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Ashitha KT, Lakshmi S, Anjali S, Krishna A, Prakash V, Anbumani S, Priya S, Somappa SB. Design and discovery of carboxamide-based pyrazole conjugates with multifaceted potential against Triple-Negative Breast cancer MDA-MB-231 cells. Bioorg Med Chem Lett 2024; 113:129960. [PMID: 39265894 DOI: 10.1016/j.bmcl.2024.129960] [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: 05/08/2024] [Revised: 08/31/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024]
Abstract
We report the design, synthesis, and validation of carboxamide-based pyrazole and isoxazole conjugates with a multifaceted activity against Breast Cancer Cell Line MDA-MB-231. The study established that amongst the series, N-(3,5-bis(trifluoromethyl)benzyl)-3-(3,4,5-trimethoxyphenyl)-1H-pyrazole-5-carboxamide (5g) exhibits the highest potency in inhibiting Breast Cancer Cell Line MDA-MB-231 with an IC50 value of 15.08 ± 0.04 µM. The MDA-MB-231 cells, upon treatment with compound 5g, exhibited characteristic apoptotic specific activities such as nuclear fragmentation, phosphatidylserine translocation to the outer plasma membrane, release of lactate dehydrogenase (LDH), and upregulation of caspase 3 and caspase 9 activities. Also, the modulation of pro and antiapoptotic proteins in 5g treated MDA-MB-231 cells was revealed by membrane array analysis. More importantly, the combination of paclitaxel and compound 5g has exhibited improved activity by several folds via their synergistic effects.
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Affiliation(s)
- K T Ashitha
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Lakshmi
- Agro-processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Anjali
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ajay Krishna
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ved Prakash
- Ecotoxicology Laboratory, REACT Division, C.R. Krishnamurti (CRK) Campus, CSIR-Indian Institute of Toxicology Research, Lucknow 226 008, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sadasivam Anbumani
- Ecotoxicology Laboratory, REACT Division, C.R. Krishnamurti (CRK) Campus, CSIR-Indian Institute of Toxicology Research, Lucknow 226 008, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Priya
- Agro-processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Sasidhar B Somappa
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [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: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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3
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Knockenhauer KE, Copeland RA. The importance of binding kinetics and drug-target residence time in pharmacology. Br J Pharmacol 2024; 181:4103-4116. [PMID: 37160660 DOI: 10.1111/bph.16104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
A dominant assumption in pharmacology throughout the 20th century has been that in vivo target occupancy-and attendant pharmacodynamics-depends on the systemic concentration of drug relative to the equilibrium dissociation constant for the drug-target complex. In turn, the duration of pharmacodynamics is temporally linked to the systemic pharmacokinetics of the drug. Yet, there are many examples of drugs for which pharmacodynamic effect endures long after the systemic concentration of a drug has waned to (equilibrium) insignificant levels. To reconcile such data, the drug-target residence time model was formulated, positing that it is the lifetime (or residence time) of the binary drug-target complex, and not its equilibrium affinity per se, that determines the extent and duration of drug pharmacodynamics. Here, we review this model, its evolution over time, and its applications to natural ligand-macromolecule biology and synthetic drug-target pharmacology.
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4
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S Mantilla B, White JS, Mosedale WRT, Gomm A, Nelson A, Smith TK, Wright MH. Discovery of Trypanosoma brucei inhibitors enabled by a unified synthesis of diverse sulfonyl fluorides. Commun Chem 2024; 7:237. [PMID: 39427042 DOI: 10.1038/s42004-024-01327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 10/10/2024] [Indexed: 10/21/2024] Open
Abstract
Sets of electrophilic probes are generally prepared using a narrow toolkit of robust reactions, which tends to limit both their structural and functional diversity. A unified synthesis of skeletally-diverse sulfonyl fluorides was developed that relied upon photoredox-catalysed dehydrogenative couplings between hetaryl sulfonyl fluorides and hydrogen donor building blocks. A set of 32 diverse probes was prepared, and then screened against Trypanosoma brucei. Four of the probes were found to have sub-micromolar anti-trypanosomal activity. A chemical proteomic approach, harnessing an alkynylated analogue and broad-spectrum fluorophosphonate tools, provided insights into the observed anti-trypanosomal activity, which likely stems from covalent modification of multiple protein targets. It is envisaged that the unified diversity-oriented approach may enable the discovery of electrophilic probes that have value in the elucidation of biological and biomedical mechanisms.
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Affiliation(s)
- Brian S Mantilla
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Jack S White
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - William R T Mosedale
- Schools of Biology and Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Andrew Gomm
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Terry K Smith
- Schools of Biology and Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
| | - Megan H Wright
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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5
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Winter GE. Extrapolating Lessons from Targeted Protein Degradation to Other Proximity-Inducing Drugs. ACS Chem Biol 2024; 19:2089-2102. [PMID: 39264973 DOI: 10.1021/acschembio.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Targeted protein degradation (TPD) is an emerging pharmacologic strategy. It relies on small-molecule "degraders" that induce proximity of a component of an E3 ubiquitin ligase complex and a target protein to induce target ubiquitination and subsequent proteasomal degradation. Essentially, degraders thus expand the function of E3 ligases, allowing them to degrade proteins they would not recognize in the absence of the small molecule. Over the past decade, insights gained from identifying, designing, and characterizing various degraders have significantly enhanced our understanding of TPD mechanisms, precipitating in rational degrader discovery strategies. In this Account, I aim to explore how these insights can be extrapolated to anticipate both opportunities and challenges of utilizing the overarching concept of proximity-inducing pharmacology to manipulate other cellular circuits for the dissection of biological mechanisms and for therapeutic purposes.
