sites and ligands.
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Affiliation(s)
- Maria-Jesus Blanco
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Melissa J Buskes
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Rajiv G Govindaraj
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jonathan J Ipsaro
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Joann E Prescott-Roy
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Anil K Padyana
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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3
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Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Nat Chem Biol 2024; 20:1199-1209. [PMID: 38671223 PMCID: PMC11358040 DOI: 10.1038/s41589-024-01609-1] [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: 05/20/2023] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.
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Affiliation(s)
- Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Todd M Link
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runze Shen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davide Moiani
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn Burnett
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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4
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Nussinov R, Jang H. The value of protein allostery in rational anticancer drug design: an update. Expert Opin Drug Discov 2024; 19:1071-1085. [PMID: 39068599 PMCID: PMC11390313 DOI: 10.1080/17460441.2024.2384467] [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: 04/15/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
INTRODUCTION Allosteric drugs are advantageous. However, they still face hurdles, including identification of allosteric sites that will effectively alter the active site. Current strategies largely focus on identifying pockets away from the active sites into which the allosteric ligand will dock and do not account for exactly how the active site is altered. Favorable allosteric inhibitors dock into sites that are nearby the active sites and follow nature, mimicking diverse allosteric regulation strategies. AREAS COVERED The following article underscores the immense significance of allostery in drug design, describes current allosteric strategies, and especially offers a direction going forward. The article concludes with the authors' expert perspectives on the subject. EXPERT OPINION To select a productive venue in allosteric inhibitor development, we should learn from nature. Currently, useful strategies follow this route. Consider, for example, the mechanisms exploited in relieving autoinhibition and in harnessing allosteric degraders. Mimicking compensatory, or rescue mutations may also fall into such a thesis, as can molecular glues that capture features of scaffolding proteins. Capturing nature and creatively tailoring its mimicry can continue to innovate allosteric drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, USA
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5
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Ding T, Guseinov AA, Milligan G, Plouffe B, Tikhonova IG. Exploring an Intracellular Allosteric Site of CC-Chemokine Receptor 4 from 3D Models, Probe Simulations, and Mutagenesis. ACS Pharmacol Transl Sci 2024; 7:2516-2526. [PMID: 39144548 PMCID: PMC11320731 DOI: 10.1021/acsptsci.4c00330] [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: 06/01/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024]
Abstract
We applied our previously developed probe confined dynamic mapping protocol, which combines enhanced sampling molecular dynamics (MD) simulations and fragment-based approaches, to identify the binding site of GSK2239633A (N-[[3-[[3-[(5-chlorothiophen-2-yl)sulfonylamino]-4-methoxyindazol-1-yl]methyl]phenyl]methyl]-2-hydroxy-2-methylpropanamide), a selective CC-chemokine receptor type 4 (CCR4) negative allosteric modulator, using CCR4 homology and AlphaFold models. By comparing the performance across five computational models, we identified conserved (K3108.49 and Y3047.53) and non-conserved (M2436.36) residue hotspots for GSK2239633A binding, which were validated by mutagenesis and bioluminescence resonance energy transfer assay. Further analysis of 3D models and MD simulations highlighted the pair of residues 6.36 and 7.56 that might account for antagonist selectivity among chemokine receptors. Our in silico protocol provides a promising approach for characterizing ligand binding sites in membrane proteins, considering receptor dynamics and adaptability and guiding protein template selection for ligand design.
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Affiliation(s)
- Tianyi Ding
- School
of Pharmacy, Queen’s University Belfast, Belfast Bt9 7BL, Northern Ireland, U.K.
| | - Abdul-Akim Guseinov
- School
of Pharmacy, Queen’s University Belfast, Belfast Bt9 7BL, Northern Ireland, U.K.
| | - Graeme Milligan
- Centre
for Translational Pharmacology, School of Molecular Biosciences, College
of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland G12 8QQ, U.K.
| | - Bianca Plouffe
- Wellcome-Wolfson
Institute for Experimental Medicine, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, Belfast Bt9 7BL, Northern Ireland, U.K.
| | - Irina G. Tikhonova
- School
of Pharmacy, Queen’s University Belfast, Belfast Bt9 7BL, Northern Ireland, U.K.
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6
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Koenig A, Lewis M, Wald J, Li S, Varoglu M, Dai J, Sankoh A, Paumier K, Doherty J, Quirk M. Dalzanemdor (SAGE-718), a novel, investigational N-methyl-D-aspartate receptor positive allosteric modulator: Safety, tolerability, and clinical pharmacology in randomized dose-finding studies in healthy participants and an open-label study in participants with Huntington's disease. Clin Transl Sci 2024; 17:e13852. [PMID: 38988035 PMCID: PMC11236904 DOI: 10.1111/cts.13852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/12/2024] Open
Abstract
N-methyl-D-aspartate receptor (NMDAR)-positive allosteric modulators (PAMs) represent a potential therapeutic strategy for cognitive impairment in disorders associated with NMDAR hypofunction, including Huntington's disease (HD) and Alzheimer's disease. Dalzanemdor (SAGE-718) is a novel, investigational NMDAR PAM being evaluated for the potential treatment of cognitive impairment in these disorders. We report first-in-human, phase I, double-blind, dose-finding studies to assess the safety, tolerability, and clinical pharmacology of dalzanemdor. A single-ascending dose study (dalzanemdor 0.35, 0.75, 1.5, or 3.0 mg vs. placebo) was conducted in healthy participants and included food effects. A multiple-ascending dose study (14 days) was conducted in healthy participants (dalzanemdor 0.5 or 1.0 mg vs. placebo) and HD participants (open-label dalzanemdor 1.0 mg) and included exploratory pharmacodynamics on cognitive performance. Dalzanemdor was generally well tolerated with no adverse events leading to discontinuation. Dalzanemdor exhibited pharmacokinetic parameters appropriate for once-daily dosing. Following single and multiple doses in healthy participants, median terminal half-life was 8-118 h, and the median time to reach maximum plasma concentration was 4-7 h. Exposures were dose-proportional after single dose (6-46 ng/mL) and more than dose-proportional after multiple doses (6-41 ng/mL). With multiple dosing, a steady state was achieved after 11 days in healthy participants and 13 days in HD participants. Dalzanemdor exposure decreased slightly with food. In HD participants, results suggest that dalzanemdor may improve cognitive performance on tests of executive function. These results support continued clinical development of dalzanemdor for the potential treatment of cognitive impairment in disorders of NMDAR hypofunction.
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Affiliation(s)
| | | | - Jeff Wald
- Sage Therapeutics, IncCambridgeMassachusettsUSA
| | - Sigui Li
- Sage Therapeutics, IncCambridgeMassachusettsUSA
| | | | - Jing Dai
- Sage Therapeutics, IncCambridgeMassachusettsUSA
| | | | | | | | - Mike Quirk
- Sage Therapeutics, IncCambridgeMassachusettsUSA
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7
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Ramírez-Valle F, Maranville JC, Roy S, Plenge RM. Sequential immunotherapy: towards cures for autoimmunity. Nat Rev Drug Discov 2024; 23:501-524. [PMID: 38839912 DOI: 10.1038/s41573-024-00959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Despite major progress in the treatment of autoimmune diseases in the past two decades, most therapies do not cure disease and can be associated with increased risk of infection through broad suppression of the immune system. However, advances in understanding the causes of autoimmune disease and clinical data from novel therapeutic modalities such as chimeric antigen receptor T cell therapies provide evidence that it may be possible to re-establish immune homeostasis and, potentially, prolong remission or even cure autoimmune diseases. Here, we propose a 'sequential immunotherapy' framework for immune system modulation to help achieve this ambitious goal. This framework encompasses three steps: controlling inflammation; resetting the immune system through elimination of pathogenic immune memory cells; and promoting and maintaining immune homeostasis via immune regulatory agents and tissue repair. We discuss existing drugs and those in development for each of the three steps. We also highlight the importance of causal human biology in identifying and prioritizing novel immunotherapeutic strategies as well as informing their application in specific patient subsets, enabling precision medicine approaches that have the potential to transform clinical care.
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8
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Bernetti M, Bosio S, Bresciani V, Falchi F, Masetti M. Probing allosteric communication with combined molecular dynamics simulations and network analysis. Curr Opin Struct Biol 2024; 86:102820. [PMID: 38688074 DOI: 10.1016/j.sbi.2024.102820] [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: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Understanding the allosteric mechanisms within biomolecules involved in diseases is of paramount importance for drug discovery. Indeed, characterizing communication pathways and critical hotspots in signal transduction can guide a rational approach to leverage allosteric modulation for therapeutic purposes. While the atomistic signatures of allosteric processes are difficult to determine experimentally, computational methods can be a remarkable resource. Network analysis built on Molecular Dynamics simulation data is particularly suited in this respect and is gradually becoming of routine use. Herein, we collect the recent literature in the field, discussing different aspects and available options for network construction and analysis. We further highlight interesting refinements and extensions, eventually providing our perspective on this topic.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
| | - Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/Stefano__Bosio
| | - Veronica Bresciani
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/V_Bresciani
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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9
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Janero DR. Current strategic trends in drug discovery: the present as prologue. Expert Opin Drug Discov 2024; 19:147-159. [PMID: 37936504 DOI: 10.1080/17460441.2023.2275640] [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: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION Escalating costs and inherent uncertainties associated with drug discovery invite initiatives to improve its efficiency and de-risk campaigns for inventing better therapeutics. One such initiative involves recognizing and exploiting current approaches in therapeutics invention with molecular mechanisms of action that hold promise for designing and targeting new chemical entities as drugs. AREAS COVERED This perspective considers the current contextual framework around three drug-discovery approaches and evaluates their potential to help identify new targets/modalities in small-molecule molecular pharmacology: diversifying ligand-directed phenotypes for G protein-coupled receptor (GPCR) pharmacotherapeutic signaling; developing therapeutic-protein degraders and stabilizers for proximity-inducing pharmacology; and mining organelle biology for druggable therapeutic targets. EXPERT OPINION The contemporary drug-discovery approaches examined appear generalizable and versatile to have applications in therapeutics invention beyond those case studies discussed herein. Accordingly, they may be considered strategic trends worthy of note in advancing the field toward novel ways of addressing pharmacotherapeutically unmet medical needs.
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Affiliation(s)
- David R Janero
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, and Health Sciences Entrepreneurs, Northeastern University, Boston, MA, USA
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10
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Jovičić SM. Enzyme ChE, cholinergic therapy and molecular docking: Significant considerations and future perspectives. Int J Immunopathol Pharmacol 2024; 38:3946320241289013. [PMID: 39367568 DOI: 10.1177/03946320241289013] [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: 10/06/2024] Open
Abstract
Enzyme Che plays an essential role in cholinergic and non-cholinergic functions. It is present in the fertilized/unfertilized eggs and sperm of different species. Inclusion criteria for data collection from electronic databases NCBI and Google Scholar are enzyme AChE/BChE, cholinergic therapy, genomic organization and gene transcription, enzyme structure, biogenesis, transport, processing and localization, molecular signaling and biological function, polymorphism and influencing factors. Enzyme Che acts as a signaling receptor during hematopoiesis, protein adhesion, amyloid fiber formation, neurite outgrowth, bone development, and maturation, explaining the activity out of synaptic neurotransmission. Polymorphism in the Che genes correlates to various diseases and diverse drug responses. In particular, change accompanies cancer, neurodegenerative, and cardiovascular disease. Literature knowledge indicates the importance of Che inhibitors that influence biochemical and molecular pathways in disease treatment, genomic organization, gene transcription, structure, biogenesis, transport, processing, and localization of Che enzyme. Enzyme Che polymorphism changes indicate the possibility of efficient and new inhibitor drug target mechanisms in diverse research areas.
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Affiliation(s)
- Snežana M Jovičić
- Department of Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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11
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Šeflová J, Cruz-Cortés C, Guerrero-Serna G, Robia SL, Espinoza-Fonseca LM. Mechanisms for cardiac calcium pump activation by its substrate and a synthetic allosteric modulator using fluorescence lifetime imaging. PNAS NEXUS 2024; 3:pgad453. [PMID: 38222469 PMCID: PMC10785037 DOI: 10.1093/pnasnexus/pgad453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
The discovery of allosteric modulators is an emerging paradigm in drug discovery, and signal transduction is a subtle and dynamic process that is challenging to characterize. We developed a time-correlated single photon-counting imaging approach to investigate the structural mechanisms for small-molecule activation of the cardiac sarcoplasmic reticulum Ca2+-ATPase, a pharmacologically important pump that transports Ca2+ at the expense of adenosine triphosphate (ATP) hydrolysis. We first tested whether the dissociation of sarcoplasmic reticulum Ca2+-ATPase from its regulatory protein phospholamban is required for small-molecule activation. We found that CDN1163, a validated sarcoplasmic reticulum Ca2+-ATPase activator, does not have significant effects on the stability of the sarcoplasmic reticulum Ca2+-ATPase-phospholamban complex. Time-correlated single photon-counting imaging experiments using the nonhydrolyzable ATP analog β,γ-Methyleneadenosine 5'-triphosphate (AMP-PCP) showed ATP is an allosteric modulator of sarcoplasmic reticulum Ca2+-ATPase, increasing the fraction of catalytically competent structures at physiologically relevant Ca2+ concentrations. Unlike ATP, CDN1163 alone has no significant effects on the Ca2+-dependent shifts in the structural populations of sarcoplasmic reticulum Ca2+-ATPase, and it does not increase the pump's affinity for Ca2+ ions. However, we found that CDN1163 enhances the ATP-mediated modulatory effects to increase the population of catalytically competent sarcoplasmic reticulum Ca2+-ATPase structures. Importantly, this structural shift occurs within the physiological window of Ca2+ concentrations at which sarcoplasmic reticulum Ca2+-ATPase operates. We demonstrated that ATP is both a substrate and modulator of sarcoplasmic reticulum Ca2+-ATPase and showed that CDN1163 and ATP act synergistically to populate sarcoplasmic reticulum Ca2+-ATPase structures that are primed for phosphorylation. This study provides novel insights into the structural mechanisms for sarcoplasmic reticulum Ca2+-ATPase activation by its substrate and a synthetic allosteric modulator.