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Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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6
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Mahran R, Kapp JN, Valtonen S, Champagne A, Ning J, Gillette W, Stephen AG, Hao F, Plückthun A, Härmä H, Pantsar T, Kopra K. Beyond KRAS(G12C): Biochemical and Computational Characterization of Sotorasib and Adagrasib Binding Specificity and the Critical Role of H95 and Y96. ACS Chem Biol 2024; 19:2152-2164. [PMID: 39283696 DOI: 10.1021/acschembio.4c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Mutated KRAS proteins are frequently expressed in some of the most lethal human cancers and thus have been a target of intensive drug discovery efforts for decades. Lately, KRAS(G12C) switch-II pocket (SII-P)-targeting covalent small molecule inhibitors have finally reached clinical practice. Sotorasib (AMG-510) was the first FDA-approved covalent inhibitor to treat KRAS(G12C)-positive nonsmall cell lung cancer (NSCLC), followed soon by adagrasib (MRTX849). Both drugs target the GDP-bound state of KRAS(G12C), exploiting the strong nucleophilicity of acquired cysteine. Here, we evaluate the similarities and differences between sotorasib and adagrasib in their RAS SII-P binding by applying biochemical, cellular, and computational methods. Exact knowledge of SII-P engagement can enable targeting this site by reversible inhibitors for KRAS mutants beyond G12C. We show that adagrasib is strictly KRAS- but not KRAS(G12C)-specific due to its strong and unreplaceable interaction with H95. Unlike adagrasib, sotorasib is less dependent on H95 for its binding, making it a RAS isoform-agnostic compound, having a similar functionality also with NRAS and HRAS G12C mutants. Our results emphasize the accessibility of SII-P beyond oncogenic G12C and aid in understanding the molecular mechanism behind the clinically observed drug resistance, associated especially with secondary mutations on KRAS H95 and Y96.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Jonas N Kapp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Salla Valtonen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Allison Champagne
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21702, United States
| | - Jinying Ning
- KYinno Biotechnology Co., Ltd., Yizhuang Biomedical Park, No. 88 Kechuang Six Street, BDA, Beijing 101111, China
| | - William Gillette
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21702, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21702, United States
| | - Feng Hao
- KYinno Biotechnology Co., Ltd., Yizhuang Biomedical Park, No. 88 Kechuang Six Street, BDA, Beijing 101111, China
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonrinne 3, 70210 Kuopio, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
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7
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Merten EM, Sears JD, Leisner TM, Hardy PB, Ghoshal A, Hossain MA, Asressu KH, Brown PJ, Tse EG, Stashko MA, Li K, Norris-Drouin JL, Herring LE, Mordant AL, Webb TS, Mills CA, Barker NK, Streblow ZJ, Perveen S, Arrowsmith CH, Couñago RM, Arnold JJ, Cameron CE, Streblow DN, Moorman NJ, Heise MT, Willson TM, Popov KI, Pearce KH. Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach. Proc Natl Acad Sci U S A 2024; 121:e2409166121. [PMID: 39388272 DOI: 10.1073/pnas.2409166121] [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: 05/21/2024] [Accepted: 09/09/2024] [Indexed: 10/12/2024] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV nonstructural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow-up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a kinact /KI of 6.4 × 103 M-1s-1. LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity in proteomic experiments or against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the identification and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic.
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Affiliation(s)
- Eric M Merten
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - John D Sears
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Tina M Leisner
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - P Brian Hardy
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Anirban Ghoshal
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kesatebrhan Haile Asressu
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Peter J Brown
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Edwin G Tse
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Michael A Stashko
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kelin Li
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jacqueline L Norris-Drouin
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Laura E Herring
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Angie L Mordant
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Thomas S Webb
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Christine A Mills
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Natalie K Barker
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zachary J Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Sumera Perveen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Rafael Miguez Couñago
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Center of Medicinal Chemistry, Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP 13083-886, Brazil
| | - Jamie J Arnold
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Craig E Cameron
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daniel N Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Timothy M Willson
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Konstantin I Popov
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kenneth H Pearce
- Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, Molecular Therapeutics Research Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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8
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Qian R, Xue J, Xu Y, Huang J. Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery. J Chem Inf Model 2024; 64:7214-7237. [PMID: 39360948 DOI: 10.1021/acs.jcim.4c01024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Computational methods constitute efficient strategies for screening and optimizing potential drug molecules. A critical factor in this process is the binding affinity between candidate molecules and targets, quantified as binding free energy. Among various estimation methods, alchemical transformation methods stand out for their theoretical rigor. Despite challenges in force field accuracy and sampling efficiency, advancements in algorithms, software, and hardware have increased the application of free energy perturbation (FEP) calculations in the pharmaceutical industry. Here, we review the practical applications of FEP in drug discovery projects since 2018, covering both ligand-centric and residue-centric transformations. We show that relative binding free energy calculations have steadily achieved chemical accuracy in real-world applications. In addition, we discuss alternative physics-based simulation methods and the incorporation of deep learning into free energy calculations.
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Affiliation(s)
- Runtong Qian
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jing Xue
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - You Xu
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
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9
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Chaudhuri S, Rogers DM, Hayes CJ, Inzani K, Hirst JD. Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors. J Chem Inf Model 2024; 64:7687-7697. [PMID: 39265068 PMCID: PMC11480980 DOI: 10.1021/acs.jcim.4c01379] [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: 07/31/2024] [Revised: 09/05/2024] [Accepted: 09/05/2024] [Indexed: 09/14/2024]
Abstract
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed as targeted covalent inhibitors that have some selectivity for and covalently inhibit cyclin-dependent kinase 12 (CDK12). CDK12 is involved in the transcription of elongated RNA sections that results in the DM1 condition. The covalent bond is achieved after nucleophilic addition to a Michael acceptor warhead. Previous studies of the conformational preferences of thio-Michael additions have focused on characterizing the reaction profile based on the distance between the sulfur and β-carbon atoms. Rotamerism, however, has not been investigated extensively. Here, we use high-level quantum chemistry calculations, up to coupled cluster with single, double, and perturbative triple excitations [CCSD(T)], to characterize the nucleophilic addition of an archetypal nucleophile, methanethiolate, to various nitrogen-containing Michael acceptors which are representative of the small-molecule covalent inhibitors. By investigating the structural, energetic, and electronic properties of the resulting enolates, as well as their reaction profiles, we show that synclinal additions are generally energetically favored over other additions due to the greater magnitude of attractive noncovalent interactions permitted by the conformation. The calculated transition states associated with the addition process indicate that synclinal addition proceeds via lower energetic barriers than antiperiplanar addition and is the preferred reaction pathway.
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Affiliation(s)
| | - David M. Rogers
- School of Chemistry, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | | | - Katherine Inzani
- School of Chemistry, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | - Jonathan D. Hirst
- School of Chemistry, University
of Nottingham, Nottingham NG7 2RD, U.K.