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Affiliation(s)
- Jaroslava Šeflová
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carlos Cruz-Cortés
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guadalupe Guerrero-Serna
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Talevi A. Computer-Aided Drug Discovery and Design: Recent Advances and Future Prospects. Methods Mol Biol 2024; 2714:1-20. [PMID: 37676590 DOI: 10.1007/978-1-0716-3441-7_1] [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: 09/08/2023]
Abstract
Computer-aided drug discovery and design involve the use of information technologies to identify and develop, on a rational ground, chemical compounds that align a set of desired physicochemical and biological properties. In its most common form, it involves the identification and/or modification of an active scaffold (or the combination of known active scaffolds), although de novo drug design from scratch is also possible. Traditionally, the drug discovery and design processes have focused on the molecular determinants of the interactions between drug candidates and their known or intended pharmacological target(s). Nevertheless, in modern times, drug discovery and design are conceived as a particularly complex multiparameter optimization task, due to the complicated, often conflicting, property requirements.This chapter provides an updated overview of in silico approaches for identifying active scaffolds and guiding the subsequent optimization process. Recent groundbreaking advances in the field have also analyzed the integration of state-of-the-art machine learning approaches in every step of the drug discovery process (from prediction of target structure to customized molecular docking scoring functions), integration of multilevel omics data, and the use of a diversity of computational approaches to assist target validation and assess plausible binding pockets.
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Affiliation(s)
- Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata, Argentina.
- Argentinean National Council of Scientific and Technical Research (CONICET), La Plata, Argentina.
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13
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Zhang W, Miura A, Abu Saleh MM, Shimizu K, Mita Y, Tanida R, Hirako S, Shioda S, Gmyr V, Kerr-Conte J, Pattou F, Jin C, Kanai Y, Sasaki K, Minamino N, Sakoda H, Nakazato M. The NERP-4-SNAT2 axis regulates pancreatic β-cell maintenance and function. Nat Commun 2023; 14:8158. [PMID: 38071217 PMCID: PMC10710447 DOI: 10.1038/s41467-023-43976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Insulin secretion from pancreatic β cells is regulated by multiple stimuli, including nutrients, hormones, neuronal inputs, and local signalling. Amino acids modulate insulin secretion via amino acid transporters expressed on β cells. The granin protein VGF has dual roles in β cells: regulating secretory granule formation and functioning as a multiple peptide precursor. A VGF-derived peptide, neuroendocrine regulatory peptide-4 (NERP-4), increases Ca2+ influx in the pancreata of transgenic mice expressing apoaequorin, a Ca2+-induced bioluminescent protein complex. NERP-4 enhances glucose-stimulated insulin secretion from isolated human and mouse islets and β-cell-derived MIN6-K8 cells. NERP-4 administration reverses the impairment of β-cell maintenance and function in db/db mice by enhancing mitochondrial function and reducing metabolic stress. NERP-4 acts on sodium-coupled neutral amino acid transporter 2 (SNAT2), thereby increasing glutamine, alanine, and proline uptake into β cells and stimulating insulin secretion. SNAT2 deletion and inhibition abolish the protective effects of NERP-4 on β-cell maintenance. These findings demonstrate a novel autocrine mechanism of β-cell maintenance and function that is mediated by the peptide-amino acid transporter axis.
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Affiliation(s)
- Weidong Zhang
- Department of Bioregulatory Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ayako Miura
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Department of Pharmacology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Md Moin Abu Saleh
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Department of Postgraduate Studies and Research, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Bahrain
| | - Koichiro Shimizu
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuichiro Mita
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Ryota Tanida
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Satoshi Hirako
- Department of Health and Nutrition, University of Human Arts and Sciences, Saitama, Japan
| | - Seiji Shioda
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, Yokohama, Japan
| | - Valery Gmyr
- Université de Lille, Inserm, Campus Hospitalo-Universitaire de Lille, Institut Pasteur de Lille, U1190-EGID, F-59000, Lille, France
| | - Julie Kerr-Conte
- Université de Lille, Inserm, Campus Hospitalo-Universitaire de Lille, Institut Pasteur de Lille, U1190-EGID, F-59000, Lille, France
| | - Francois Pattou
- Université de Lille, Inserm, Campus Hospitalo-Universitaire de Lille, Institut Pasteur de Lille, U1190-EGID, F-59000, Lille, France
| | - Chunhuan Jin
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kazuki Sasaki
- Department of Peptidomics, Sasaki Foundation, Tokyo, Japan
| | - Naoto Minamino
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research, Suita, Japan
| | - Hideyuki Sakoda
- Department of Bioregulatory Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masamitsu Nakazato
- Department of Bioregulatory Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Institute for Protein Research, Osaka University, Osaka, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.
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14
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Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023; 83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The concept of allostery has become a central tenet in the study of biological systems. In parallel, the discovery of allosteric drugs is generating new opportunities to selectively modulate difficult targets involved in pathologic mechanisms. Molecular simulations can provide atomistically detailed insight into the processes involved in allosteric regulation and signaling, and at the same time, they have the potential to unveil regulatory hotspots or cryptic sites that are not immediately evident from the analysis of static structures. In this context, computational approaches should be able to connect the study of allosteric regulation at different scales to the possibility of leveraging this knowledge to expand the chemical space of new, active drugs. Here, we will discuss recent advances in the study of allosteric regulation via computational methods and connect the mechanistic knowledge generated to the possibility of designing new small molecules that can tweak the functions of their receptors.
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Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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15
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Raza SHA, Zhong R, Yu X, Zhao G, Wei X, Lei H. Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application. Mol Biotechnol 2023:10.1007/s12033-023-00951-4. [PMID: 37957479 DOI: 10.1007/s12033-023-00951-4] [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: 07/14/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Allostery is an intriguing phenomenon wherein the binding activity of a biological macromolecule is modulated via non-canonical binding site, resulting in synchronized functional changes. The mechanics underlying allostery are relatively complex and this review is focused on common methodologies used to study allostery, such as X-ray crystallography, NMR spectroscopy, and HDXMS. Different methodological approaches are used to generate data in different scenarios. For example, X-ray crystallography provides high-resolution structural information, NMR spectroscopy offers dynamic insights into allosteric interactions in solution, and HDXMS provides information on protein dynamics. The residue transition state (RTS) approach has emerged as a critical tool in understanding the energetics and conformational changes associated with allosteric regulation. Allostery has significant implications in drug discovery, gene transcription, disease diagnosis, and enzyme catalysis. Enzymes' catalytic activity can be modulated by allosteric regulation, offering opportunities to develop novel therapeutic alternatives. Understanding allosteric mechanisms associated with infectious organisms like SARS-CoV and bacterial pathogens can aid in the development of new antiviral drugs and antibiotics. Allosteric mechanisms are crucial in the regulation of a variety of signal transduction and cell metabolism pathways, which in turn govern various cellular processes. Despite progress, challenges remain in identifying allosteric sites and characterizing their contribution to a variety of biological processes. Increased understanding of these mechanisms can help develop allosteric systems specifically designed to modulate key biological mechanisms, providing novel opportunities for the development of targeted therapeutics. Therefore, the current review aims to summarize common methodologies that are used to further our understanding of allosteric mechanisms. In conclusion, this review provides insights into the methodologies used for the study of allostery, its applications in in silico modeling, the mechanisms underlying antibody allostery, and the ongoing challenges and prospects in advancing our comprehension of this intriguing phenomenon.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruimin Zhong
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoting Yu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Zhao
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- Licheng Detection and Certification Group Co., Ltd., Zhongshan, 528403, Guangdong, China.
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16
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Fancher AT, Hua Y, Close DA, Xu W, McDermott LA, Strock CJ, Santiago U, Camacho CJ, Johnston PA. Characterization of allosteric modulators that disrupt androgen receptor co-activator protein-protein interactions to alter transactivation-Drug leads for metastatic castration resistant prostate cancer. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:325-343. [PMID: 37549772 DOI: 10.1016/j.slasd.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/06/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Three series of compounds were prioritized from a high content screening campaign that identified molecules that blocked dihydrotestosterone (DHT) induced formation of Androgen Receptor (AR) protein-protein interactions (PPIs) with the Transcriptional Intermediary Factor 2 (TIF2) coactivator and also disrupted preformed AR-TIF2 PPI complexes; the hydrobenzo-oxazepins (S1), thiadiazol-5-piperidine-carboxamides (S2), and phenyl-methyl-indoles (S3). Compounds from these series inhibited AR PPIs with TIF2 and SRC-1, another p160 coactivator, in mammalian 2-hybrid assays and blocked transcriptional activation in reporter assays driven by full length AR or AR-V7 splice variants. Compounds inhibited the growth of five prostate cancer cell lines, with many exhibiting differential cytotoxicity towards AR positive cell lines. Representative compounds from the 3 series substantially reduced both endogenous and DHT-enhanced expression and secretion of the prostate specific antigen (PSA) cancer biomarker in the C4-2 castration resistant prostate cancer (CRPC) cell line. The comparatively weak activities of series compounds in the H3-DHT and/or TIF2 box 3 LXXLL-peptide binding assays to the recombinant ligand binding domain of AR suggest that direct antagonism at the orthosteric ligand binding site or AF-2 surface respectively are unlikely mechanisms of action. Cellular enhanced thermal stability assays (CETSA) indicated that compounds engaged AR and reduced the maximum efficacy and right shifted the EC50 of DHT-enhanced AR thermal stabilization consistent with the effects of negative allosteric modulators. Molecular docking of potent representative hits from each series to AR structures suggest that S1-1 and S2-6 engage a novel binding pocket (BP-1) adjacent to the orthosteric ligand binding site, while S3-11 occupies the AR binding function 3 (BF-3) allosteric pocket. Hit binding poses indicate spaces and residues adjacent to the BP-1 and BF-3 pockets that will be exploited in future medicinal chemistry optimization studies. Small molecule allosteric modulators that prevent/disrupt AR PPIs with coactivators like TIF2 to alter transcriptional activation in the presence of orthosteric agonists might evade the resistance mechanisms to existing prostate cancer drugs and provide novel starting points for medicinal chemistry lead optimization and future development into therapies for metastatic CRPC.
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Affiliation(s)
- Ashley T Fancher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Nucleus Global, 2 Ravinia Drive, Suite 605, Atlanta, GA 30346, USA
| | - Yun Hua
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David A Close
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lee A McDermott
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; PsychoGenics Inc, 215 College Road, Paramus, NJ 07652, USA
| | | | - Ulises Santiago
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15232, USA.
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17
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Maschietto F, Morzan UN, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro GW, Nekrasov P, Brooks B, Loria JP, Rivalta I, Batista VS. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nat Commun 2023; 14:2239. [PMID: 37076500 PMCID: PMC10115891 DOI: 10.1038/s41467-023-37956-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.
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Affiliation(s)
- Federica Maschietto
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
| | - Uriel N Morzan
- International Center for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Florentina Tofoleanu
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
- Treeline Biosciences, 500 Arsenal Street, Watertown, MA, 02472, USA
| | - Aria Gheeraert
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Apala Chaudhuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gregory W Kyro
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Peter Nekrasov
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Bernard Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - J Patrick Loria
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Ivan Rivalta
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France.
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy.
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
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18
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Vavers E, Zvejniece L, Dambrova M. Sigma-1 receptor and seizures. Pharmacol Res 2023; 191:106771. [PMID: 37068533 PMCID: PMC10176040 DOI: 10.1016/j.phrs.2023.106771] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/19/2023]
Abstract
Over the last decade, sigma-1 receptor (Sig1R) has been recognized as a valid target for the treatment of seizure disorders and seizure-related comorbidities. Clinical trials with Sig1R ligands are underway testing therapies for the treatment of drug-resistant seizures, developmental and epileptic encephalopathies, and photosensitive epilepsy. However, the direct molecular mechanism by which Sig1R modulates seizures and the balance between excitatory and inhibitory pathways has not been fully elucidated. This review article aims to summarize existing knowledge of Sig1R and its involvement in seizures by focusing on the evidence obtained from Sig1R knockout animals and the anti-seizure effects of Sig1R ligands. In addition, this review article includes a discussion of the advantages and disadvantages of the use of existing compounds and describes the challenges and future perspectives on the use of Sig1R as a target for the treatment of seizure disorders.