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10
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Yang Y, Tse YS, Zhang Q, Wong KY, Yang C, Yang Y, Li S, Lau KW, Charles TC, Lam TC, Zhao Q. Multiplexed Target Profiling with Integrated Chemical Genomics and Chemical Proteomics. J Med Chem 2024; 67:17542-17550. [PMID: 39340453 DOI: 10.1021/acs.jmedchem.4c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2024]
Abstract
Target identification is crucial for elucidating the mechanisms of bioactive molecules in drug discovery. However, traditional methods assess compounds individually, making it challenging to efficiently examine multiple compounds in parallel, especially for structurally diverse compounds. This study reports a novel strategy called chemical genomics-facilitated chemical proteomics (CGCP) for multiplexing the target identification of bioactive small molecules. CGCP correlates compounds' perturbation of global transcription, or chemical genomic profiles, with their reactivity toward target proteins, enabling simultaneous identification of targets. We demonstrated the utility of CGCP by studying the targets of celastrol (Cel) and four other electrophilic compounds with varying levels of similarity to Cel based on their chemical genomic profiles. We identified multiple novel targets and binding sites shared by the compounds in a single experiment. CGCP enabled multiplexity and improved the efficiency of target identification for structurally distinct compounds, indicating its potential to accelerate drug discovery.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
| | - Yin-Suen Tse
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong, SAR 999077, China
| | - Qi Zhang
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
| | - Kin-Yau Wong
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Chenxi Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Shuqi Li
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Kin-Wa Lau
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Trevor C Charles
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Thomas C Lam
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
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11
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Bálint D, Póti ÁL, Alexa A, Sok P, Albert K, Torda L, Földesi-Nagy D, Csókás D, Turczel G, Imre T, Szarka E, Fekete F, Bento I, Bojtár M, Palkó R, Szabó P, Monostory K, Pápai I, Soós T, Reményi A. Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads. Nat Commun 2024; 15:8606. [PMID: 39366946 PMCID: PMC11452492 DOI: 10.1038/s41467-024-52573-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/13/2024] [Indexed: 10/06/2024] Open
Abstract
There has been a surge of interest in covalent inhibitors for protein kinases in recent years. Despite success in oncology, the off-target reactivity of these molecules is still hampering the use of covalent warhead-based strategies. Herein, we disclose the development of precision-guided warheads to mitigate the off-target challenge. These reversible warheads have a complex and cyclic structure with optional chirality center and tailored steric and electronic properties. To validate our proof-of-concept, we modified acrylamide-based covalent inhibitors of c-Jun N-terminal kinases (JNKs). We show that the cyclic warheads have high resilience against off-target thiols. Additionally, the binding affinity, residence time, and even JNK isoform specificity can be fine-tuned by adjusting the substitution pattern or using divergent and orthogonal synthetic elaboration of the warhead. Taken together, the cyclic warheads presented in this study will be a useful tool for medicinal chemists for the deliberate design of safer and functionally fine-tuned covalent inhibitors.
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Affiliation(s)
- Dániel Bálint
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Ádám Levente Póti
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Doctoral School of Biology, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Anita Alexa
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Krisztián Albert
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Lili Torda
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Dóra Földesi-Nagy
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Dániel Csókás
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Tímea Imre
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Eszter Szarka
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Ferenc Fekete
- Metabolic Drug-interactions Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Isabel Bento
- European Molecular Biology Laboratory, EMBL, Hamburg, Germany
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Roberta Palkó
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Pál Szabó
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Katalin Monostory
- Metabolic Drug-interactions Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Imre Pápai
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Tibor Soós
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
| | - Attila Reményi
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
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12
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Póti ÁL, Bálint D, Alexa A, Sok P, Ozsváth K, Albert K, Turczel G, Magyari S, Ember O, Papp K, Király SB, Imre T, Németh K, Kurtán T, Gógl G, Varga S, Soós T, Reményi A. Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold. Nat Commun 2024; 15:8607. [PMID: 39366929 PMCID: PMC11452651 DOI: 10.1038/s41467-024-52574-1] [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] [Received: 08/22/2023] [Accepted: 08/22/2024] [Indexed: 10/06/2024] Open
Abstract
For mitogen-activated protein kinases (MAPKs) a shallow surface-distinct from the substrate binding pocket-called the D(ocking)-groove governs partner protein binding. Screening of broad range of Michael acceptor compounds identified a double-activated, sterically crowded cyclohexenone moiety as a promising scaffold. We show that compounds bearing this structurally complex chiral warhead are able to target the conserved MAPK D-groove cysteine via reversible covalent modification and interfere with the protein-protein interactions of MAPKs. The electronic and steric properties of the Michael acceptor can be tailored via different substitution patterns. The inversion of the chiral center of the warhead can reroute chemical bond formation with the targeted cysteine towards the neighboring, but less nucleophilic histidine. Compounds bind to the shallow MAPK D-groove with low micromolar affinity in vitro and perturb MAPK signaling networks in the cell. This class of chiral, cyclic and enhanced 3D shaped Michael acceptor scaffolds offers an alternative to conventional ATP-competitive drugs modulating MAPK signaling pathways.
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Affiliation(s)
- Ádám Levente Póti
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Dániel Bálint
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Anita Alexa
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kristóf Ozsváth
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Krisztián Albert
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sarolt Magyari
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Orsolya Ember
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kinga Papp
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Tímea Imre
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, Budapest, Hungary
| | - Krisztina Németh
- MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
| | - Gergő Gógl
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Szilárd Varga
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tibor Soós
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Attila Reményi
- Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.
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13
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Ming Y, Gong Y, Fu X, Ouyang X, Peng Y, Pu W. Small-molecule-based targeted therapy in liver cancer. Mol Ther 2024; 32:3260-3287. [PMID: 39113358 DOI: 10.1016/j.ymthe.2024.08.001] [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: 11/22/2023] [Revised: 03/13/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
Liver cancer is one of the most prevalent malignant tumors worldwide. According to the Barcelona Clinic Liver Cancer staging criteria, clinical guidelines provide tutorials to clinical management of liver cancer at their individual stages. However, most patients diagnosed with liver cancer are at advanced stage; therefore, many researchers conduct investigations on targeted therapy, aiming to improve the overall survival of these patients. To date, small-molecule-based targeted therapies are highly recommended (first line: sorafenib and lenvatinib; second line: regorafenib and cabozantinib) by current the clinical guidelines of the American Society of Clinical Oncology, European Society for Medical Oncology, and National Comprehensive Cancer Network. Herein, we summarize the small-molecule-based targeted therapies in liver cancer, including the approved and preclinical therapies as well as the therapies under clinical trials, and introduce their history of discovery, clinical trials, indications, and molecular mechanisms. For drug resistance, the revealed mechanisms of action and the combination therapies are also discussed. In fact, the known small-molecule-based therapies still have limited clinical benefits to liver cancer patients. Therefore, we analyze the current status and give our ideas for the urgent issues and future directions in this field, suggesting clues for novel techniques in liver cancer treatment.
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Affiliation(s)
- Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuewen Fu
- Jinhua Huanke Environmental Technology Co., Ltd., Jinhua 321000, China
| | - Xinyu Ouyang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, China.
| | - Wenchen Pu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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14
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Liang L, Zhang Z, You Q, Guo X. Recent advances in the design of small molecular drugs with acrylamides covalent warheads. Bioorg Med Chem 2024; 112:117902. [PMID: 39236467 DOI: 10.1016/j.bmc.2024.117902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024]
Abstract
In the development of covalent inhibitors, acrylamides warhead is one of the most popular classes of covalent warheads. In recent years, researchers have made different structural modifications to acrylamides warheads, resulting in the creation of fluorinated acrylamide warheads and cyano acrylamide warheads. These new warheads exhibit superior selectivity, intracellular accumulation, and pharmacokinetic properties. Additionally, although ketoamide warheads have been applied in the design of covalent inhibitors for viral proteins, it has not received sufficient attention. Combined with the studies in kinase inhibitors and antiviral drugs, this review presents the structural features and the progression of acrylamides warheads, offering a perspective on future research and development in this field.