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Affiliation(s)
- Edijs Vavers
- Latvian Institute of Organic Synthesis, Laboratory of Pharmaceutical Pharmacology, Aizkraukles 21, LV-1006, Riga, Latvia; University of Tartu, Faculty of Science and Technology, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Liga Zvejniece
- Latvian Institute of Organic Synthesis, Laboratory of Pharmaceutical Pharmacology, Aizkraukles 21, LV-1006, Riga, Latvia
| | - Maija Dambrova
- Latvian Institute of Organic Synthesis, Laboratory of Pharmaceutical Pharmacology, Aizkraukles 21, LV-1006, Riga, Latvia; Riga Stradiņš University, Faculty of Pharmacy, Konsula 21, LV-1007, Riga, Latvia
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19
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Govindaraj RG, Thangapandian S, Schauperl M, Denny RA, Diller DJ. Recent applications of computational methods to allosteric drug discovery. Front Mol Biosci 2023; 9:1070328. [PMID: 36710877 PMCID: PMC9877542 DOI: 10.3389/fmolb.2022.1070328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Interest in exploiting allosteric sites for the development of new therapeutics has grown considerably over the last two decades. The chief driving force behind the interest in allostery for drug discovery stems from the fact that in comparison to orthosteric sites, allosteric sites are less conserved across a protein family, thereby offering greater opportunity for selectivity and ultimately tolerability. While there is significant overlap between structure-based drug design for orthosteric and allosteric sites, allosteric sites offer additional challenges mostly involving the need to better understand protein flexibility and its relationship to protein function. Here we examine the extent to which structure-based drug design is impacting allosteric drug design by highlighting several targets across a variety of target classes.
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Affiliation(s)
- Rajiv Gandhi Govindaraj
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States,*Correspondence: Rajiv Gandhi Govindaraj,
| | | | - Michael Schauperl
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
| | | | - David J. Diller
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
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20
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Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Bioorg Chem 2023; 135:106390. [PMID: 37037129 PMCID: PMC9883075 DOI: 10.1016/j.bioorg.2023.106390] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl2•8H2O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (MPro) and papain-like protease (PLPro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent MPro protein that surprisingly contains zincII (ZnII) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 MPro inhibitors, is performed for the first time in this paper, to the best of our knowledge.
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21
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Blanco MJ, Gardinier KM, Namchuk MN. Advancing New Chemical Modalities into Clinical Studies. ACS Med Chem Lett 2022; 13:1691-1698. [PMID: 36385931 PMCID: PMC9661701 DOI: 10.1021/acsmedchemlett.2c00375] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 11/29/2022] Open
Abstract
Drug discovery and development has experienced an incredible paradigm shift in the past two decades. What once was considered a predominant R&D landscape of small molecules within a prescribed properties and mechanism space now includes an innovative wave of new chemical modalities. Scientists in the pharmaceutical industry can now strategize across a variety of modalities to find the best option to modulate a given target and provide treatment for a specific disease. We have witnessed a remarkable change not only in molecular design but also in creative approaches to drug delivery that have enabled advancement of novel modalities to clinical studies. In this Microperspective, we evaluate the critical differences between traditional small molecules and beyond rule of 5 compounds, peptides, oligonucleotides, and biologics for advancing into development, particularly their pharmacokinetic profiles and drug delivery strategies.
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Affiliation(s)
- Maria-Jesus Blanco
- Chemical
Sciences, Atavistik Bio, 75 Sidney Street, Cambridge Massachusetts 02139, United States
| | - Kevin M. Gardinier
- Discovery
Research, Karuna Therapeutics, 99 High Street Boston, Massachusetts 02110, United States
| | - Mark N. Namchuk
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street Boston, Massachusetts 02115, United States
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22
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Pagano K, Longhi E, Molinari H, Taraboletti G, Ragona L. Inhibition of FGFR Signaling by Targeting FGF/FGFR Extracellular Interactions: Towards the Comprehension of the Molecular Mechanism through NMR Approaches. Int J Mol Sci 2022; 23:ijms231810860. [PMID: 36142770 PMCID: PMC9503799 DOI: 10.3390/ijms231810860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
NMR-based approaches play a pivotal role in providing insight into molecular recognition mechanisms, affording the required atomic-level description and enabling the identification of promising inhibitors of protein–protein interactions. The aberrant activation of the fibroblast growth factor 2 (FGF2)/fibroblast growth factor receptor (FGFR) signaling pathway drives several pathologies, including cancer development, metastasis formation, resistance to therapy, angiogenesis-driven pathologies, vascular diseases, and viral infections. Most FGFR inhibitors targeting the intracellular ATP binding pocket of FGFR have adverse effects, such as limited specificity and relevant toxicity. A viable alternative is represented by targeting the FGF/FGFR extracellular interactions. We previously identified a few small-molecule inhibitors acting extracellularly, targeting FGFR or FGF. We have now built a small library of natural and synthetic molecules that potentially act as inhibitors of FGF2/FGFR interactions to improve our understanding of the molecular mechanisms of inhibitory activity. Here, we provide a comparative analysis of the interaction mode of small molecules with the FGF2/FGFR complex and the single protein domains. DOSY and residue-level NMR analysis afforded insights into the capability of the potential inhibitors to destabilize complex formation, highlighting different mechanisms of inhibition of FGF2-induced cell proliferation.
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Affiliation(s)
- Katiuscia Pagano
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), via Corti 12, 20133 Milano, Italy
- Correspondence: (K.P.); (L.R.)
| | - Elisa Longhi
- Laboratory of Tumour Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Henriette Molinari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), via Corti 12, 20133 Milano, Italy
| | - Giulia Taraboletti
- Laboratory of Tumour Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Laura Ragona
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), via Corti 12, 20133 Milano, Italy
- Correspondence: (K.P.); (L.R.)
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23
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Abram M, Jakubiec M, Reeb K, Cheng MH, Gedschold R, Rapacz A, Mogilski S, Socała K, Nieoczym D, Szafarz M, Latacz G, Szulczyk B, Kalinowska-Tłuścik J, Gawel K, Esguerra CV, Wyska E, Müller CE, Bahar I, Fontana ACK, Wlaź P, Kamiński RM, Kamiński K. Discovery of ( R)- N-Benzyl-2-(2,5-dioxopyrrolidin-1-yl)propanamide [ (R)-AS-1], a Novel Orally Bioavailable EAAT2 Modulator with Drug-like Properties and Potent Antiseizure Activity In Vivo. J Med Chem 2022; 65:11703-11725. [PMID: 35984707 PMCID: PMC9469208 DOI: 10.1021/acs.jmedchem.2c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(R)-7 [(R)-AS-1] showed broad-spectrum antiseizure activity across in vivo mouse seizure models: maximal electroshock (MES), 6 Hz (32/44 mA), acute pentylenetetrazol (PTZ), and PTZ-kindling. A remarkable separation between antiseizure activity and CNS-related adverse effects was also observed. In vitro studies with primary glia cultures and COS-7 cells expressing the glutamate transporter EAAT2 showed enhancement of glutamate uptake, revealing a stereoselective positive allosteric modulator (PAM) effect, further supported by molecular docking simulations. (R)-7 [(R)-AS-1] was not active in EAAT1 and EAAT3 assays and did not show significant off-target activity, including interactions with targets reported for marketed antiseizure drugs, indicative of a novel and unprecedented mechanism of action. Both in vivo pharmacokinetic and in vitro absorption, distribution, metabolism, excretion, toxicity (ADME-Tox) profiles confirmed the favorable drug-like potential of the compound. Thus, (R)-7 [(R)-AS-1] may be considered as the first-in-class small-molecule PAM of EAAT2 with potential for further preclinical and clinical development in epilepsy and possibly other CNS disorders.