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Affiliation(s)
- Luxia Liang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ze Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiaoke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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15
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Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem 2024; 16:1592-1604. [PMID: 39138346 DOI: 10.1038/s41557-024-01601-1] [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: 06/05/2023] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds-termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | | | | | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | | | | | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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16
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Cao Z, Wang Q, Neumann H, Beller M. Modular and Diverse Synthesis of Acrylamides by Palladium-Catalyzed Hydroaminocarbonylation of Acetylene. Angew Chem Int Ed Engl 2024; 63:e202410597. [PMID: 38986016 DOI: 10.1002/anie.202410597] [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: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024]
Abstract
The development of all kinds of covalent drugs had a major impact on the improvement of the human health system. Covalent binding to target proteins is achieved by so-called electrophilic warheads, which are incorporated in the respective drug molecule. In the last decade, specifically acrylamides emerged as attractive warheads in covalent drug design. Herein, a straightforward palladium-catalyzed hydroaminocarbonylation of acetylene has been developed, allowing a modular and diverse synthesis of bio-active acrylamides. This general protocol features high atom efficiency, wide functional group compatibility, high chemoselectivity and proceeds additive free under mild reaction conditions. The synthetic utility of this protocol is showcased in the synthesis of ibrutinib, osimertinib, and other bio-active compound derivatives.
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Affiliation(s)
- Zhusong Cao
- Leibniz-Institut für Katalyse e. V. an der, Universität Rostock, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Qiang Wang
- Leibniz-Institut für Katalyse e. V. an der, Universität Rostock, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Helfried Neumann
- Leibniz-Institut für Katalyse e. V. an der, Universität Rostock, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Matthias Beller
- Leibniz-Institut für Katalyse e. V. an der, Universität Rostock, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
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17
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Pezacki JP, Lundrigan E, Evers P, Uguccioni S. Charting the ligandable proteome for stereoselective interactions. Nat Chem 2024; 16:1571-1573. [PMID: 39354165 DOI: 10.1038/s41557-024-01639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Affiliation(s)
- John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada.
- Fulbright Canada Research Chair, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Eryn Lundrigan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Parrish Evers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Spencer Uguccioni
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
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18
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Scholtes JF, Alhambra C, Carpino PA. Trends in covalent drug discovery: a 2020-23 patent landscape analysis focused on select covalent reacting groups (CRGs) found in FDA-approved drugs. Expert Opin Ther Pat 2024; 34:843-861. [PMID: 39219095 DOI: 10.1080/13543776.2024.2400175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/02/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Covalent drugs contain electrophilic groups that can react with nucleophilic amino acids located in the active sites of proteins, particularly enzymes. Recently, there has been considerable interest in using covalent drugs to target non-catalytic amino acids in proteins to modulate difficult targets (i.e. targeted covalent inhibitors). Covalent compounds contain a wide variety of covalent reacting groups (CRGs), but only a few of these CRGs are present in FDA-approved covalent drugs. AREAS COVERED This review summarizes a 2020-23 patent landscape analysis that examined trends in the field of covalent drug discovery around targets and organizations. The analysis focused on patent applications that were submitted to the World International Patent Organization and selected using a combination of keywords and structural searches based on CRGs present in FDA-approved drugs. EXPERT OPINION A total of 707 patent applications from >300 organizations were identified, disclosing compounds that acted at 71 targets. Patent application counts for five targets accounted for ~63% of the total counts (i.e. BTK, EGFR, FGFR, KRAS, and SARS-CoV-2 Mpro). The organization with the largest number of patent counts was an academic institution (Dana-Farber Cancer Institute). For one target, KRAS G12C, the discovery of new drugs was highly competitive (>100 organizations, 186 patent applications).
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19
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Xu G, Torri D, Cuesta-Hoyos S, Panda D, Yates LRL, Zallot R, Bian K, Jia D, Iorgu AI, Levy C, Shepherd SA, Micklefield J. Cryptic enzymatic assembly of peptides armed with β-lactone warheads. Nat Chem Biol 2024; 20:1371-1379. [PMID: 38951647 PMCID: PMC11427300 DOI: 10.1038/s41589-024-01657-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/29/2024] [Indexed: 07/03/2024]
Abstract
Nature has evolved biosynthetic pathways to molecules possessing reactive warheads that inspired the development of many therapeutic agents, including penicillin antibiotics. Peptides armed with electrophilic warheads have proven to be particularly effective covalent inhibitors, providing essential antimicrobial, antiviral and anticancer agents. Here we provide a full characterization of the pathways that nature deploys to assemble peptides with β-lactone warheads, which are potent proteasome inhibitors with promising anticancer activity. Warhead assembly involves a three-step cryptic methylation sequence, which is likely required to reduce unfavorable electrostatic interactions during the sterically demanding β-lactonization. Amide-bond synthetase and adenosine triphosphate (ATP)-grasp enzymes couple amino acids to the β-lactone warhead, generating the bioactive peptide products. After reconstituting the entire pathway to β-lactone peptides in vitro, we go on to deliver a diverse range of analogs through enzymatic cascade reactions. Our approach is more efficient and cleaner than the synthetic methods currently used to produce clinically important warhead-containing peptides.
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Affiliation(s)
- Guangcai Xu
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Daniele Torri
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Sebastian Cuesta-Hoyos
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Deepanjan Panda
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Luke R L Yates
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Rémi Zallot
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Kehan Bian
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Dongxu Jia
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Andreea I Iorgu
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Colin Levy
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Sarah A Shepherd
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Jason Micklefield
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.
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20
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Molitor M, Menge A, Mandel S, George S, Müller S, Knapp S, Hofmann B, Steinhilber D, Häfner AK. Unlocking the potential: unveiling tyrphostins with Michael-reactive cyanoacrylate motif as promising inhibitors of human 5-lipoxygenase. Pflugers Arch 2024:10.1007/s00424-024-03019-7. [PMID: 39347835 DOI: 10.1007/s00424-024-03019-7] [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: 04/19/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024]
Abstract
Human 5-lipoxygenase (5-LO) is the key enzyme in the biosynthesis of leukotrienes, mediators of the innate immune system that also play an important role in inflammatory diseases and cancer. In this study, we present compounds, containing a Michael-reactive cyanoacrylate moiety as potent inhibitors of 5-LO. Representatives of the tyrosine kinase inhibitor family called tyrphostins, structurally related to known 5-LO inhibitors, were screened for their 5-LO inhibitory properties using recombinant human 5-LO, intact human PMNL (polymorphonuclear leukocytes), and PMNL homogenates. Their mode of action was characterized by the addition of glutathione, using a fourfold cysteine 5-LO mutant and mass spectrometry analysis. SAR studies revealed several members of the tyrphostin family containing a Michael-reactive cyanoacrylate to efficiently inhibit 5-LO. We identified degrasyn (IC50 0.11 µM), tyrphostin A9 (IC50 0.8 µM), AG879 (IC50 78 nM), and AG556 (IC50 64 nM) as potent 5-LO inhibitors. Mass spectrometry analysis revealed that degrasyn and AG556 covalently bound to up to four cysteines, including C416 and/or C418 which surround the substrate entry site. Furthermore, the 5-LO inhibitory effect of degrasyn was remarkably impaired by the addition of glutathione or by the mutation of cysteines to serines at the surface of 5-LO. We successfully identified several tyrphostins as potent inhibitors of human 5-LO. Degrasyn and AG556 were able to covalently bind to 5-LO via their cyanoacrylate moiety. This provides a promising mechanism for targeting 5-LO by Michael acceptors, leading to new therapeutic opportunities in the field of inflammation and cancer.
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Affiliation(s)
- Maximilian Molitor
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt Am Main, Germany
| | - Sebastian Mandel
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Sven George
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt Am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt Am Main, Germany
| | - Bettina Hofmann
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany
| | - Ann-Kathrin Häfner
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt Am Main, Germany.
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21
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Su Z, Yin S, Wu Y. Rationalize the Functional Roles of Protein-Protein Interactions in Targeted Protein Degradation by Kinetic Monte-Carlo Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615190. [PMID: 39386564 PMCID: PMC11463391 DOI: 10.1101/2024.09.26.615190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Targeted protein degradation is a promising therapeutic strategy to tackle disease-causing proteins that lack binding pockets for traditional small-molecule inhibitors. Its first step is to trigger the proximity between a ubiquitin ligase complex and a target protein through a heterobifunctional molecule, such as proteolysis targeting chimeras (PROTACs), leading to the formation of a ternary complex. The properties of protein-protein interactions play an important regulatory role during this process, which can be reflected by binding cooperativity. Unfortunately, although computer-aided drug design has become a cornerstone of modern drug development, the endeavor to model targeted protein degradation is still in its infancy. The development of computational tools to understand the impacts of protein-protein interactions on targeted protein degradation, therefore, is highly demanded. To reach this goal, we constructed a non-redundant structural benchmark of the most updated ternary complexes and applied a kinetic Monte-Carlo method to simulate the association between ligases and PROTAC-targeted proteins in the benchmark. Our results show that proteins in most complexes with positive cooperativity tend to associate into native-like configurations more often. In contrast, proteins very likely failed to associate into native-like configurations in complexes with negative cooperativity. Moreover, we compared the protein-protein association through different interfaces generated from molecular docking. The native-like binding interface shows a higher association probability than all the other alternative interfaces only in the complex with positive cooperativity. These observations support the idea that the formation of ternary complexes is closely regulated by the binary interactions between proteins. Finally, we applied our method to cyclin-dependent kinases 4 and 6 (CDK4/6). We found that their interactions with the ligase are not as similar as their structures. Altogether, our study paves the way for understanding the role of protein-protein interactions in PROTACE-induced ternary complex formation. It can potentially help in searching for degraders that selectively target specific proteins.
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Affiliation(s)
- Zhaoqian Su
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212
| | - Shanye Yin
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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22
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Tsuruno A, Kamoshita S, Hosoya S, Sakurai K. Dichlorotriazine-based multivalent probe for selective affinity labeling of carbohydrate-binding proteins. Org Biomol Chem 2024; 22:7659-7663. [PMID: 39193651 DOI: 10.1039/d4ob01285b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
A new series of multivalent gold nanoparticle probes bearing different electrophilic groups were synthesized and their affinity labeling reactivities were evaluated. The dichlorotriazine group was identified as a useful protein-reactive label, allowing selective capture of a target protein at nanomolar probe concentrations.
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Affiliation(s)
- Ayaka Tsuruno
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
| | - Shione Kamoshita
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
| | - Shoichi Hosoya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kaori Sakurai
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
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23
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Stefan SM, Stefan K, Namasivayam V. Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action. J Cheminform 2024; 16:108. [PMID: 39313842 PMCID: PMC11421111 DOI: 10.1186/s13321-024-00901-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
The identification, establishment, and exploration of potential pharmacological drug targets are major steps of the drug development pipeline. Target validation requires diverse chemical tools that come with a spectrum of functionality, e.g., inhibitors, activators, and other modulators. Particularly tools with rare modes-of-action allow for a proper kinetic and functional characterization of the targets-of-interest (e.g., channels, enzymes, receptors, or transporters). Despite, functional innovation is a prime criterion for patentability and commercial exploitation, which may lead to therapeutic benefit. Unfortunately, data on new, and thus, undruggable or barely druggable targets are scarce and mostly available for mainstream modes-of-action only (e.g., inhibition). Here we present a novel cheminformatic workflow-computer-aided pattern scoring (C@PS)-which was specifically designed to project its prediction capabilities into an uncharted domain of applicability.
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Affiliation(s)
- Sven Marcel Stefan
- Department of Pathology, University of Oslo and Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, 0372, Oslo, Norway
- Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093, Lublin, Poland
| | - Katja Stefan
- Department of Pathology, University of Oslo and Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, 0372, Oslo, Norway
- Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Vigneshwaran Namasivayam
- Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- Pharmaceutical Institute, Department of Pharmaceutical and Cellbiological Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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24
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Szupryczyński K, Czeleń P, Jeliński T, Szefler B. What is the Reason That the Pharmacological Future of Chemotherapeutics in the Treatment of Lung Cancer Could Be Most Closely Related to Nanostructures? Platinum Drugs in Therapy of Non-Small and Small Cell Lung Cancer and Their Unexpected, Possible Interactions. The Review. Int J Nanomedicine 2024; 19:9503-9547. [PMID: 39296940 PMCID: PMC11410046 DOI: 10.2147/ijn.s469217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/19/2024] [Indexed: 09/21/2024] Open
Abstract
Over the course of several decades, anticancer treatment with chemotherapy drugs for lung cancer has not changed significantly. Unfortunately, this treatment prolongs the patient's life only by a few months, causing many side effects in the human body. It has also been proven that drugs such as Cisplatin, Carboplatin, Oxaliplatin and others can react with other substances containing an aromatic ring in which the nitrogen atom has a free electron group in its structure. Thus, such structures may have a competitive effect on the nucleobases of DNA. Therefore, scientists are looking not only for new drugs, but also for new alternative ways of delivering the drug to the cancer site. Nanotechnology seems to be a great hope in this matter. Creating a new nanomedicine would reduce the dose of the drug to an absolute minimum, and thus limit the toxic effect of the drug; it would allow for the exclusion of interactions with competitive compounds with a structure similar to nucleobases; it would also permit using the so-called targeted treatment and bypassing healthy cells; it would allow for the introduction of other treatment options, such as radiotherapy directly to the cancer site; and it would provide diagnostic possibilities. This article is a review that aims to systematize the knowledge regarding the anticancer treatment of lung cancer, but not only. It shows the clear possibility of interactions of chemotherapeutics with compounds competitive to the nitrogenous bases of DNA. It also shows the possibilities of using nanostructures as potential Platinum drug carriers, and proves that nanomedicine can easily become a new medicinal product in personalized medicine.