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Affiliation(s)
- Michał Abram
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Marcin Jakubiec
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Katelyn Reeb
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania19102, United States
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15213, United States
| | - Robin Gedschold
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Anna Rapacz
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Szczepan Mogilski
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Katarzyna Socała
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Dorota Nieoczym
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Małgorzata Szafarz
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Bartłomiej Szulczyk
- Department of Pharmacodynamics, Centre for Preclinical Research and Technology, Medical University of Warsaw, Banacha 1B, 02-097Warsaw, Poland
| | - Justyna Kalinowska-Tłuścik
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Krakow, Poland
| | - Kinga Gawel
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego 8B, 20-090Lublin, Poland
| | - Camila V Esguerra
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway, University of Oslo, Gaustadalléen 21, Forskningsparken, 0349Oslo, Norway
| | - Elżbieta Wyska
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15213, United States
| | - Andréia C K Fontana
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania19102, United States
| | - Piotr Wlaź
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Rafał M Kamiński
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Krzysztof Kamiński
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
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24
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Buey RM, Fernández‐Justel D, Jiménez A, Revuelta JL. The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases. Protein Sci 2022; 31:e4399. [PMID: 36040265 PMCID: PMC9375230 DOI: 10.1002/pro.4399] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) is an evolutionarily conserved enzyme that mediates the first committed step in de novo guanine nucleotide biosynthetic pathway. It is an essential enzyme in purine nucleotide biosynthesis that modulates the metabolic flux at the branch point between adenine and guanine nucleotides. IMPDH plays key roles in cell homeostasis, proliferation, and the immune response, and is the cellular target of several drugs that are widely used for antiviral and immunosuppressive chemotherapy. IMPDH enzyme is tightly regulated at multiple levels, from transcriptional control to allosteric modulation, enzyme filamentation, and posttranslational modifications. Herein, we review recent developments in our understanding of the mechanisms of IMPDH regulation, including all layers of allosteric control that fine-tune the enzyme activity.
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Affiliation(s)
- Rubén M. Buey
- Metabolic Engineering Group, Department of Microbiology and GeneticsUniversidad de SalamancaSalamancaSpain
| | - David Fernández‐Justel
- Metabolic Engineering Group, Department of Microbiology and GeneticsUniversidad de SalamancaSalamancaSpain
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and GeneticsUniversidad de SalamancaSalamancaSpain
| | - José L. Revuelta
- Metabolic Engineering Group, Department of Microbiology and GeneticsUniversidad de SalamancaSalamancaSpain
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25
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García-Cárceles J, Vázquez-Villa H, Brea J, Ladron de Guevara-Miranda D, Cincilla G, Sánchez-Martínez M, Sánchez-Merino A, Algar S, Teresa de Los Frailes M, Roberts RS, Ballesteros JA, Rodríguez de Fonseca F, Benhamú B, Loza MI, López-Rodríguez ML. 2-(Fluoromethoxy)-4'-( S-methanesulfonimidoyl)-1,1'-biphenyl (UCM-1306), an Orally Bioavailable Positive Allosteric Modulator of the Human Dopamine D 1 Receptor for Parkinson's Disease. J Med Chem 2022; 65:12256-12272. [PMID: 36044544 PMCID: PMC9511493 DOI: 10.1021/acs.jmedchem.2c00949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
![]()
Tolerance development caused by dopamine replacement
with l-DOPA and therapeutic drawbacks upon activation of
dopaminergic receptors
with orthosteric agonists reveal a significant unmet need for safe
and effective treatment of Parkinson’s disease. In search for
selective modulators of the D1 receptor, the screening
of a chemical library and subsequent medicinal chemistry program around
an identified hit resulted in new synthetic compound 26 [UCM-1306, 2-(fluoromethoxy)-4′-(S-methanesulfonimidoyl)-1,1′-biphenyl]
that increases the dopamine maximal effect in a dose-dependent manner
in human and mouse D1 receptors, is inactive in the absence
of dopamine, modulates dopamine affinity for the receptor, exhibits
subtype selectivity, and displays low binding competition with orthosteric
ligands. The new allosteric modulator potentiates cocaine-induced
locomotion and enhances l-DOPA recovery of decreased locomotor
activity in reserpinized mice after oral administration. The behavior
of compound 26 supports the interest of a positive allosteric
modulator of the D1 receptor as a promising therapeutic
approach for Parkinson’s disease.
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Affiliation(s)
- Javier García-Cárceles
- Departamento de Química Orgánica, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - José Brea
- Biofarma Research Group, USEF Screening Platform, CIMUS, USC, E-15782 Santiago de Compostela, Spain
| | | | - Giovanni Cincilla
- Molomics S.L., Parc Científic de Barcelona, Baldiri Reixac 4-8, E-08028 Barcelona, Spain
| | | | - Anabel Sánchez-Merino
- Departamento de Química Orgánica, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Sergio Algar
- Departamento de Química Orgánica, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - María Teresa de Los Frailes
- Fundación Kærtor, Edificio EMPRENDIA, Planta 2, Oficina 4. Campus Vida, E-15706 Santiago de Compostela, Spain
| | - Richard S Roberts
- Fundación Kærtor, Edificio EMPRENDIA, Planta 2, Oficina 4. Campus Vida, E-15706 Santiago de Compostela, Spain
| | | | | | - Bellinda Benhamú
- Departamento de Química Orgánica, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - María I Loza
- Biofarma Research Group, USEF Screening Platform, CIMUS, USC, E-15782 Santiago de Compostela, Spain.,Fundación Kærtor, Edificio EMPRENDIA, Planta 2, Oficina 4. Campus Vida, E-15706 Santiago de Compostela, Spain
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26
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Protein Folding Interdiction Strategy for Therapeutic Drug Development in Viral Diseases: Ebola VP40 and Influenza A M1. Int J Mol Sci 2022; 23:ijms23073906. [PMID: 35409264 PMCID: PMC8998936 DOI: 10.3390/ijms23073906] [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: 03/07/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
In a recent paper, we proposed the folding interdiction target region (FITR) strategy for therapeutic drug design in SARS-CoV-2. This paper expands the application of the FITR strategy by proposing therapeutic drug design approaches against Ebola virus disease and influenza A. We predict target regions for folding interdicting drugs on correspondingly relevant structural proteins of both pathogenic viruses: VP40 of Ebola, and matrix protein M1 of influenza A. Identification of the protein targets employs the sequential collapse model (SCM) for protein folding. It is explained that the model predicts natural peptide candidates in each case from which to start the search for therapeutic drugs. The paper also discusses how these predictions could be tested, as well as some challenges likely to be found when designing effective therapeutic drugs from the proposed peptide candidates. The FITR strategy opens a potential new avenue for the design of therapeutic drugs that promises to be effective against infectious diseases.