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Affiliation(s)
- Kamil Szupryczyński
- Doctoral School of Medical and Health Sciences, Faculty of Pharmacy, Collegium Medicum, Nicolaus, Copernicus University, Bydgoszcz, Poland
| | - Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Tomasz Jeliński
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Beata Szefler
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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25
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Heppner DE, Ogboo BC, Urul DA, May EW, Schaefer EM, Murkin AS, Gehringer M. Demystifying Functional Parameters for Irreversible Enzyme Inhibitors. J Med Chem 2024; 67:14693-14696. [PMID: 39115869 DOI: 10.1021/acs.jmedchem.4c01721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Affiliation(s)
- David E Heppner
- Department of Chemistry, The State University of New York at Buffalo. Buffalo, New York 14221, United States
| | - Blessing C Ogboo
- Department of Chemistry, The State University of New York at Buffalo. Buffalo, New York 14221, United States
| | - Daniel A Urul
- AssayQuant Technologies Inc., Marlboro, Massachusetts 01752, United States
| | - Earl W May
- AssayQuant Technologies Inc., Marlboro, Massachusetts 01752, United States
| | - Erik M Schaefer
- AssayQuant Technologies Inc., Marlboro, Massachusetts 01752, United States
| | - Andrew S Murkin
- Department of Chemistry, The State University of New York at Buffalo. Buffalo, New York 14221, United States
| | - Matthias Gehringer
- Division of Medicinal Chemistry, Institute of Biomedical Engineering, University Hospital Tübingen and Institute of Pharmaceutical Sciences, University of Tübingen. 72076 Tübingen, Germany
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26
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Wiest A, Kielkowski P. Improved deconvolution of natural products' protein targets using diagnostic ions from chemical proteomics linkers. Beilstein J Org Chem 2024; 20:2323-2341. [PMID: 39290210 PMCID: PMC11406061 DOI: 10.3762/bjoc.20.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Identification of interactions between proteins and natural products or similar active small molecules is crucial for understanding of their mechanism of action on a molecular level. To search elusive, often labile, and low-abundant conjugates between proteins and active compounds, chemical proteomics introduces a feasible strategy that allows to enrich and detect these conjugates. Recent advances in mass spectrometry techniques and search algorithms provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical 'linker' connecting an active compound-protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we discuss the properties and applications of different chemical proteomics linkers with special focus on their fragmentation releasing diagnostic ions and how these may improve the confidence in identified active compound-peptide conjugates. The application of advanced search options improves the identification rates and may help to identify otherwise difficult to find interactions between active compounds and proteins, which may result from unperturbed conditions, and thus are of high physiological relevance.
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Affiliation(s)
- Andreas Wiest
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Pavel Kielkowski
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
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27
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Schnaider L, Tan S, Singh PR, Capuano F, Scott AJ, Hambley R, Lu L, Yang H, Wallace EJ, Jo H, DeGrado WF. SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex. J Am Chem Soc 2024; 146:25047-25057. [PMID: 39190920 DOI: 10.1021/jacs.4c07920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Proximity-enhanced chemical cross-linking is an invaluable tool for probing protein-protein interactions and enhancing the potency of potential peptide and protein drugs. Here, we extend this approach to covalently stabilize large macromolecular assemblies. We used SuFEx chemistry to covalently stabilize an 18-subunit pore-forming complex, CsgG:CsgF, consisting of nine CsgG membrane protein subunits that noncovalently associate with nine CsgF peptides. Derivatives of the CsgG:CsgF pore have been used for DNA sequencing, which places high demands on the structural stability and homogeneity of the complex. To increase the robustness of the pore, we designed and synthesized derivatives of CsgF-bearing sulfonyl fluorides, which react with CsgG in very high yield to form a covalently stabilized CsgG:CsgF complex. The resulting pores formed highly homogeneous channels when added to artificial membranes. The high yield and rapid reaction rate of the SuFEx reaction prompted molecular dynamics simulations, which revealed that the SO2F groups in the initially formed complex are poised for nucleophilic reaction with a targeted Tyr. These results demonstrate the utility of SuFEx chemistry to structurally stabilize very large (here, 280 kDa) assemblies.
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Affiliation(s)
- Lee Schnaider
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Sophia Tan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | | | | | | | - Lei Lu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
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28
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Liu CH, Rethi L, Weng PW, Trung Nguyen H, Chuang AEY. Cutting-edge advances in nano/biomedicine: A review on transforming thrombolytic therapy. Biochem Pharmacol 2024:116523. [PMID: 39251141 DOI: 10.1016/j.bcp.2024.116523] [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: 05/06/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
Thrombotic blockages within blood vessels give rise to critical cardiovascular disorders, including ischemic stroke, venous thromboembolism, and myocardial infarction. The current approach to the therapy of thrombolysis involves administering Plasminogen Activators (PA), but it is hindered by fast drug elimination, narrow treatment window, and the potential for bleeding complications. Leveraging nanomedicine to encapsulate and deliver PA offers a solution by improving the efficacy of therapy, safeguarding the medicine from proteinase biodegradation, and reducing unwanted effects in in vivo trials. In this review, we delve into the underlying venous as well as arterial thrombus pathophysiology and provide an overview of clinically approved PA used to address acute thrombotic conditions. We explore the existing challenges and potential directions within recent pivotal research on a variety of targeted nanocarriers, such as lipid, polymeric, inorganic, and biological carriers, designed for precise delivery of PA to specific sites. We also discuss the promising role of microbubbles and ultrasound-assisted Sono thrombolysis, which have exhibited enhanced thrombolysis in clinical studies. Furthermore, our review delves into approaches for the strategic development of nano-based carriers tailored for targeting thrombolytic action and efficient encapsulation of PA, considering the intricate interaction in biology systems as well as nanomaterials. In conclusion, the field of nanomedicine offers a valuable method for the exact and effective therapy of severe thrombus conditions, presenting a pathway toward improved patient outcomes and reduced complications.