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27
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Nussinov R, Zhang M, Maloney R, Tsai C, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2022; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Chung‐Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
- Department of Chemical and Biological Engineering, College of EngineeringKoc UniversityIstanbulTurkey
- Koc University Research Center for Translational Medicine, School of MedicineKoc UniversityIstanbulTurkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
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28
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Mannes M, Martin C, Menet C, Ballet S. Wandering beyond small molecules: peptides as allosteric protein modulators. Trends Pharmacol Sci 2021; 43:406-423. [PMID: 34857409 DOI: 10.1016/j.tips.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022]
Abstract
Recent years have seen the rise of allosteric modulation as an innovative approach for drug design and discovery, efforts which culminated in the development of several clinical candidates. Allosteric modulation of many drug targets, including mainly membrane-embedded receptors, have been vastly explored through small molecule screening campaigns, but much less attention has been paid to peptide-based allosteric modulators. However, peptides have a significant impact on the pharmaceutical industry due to the typically higher potency and selectivity for their targets, as compared with small molecule therapeutics. Therefore, peptides represent one of the most promising classes of molecules that can modulate key biological pathways. Here, we report on the allosteric modulation of proteins (ranging from G protein-coupled receptors to specific protein-protein interactions) by peptides for applications in drug discovery.
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Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
| | - Christel Menet
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 30, Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
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29
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Abstract
INTRODUCTION Undruggable targets refer to clinically meaningful therapeutic targets that are 'difficult to drug' or 'yet to be drugged' via traditional approaches. Featuring characteristics of lacking defined ligand-binding pockets, non-catalytic protein-protein interaction functional modes and less-investigated 3D structures, these undruggable targets have been targeted with novel therapeutic entities developed with the progress of unconventional drug discovery approaches, such as targeted degradation molecules and display technologies. AREA COVERED This review first presents the concept of 'undruggable' exemplified by RAS and other targets. Next, detailed strategies are illustrated in two aspects: innovation of therapeutic entities and development of unconventional drug discovery technologies. Finally, case studies covering typical undruggable targets (Bcl-2, p53, and RAS) are depicted to further demonstrate the feasibility of the strategies and entities above. EXPERT OPINION Targeting the undruggable expands the scope of therapeutically reachable targets. Consequently, it represents the drug discovery frontier. Biomedical studies are capable of dissecting disease mechanisms, thus broadening the list of undruggable targets. Encouraged by the recent approval of the KRAS inhibitor Sotorasib, we believe that merging multiple discovery approaches and exploiting various novel therapeutic entities would pave the way for dealing with more 'undruggable' targets in the future.
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Affiliation(s)
- Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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30
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Kalhor HR, Taghikhani E. Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release. J Chem Inf Model 2021; 61:4045-4057. [PMID: 34292735 DOI: 10.1021/acs.jcim.1c00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned randomly and distant from the binary complex (HSA-warfarin) in a physiologically relevant concentration. The results obtained from both approaches indicated that s-ibuprofen and ascorbic acid both displayed allosteric effects on the release of warfarin from HSA. Although ascorbic acid aided in warfarin release, leading to destabilization of HSA, ibuprofen demonstrated a stabilizing effect on releasing the anticoagulant drug through several noncovalent interactions, including hydrophobic, electrostatic, and hydrogen-bonding interactions with the protein. The calculated binding free energy and energy contribution of involved residues using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method, along with root mean square deviation (RMSD) values, protein gyration, and free energy surface (FES) mapping of the protein, provided valuable details on the nature of the interactions of each drug on the release of warfarin from HSA. These results can provide important information on the mechanisms of anticoagulant release that has not been revealed in molecular details previously.
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Affiliation(s)
- Hamid Reza Kalhor
- Biochemistry Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Elham Taghikhani
- Biochemistry Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
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31
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Karaki F, Oki T, Sakao Y, Sato N, Hirayama S, Miyano K, Uezono Y, Fujii H. Identification of a Putative β-Arrestin Superagonist of the Growth Hormone Secretagogue Receptor (GHSR). ChemMedChem 2021; 16:3463-3476. [PMID: 34278724 DOI: 10.1002/cmdc.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Ghrelin is a pleiotropic feeding hormone which also has a pivotal role in the central nervous system. Upon the activation of its receptor, growth hormone secretagogue receptor (GHSR), the Gαq/11 -mediated and the β-arrestin-mediated signaling pathways are activated. As the β-arrestin pathway is a potential drug target, there is a strong need for β-arrestin-biased GHSR modulators. Activation of the β-arrestin pathway should inhibit the Gαq/11 -mediated calcium flux through internalization of the receptor. Hence, we used the antagonistic activity in the calcium assay as the first screening for the β-arrestin activation. By conducting the second screening assay for the β-arrestin activation based on extracellular signal regulated kinase (ERK) 1/2 phosphorylation, we discovered a putative β-arrestin-biased superagonist. The activity of the compound was not completely blocked with the competitive antagonist, which implies that the effect is mediated, at least partly, by allosteric binding of the compound.
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Affiliation(s)
- Fumika Karaki
- Laboratory of Medicinal Chemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan.,Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Tomoya Oki
- Laboratory of Medicinal Chemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuma Sakao
- Laboratory of Medicinal Chemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Noriko Sato
- Analytical Unit for Organic Chemistry, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shigeto Hirayama
- Laboratory of Medicinal Chemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan.,Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kanako Miyano
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Pain Control Research, Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Yasuhito Uezono
- Department of Pain Control Research, Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Supportive and Palliative Care Research Support Office, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa city, Chiba, 277-8577, Japan
| | - Hideaki Fujii
- Laboratory of Medicinal Chemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan.,Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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32
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Matossian MD, Hoang VT, Burks HE, La J, Elliott S, Brock C, Rusch DB, Buechlein A, Nephew KP, Bhatt A, Cavanaugh JE, Flaherty PT, Collins-Burow BM, Burow ME. Constitutive activation of MEK5 promotes a mesenchymal and migratory cell phenotype in triple negative breast cancer. Oncoscience 2021; 8:64-71. [PMID: 34026925 PMCID: PMC8131078 DOI: 10.18632/oncoscience.535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited targeted therapeutic options. A defining feature of TNBC is the propensity to metastasize and acquire resistance to cytotoxic agents. Mitogen activated protein kinase (MAPK) and extracellular regulated kinase (ERK) signaling pathways have integral roles in cancer development and progression. While MEK5/ERK5 signaling drives mesenchymal and migratory cell phenotypes in breast cancer, the specific mechanisms underlying these actions remain under-characterized. To elucidate the mechanisms through which MEK5 regulates the mesenchymal and migratory phenotype, we generated stably transfected constitutively active MEK5 (MEK5-ca) TNBC cells. Downstream signaling pathways and candidate targets of MEK5-ca cells were based on RNA sequencing and confirmed using qPCR and Western blot analyses. MEK5 activation drove a mesenchymal cell phenotype independent of cell proliferation effects. Transwell migration assays demonstrated MEK5 activation significantly increased breast cancer cell migration. In this study, we provide supporting evidence that MEK5 functions through FRA-1 to regulate the mesenchymal and migratory phenotype in TNBC.