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Affiliation(s)
- Chia-Hung Liu
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan; TMU Research Center of Urology and Kidney, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan; Department of Urology, Shuang Ho Hospital, Taipei Medical University, 291 Zhongzheng Road, Zhonghe District, New Taipei City 23561, Taiwan
| | - Lekshmi Rethi
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
| | - Pei-Wei Weng
- Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Hieu Trung Nguyen
- Department of Orthopedics and Trauma, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Andrew E-Y Chuang
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan; Cell Physiology and Molecular Image Research Center, Taipei Medical University-Wan Fang Hospital, Taipei 11696, Taiwan.
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29
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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30
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Lian X, Chatterjee S, Sun Y, Dilliard SA, Moore S, Xiao Y, Bian X, Yamada K, Sung YC, Levine RM, Mayberry K, John S, Liu X, Smith C, Johnson LT, Wang X, Zhang CC, Liu DR, Newby GA, Weiss MJ, Yen JS, Siegwart DJ. Bone-marrow-homing lipid nanoparticles for genome editing in diseased and malignant haematopoietic stem cells. NATURE NANOTECHNOLOGY 2024; 19:1409-1417. [PMID: 38783058 DOI: 10.1038/s41565-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Therapeutic genome editing of haematopoietic stem cells (HSCs) would provide long-lasting treatments for multiple diseases. However, the in vivo delivery of genetic medicines to HSCs remains challenging, especially in diseased and malignant settings. Here we report on a series of bone-marrow-homing lipid nanoparticles that deliver mRNA to a broad group of at least 14 unique cell types in the bone marrow, including healthy and diseased HSCs, leukaemic stem cells, B cells, T cells, macrophages and leukaemia cells. CRISPR/Cas and base editing is achieved in a mouse model expressing human sickle cell disease phenotypes for potential foetal haemoglobin reactivation and conversion from sickle to non-sickle alleles. Bone-marrow-homing lipid nanoparticles were also able to achieve Cre-recombinase-mediated genetic deletion in bone-marrow-engrafted leukaemic stem cells and leukaemia cells. We show evidence that diverse cell types in the bone marrow niche can be edited using bone-marrow-homing lipid nanoparticles.
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Affiliation(s)
- Xizhen Lian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sumanta Chatterjee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yehui Sun
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean A Dilliard
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Moore
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yufen Xiao
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoyan Bian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohki Yamada
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yun-Chieh Sung
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rachel M Levine
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin Mayberry
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Samuel John
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoye Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Caroline Smith
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lindsay T Johnson
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xu Wang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan S Yen
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel J Siegwart
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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31
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Petruzzella A, Bruand M, Santamaria-Martínez A, Katanayeva N, Reymond L, Wehrle S, Georgeon S, Inel D, van Dalen FJ, Viertl D, Lau K, Pojer F, Schottelius M, Zoete V, Verdoes M, Arber C, Correia BE, Oricchio E. Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins. Nat Chem Biol 2024; 20:1188-1198. [PMID: 38811854 DOI: 10.1038/s41589-024-01627-z] [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: 07/10/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterious side effects. To address this problem, we developed a modular antibody-based platform for targeted drug delivery by conjugating non-natural peptide inhibitors (NNPIs) to antibodies. NNPIs were functionalized with reactive warheads for covalent inhibition, optimized with deep saturation mutagenesis and conjugated to antibodies to enable cell-type-specific delivery. Our antibody-peptide inhibitor conjugates specifically blocked the activity of cathepsins in different cancer cells, as well as osteoclasts, and showed therapeutic efficacy in vitro and in vivo. Overall, our approach allows for the rapid design of selective cathepsin inhibitors and can be generalized to inhibit a broad class of proteases in cancer and other diseases.
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Affiliation(s)
- Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Marine Bruand
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Albert Santamaria-Martínez
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Luc Reymond
- Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Damla Inel
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Floris J van Dalen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - David Viertl
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- In Vivo Imaging Facility, Department of Research and Training, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Margret Schottelius
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- AGORA Pôle de Recherche sur le Cancer, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Martijn Verdoes
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Caroline Arber
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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32
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Lan T, Peng C, Yao X, Chan RST, Wei T, Rupanya A, Radakovic A, Wang S, Chen S, Lovell S, Snyder SA, Bogyo M, Dickinson BC. Discovery of Thioether-Cyclized Macrocyclic Covalent Inhibitors by mRNA Display. J Am Chem Soc 2024; 146:24053-24060. [PMID: 39136646 DOI: 10.1021/jacs.4c07851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Macrocyclic peptides are promising scaffolds for the covalent ligand discovery. However, platforms enabling the direct identification of covalent macrocyclic ligands in a high-throughput manner are limited. In this study, we present an mRNA display platform allowing selection of covalent macrocyclic inhibitors using 1,3-dibromoacetone-vinyl sulfone (DBA-VS). Testcase selections on TEV protease resulted in potent covalent inhibitors with diverse cyclic structures, among which cTEV6-2, a macrocyclic peptide with a unique C-terminal cyclization, emerged as the most potent covalent inhibitor of TEV protease described to-date. This study outlines the workflow for integrating chemical functionalization─installation of a covalent warhead─with mRNA display and showcases its application in targeted covalent ligand discovery.
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Affiliation(s)
- Tong Lan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Cheng Peng
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Xiyuan Yao
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rachel Shu Ting Chan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Tongyao Wei
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Anuchit Rupanya
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksandar Radakovic
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sijie Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Scott A Snyder
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Chan Zuckerberg Biohub, Chicago, Illinois 60642, United States
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33
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Zhang J, Zhang Y, Wang J, Xia Y, Zhang J, Chen L. Recent advances in Alzheimer's disease: Mechanisms, clinical trials and new drug development strategies. Signal Transduct Target Ther 2024; 9:211. [PMID: 39174535 PMCID: PMC11344989 DOI: 10.1038/s41392-024-01911-3] [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: 11/09/2023] [Revised: 03/18/2024] [Accepted: 07/02/2024] [Indexed: 08/24/2024] Open
Abstract
Alzheimer's disease (AD) stands as the predominant form of dementia, presenting significant and escalating global challenges. Its etiology is intricate and diverse, stemming from a combination of factors such as aging, genetics, and environment. Our current understanding of AD pathologies involves various hypotheses, such as the cholinergic, amyloid, tau protein, inflammatory, oxidative stress, metal ion, glutamate excitotoxicity, microbiota-gut-brain axis, and abnormal autophagy. Nonetheless, unraveling the interplay among these pathological aspects and pinpointing the primary initiators of AD require further elucidation and validation. In the past decades, most clinical drugs have been discontinued due to limited effectiveness or adverse effects. Presently, available drugs primarily offer symptomatic relief and often accompanied by undesirable side effects. However, recent approvals of aducanumab (1) and lecanemab (2) by the Food and Drug Administration (FDA) present the potential in disrease-modifying effects. Nevertheless, the long-term efficacy and safety of these drugs need further validation. Consequently, the quest for safer and more effective AD drugs persists as a formidable and pressing task. This review discusses the current understanding of AD pathogenesis, advances in diagnostic biomarkers, the latest updates of clinical trials, and emerging technologies for AD drug development. We highlight recent progress in the discovery of selective inhibitors, dual-target inhibitors, allosteric modulators, covalent inhibitors, proteolysis-targeting chimeras (PROTACs), and protein-protein interaction (PPI) modulators. Our goal is to provide insights into the prospective development and clinical application of novel AD drugs.