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Affiliation(s)
- Margarite D. Matossian
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
- These authors contributed equally to this work and are shared first authors
| | - Van T. Hoang
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
- These authors contributed equally to this work and are shared first authors
| | - Hope E. Burks
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
- These authors contributed equally to this work and are shared first authors
| | - Jacqueline La
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
- These authors contributed equally to this work and are shared first authors
| | - Steven Elliott
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
| | - Courtney Brock
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN
47405, USA
| | - Aaron Buechlein
- Medical Sciences Program, Indiana University School of Medicine-Bloomington,
Bloomington, IN 47405, USA
| | - Kenneth P. Nephew
- Medical Sciences Program, Indiana University School of Medicine-Bloomington,
Bloomington, IN 47405, USA
| | - Akshita Bhatt
- Department of Pharmacology, Duquesne University School of Pharmacy, Pittsburgh,
PA 15282, USA
| | - Jane E. Cavanaugh
- Department of Pharmacology, Duquesne University School of Pharmacy, Pittsburgh,
PA 15282, USA
| | - Patrick T. Flaherty
- Department of Medicinal Chemistry, Duquesne University School of Pharmacy,
Pittsburgh, PA 15282, USA
| | - Bridgette M. Collins-Burow
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
- Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Matthew E. Burow
- Department of Medicine, Division of Hematology and Oncology, Tulane University,
New Orleans, LA 70118, USA
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33
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El-Zohairy M, Zlotos DP, Berger MR, Adwan HH, Mandour YM. Discovery of Novel CCR5 Ligands as Anticolorectal Cancer Agents by Sequential Virtual Screening. ACS OMEGA 2021; 6:10921-10935. [PMID: 34056245 PMCID: PMC8153923 DOI: 10.1021/acsomega.1c00681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/05/2021] [Indexed: 05/07/2023]
Abstract
C-C chemokine receptor type 5 (CCR5) is a member of the G protein-coupled receptor. CCR5 and its interaction with chemokine ligands have been crucial for understanding and tackling human immunodeficiency virus (HIV)-1 entry into target cells. In recent years, the change in CCR5 expression has been related to the progression of different cancer types. Patients treated with the CCR5 ligand, maraviroc (MVC), showed a deceleration in tumor development especially for metastatic colorectal cancer. Based on the crystal structure of CCR5, we herein describe a multistage virtual screening protocol including pharmacophore screening, molecular docking, and protein-ligand interaction fingerprint (PLIF) postdocking filtration for discovery of novel CCR5 ligands. The applied virtual screening protocol led to the identification of four hits with binding modes showing access to the major and minor pockets of the MVC binding site. Compounds 2-4 showed a decrease in cellular proliferation upon testing on the metastatic colorectal cancer cell line, SW620, displaying 12, 16, and 4 times higher potency compared to MVC, respectively. Compound 3 induced apoptosis by arresting cells in the G0/G1 phase of the cell cycle similar to MVC. Further in vitro assays showed compound 3 drastically decreasing the CCR5 expression and cellular migration 48 h post treatment, indicating its ability to inhibit metastatic activity in SW620 cells. The discovered hits represent potential leads for the development of novel classes of anticolorectal cancer agents targeting CCR5.
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Affiliation(s)
- Mariam
A. El-Zohairy
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt
| | - Darius P. Zlotos
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt
| | - Martin R. Berger
- Toxicology
and Chemotherapy Unit, German Cancer Research
Centre (DKFZ), 69120 Heidelberg, Germany
| | - Hassan H. Adwan
- Pharmacology
and Toxicology Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt
| | - Yasmine M. Mandour
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt
- School
of Life and Medical Sciences, University
of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, 11578 Cairo, Egypt
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Zhang Y, Wang K, Yu Z. Drug Development in Channelopathies: Allosteric Modulation of Ligand-Gated and Voltage-Gated Ion Channels. J Med Chem 2020; 63:15258-15278. [PMID: 33253554 DOI: 10.1021/acs.jmedchem.0c01304] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ion channels have been characterized as promising drug targets for treatment of numerous human diseases. Functions of ion channels can be fine-tuned by allosteric modulators, which interact with channels and modulate their activities by binding to sites spatially discrete from those of orthosteric ligands. Positive and negative allosteric modulators have presented a plethora of potential therapeutic advantages over traditionally orthosteric agonists and antagonists in terms of selectivity and safety. This thematic review highlights the discovery of representative allosteric modulators for ligand-gated and voltage-gated ion channels, discussing in particular their identifications, locations, and therapeutic uses in the treatment of a range of channelopathies. Additionally, structures and functions of selected ion channels are briefly described to aid in the rational design of channel modulators. Overall, allosteric modulation represents an innovative targeting approach, and the corresponding modulators provide an abundant but challenging landscape for novel therapeutics targeting ligand-gated and voltage-gated ion channels.
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Affiliation(s)
- Yanyun Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ke Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zhiyi Yu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
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Maryanoff BE, Wipf P. Presenting a Special Issue on "Medicinal Chemistry: From Targets to Therapies". ACS Med Chem Lett 2020; 11:1780-1782. [PMID: 33062151 PMCID: PMC7549098 DOI: 10.1021/acsmedchemlett.0c00508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Buskes MJ, Blanco MJ. Impact of Cross-Coupling Reactions in Drug Discovery and Development. Molecules 2020; 25:E3493. [PMID: 32751973 PMCID: PMC7436090 DOI: 10.3390/molecules25153493] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Cross-coupling reactions have played a critical role enabling the rapid expansion of structure-activity relationships (SAR) during the drug discovery phase to identify a clinical candidate and facilitate subsequent drug development processes. The reliability and flexibility of this methodology have attracted great interest in the pharmaceutical industry, becoming one of the most used approaches from Lead Generation to Lead Optimization. In this mini-review, we present an overview of cross-coupling reaction applications to medicinal chemistry efforts, in particular the Suzuki-Miyaura and Buchwald-Hartwig cross-coupling reactions as a remarkable resource for the generation of carbon-carbon and carbon-heteroatom bonds. To further appreciate the impact of this methodology, the authors discuss some recent examples of clinical candidates that utilize key cross-coupling reactions in their large-scale synthetic process. Looking into future opportunities, the authors highlight the versatility of the cross-coupling reactions towards new chemical modalities like DNA-encoded libraries (DELs), new generation of peptides and cyclopeptides, allosteric modulators, and proteolysis targeting chimera (PROTAC) approaches.
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Affiliation(s)
| | - Maria-Jesus Blanco
- Medicinal Chemistry. Sage Therapeutics, Inc. 215 First Street, Cambridge, MA 02142, USA;
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