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Affiliation(s)
- Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yinglu Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, TN, USA
| | - Yilin Xia
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxian Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lei Chen
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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34
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Péczka N, Ranđelović I, Orgován Z, Csorba N, Egyed A, Petri L, Ábrányi-Balogh P, Gadanecz M, Perczel A, Tóvári J, Schlosser G, Takács T, Mihalovits LM, Ferenczy G, Buday L, Keserű GM. Contribution of Noncovalent Recognition and Reactivity to the Optimization of Covalent Inhibitors: A Case Study on KRas G12C. ACS Chem Biol 2024; 19:1743-1756. [PMID: 38991015 PMCID: PMC11334105 DOI: 10.1021/acschembio.4c00217] [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: 03/31/2024] [Revised: 06/23/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Covalent drugs might bear electrophiles to chemically modify their targets and have the potential to target previously undruggable proteins with high potency. Covalent binding of drug-size molecules includes a noncovalent recognition provided by secondary interactions and a chemical reaction leading to covalent complex formation. Optimization of their covalent mechanism of action should involve both types of interactions. Noncovalent and covalent binding steps can be characterized by an equilibrium dissociation constant (KI) and a reaction rate constant (kinact), respectively, and they are affected by both the warhead and the scaffold of the ligand. The relative contribution of these two steps was investigated on a prototypic drug target KRASG12C, an oncogenic mutant of KRAS. We used a synthetically more accessible nonchiral core derived from ARS-1620 that was equipped with four different warheads and a previously described KRAS-specific basic side chain. Combining these structural changes, we have synthesized novel covalent KRASG12C inhibitors and tested their binding and biological effect on KRASG12C by various biophysical and biochemical assays. These data allowed us to dissect the effect of scaffold and warhead on the noncovalent and covalent binding event. Our results revealed that the atropisomeric core of ARS-1620 is not indispensable for KRASG12C inhibition, the basic side chain has little effect on either binding step, and warheads affect the covalent reactivity but not the noncovalent binding. This type of analysis helps identify structural determinants of efficient covalent inhibition and may find use in the design of covalent agents.
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Affiliation(s)
- Nikolett Péczka
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, Budapest 1111, Hungary
| | - Ivan Ranđelović
- Department
of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - Noémi Csorba
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, Budapest 1111, Hungary
| | - Attila Egyed
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - László Petri
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - Márton Gadanecz
- Protein
Modeling Research Group, Laboratory of Structural Chemistry and Biology, ELTE Institute of Chemistry, Budapest 1117, Hungary
- Hevesy
György PhD School of Chemistry, Eötvös
Loránd University, Pázmány Péter sétány. 1/A, Budapest 1117, Hungary
| | - András Perczel
- Protein
Modeling Research Group, Laboratory of Structural Chemistry and Biology, ELTE Institute of Chemistry, Budapest 1117, Hungary
| | - József Tóvári
- Department
of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - Gitta Schlosser
- MTA-ELTE
“Lendület”, Ion Mobility
Mass Spectrometry Research Group, Budapest 1117, Hungary
| | - Tamás Takács
- HUN-REN
Research Centre for Natural Sciences, Signal
Transduction and Functional Genomics Research Group, Budapest 1117, Hungary
- Doctoral
School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Levente M. Mihalovits
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - György
G. Ferenczy
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
| | - László Buday
- HUN-REN
Research Centre for Natural Sciences, Signal
Transduction and Functional Genomics Research Group, Budapest 1117, Hungary
| | - György M. Keserű
- Medicinal
Chemistry Research Group and National Drug Discovery and Development
Laboratory, HUN-REN Research Centre for
Natural Sciences, Budapest 1117, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, Budapest 1111, Hungary
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35
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Liu Y, Tan J, Hu S, Hussain M, Qiao C, Tu Y, Lu X, Zhou Y. Dynamics Playing a Key Role in the Covalent Binding of Inhibitors to Focal Adhesion Kinase. J Chem Inf Model 2024; 64:6053-6061. [PMID: 39051776 DOI: 10.1021/acs.jcim.4c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Covalent kinase inhibitors (CKIs) have recently garnered considerable attention, yet the rational design of CKIs continues to pose a great challenge. In the discovery of CKIs targeting focal adhesion kinase (FAK), it has been observed that the chemical structure of the linkers plays a key role in achieving covalent targeting of FAK. However, the mechanism behind the observation remains elusive. In this work, we employ a comprehensive suite of advanced computational methods to investigate the mechanism of CKIs covalently targeting FAK. We reveal that the linker of an inhibitor influences the contacts between the warhead and residue(s) and the residence time in active conformation, thereby dictating the inhibitor's capability to bind covalently to FAK. This study reflects the complexity of CKI design and underscores the importance of considering the dynamic interactions and residence times for the successful development of covalent drugs.
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Affiliation(s)
- Yiling Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jundong Tan
- School of Management, Jinan University, Guangzhou 511400, China
| | - Shiliang Hu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Muzammal Hussain
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Chang Qiao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Xiaoyun Lu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
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36
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Xu B, Zhang Z, Tantillo DJ, Dai M. Concise Total Syntheses of ( -)-Crinipellins A and B Enabled by a Controlled Cargill Rearrangement. J Am Chem Soc 2024; 146:21250-21256. [PMID: 39052841 PMCID: PMC11311239 DOI: 10.1021/jacs.4c07900] [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: 06/11/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Herein, we report concise total syntheses of diterpene natural products (-)-crinipellins A and B with a tetraquinane skeleton, three adjacent all-carbon quaternary centers, and multiple oxygenated and labile functional groups. Our synthesis features a convergent Kozikowski β-alkylation to unite two readily available building blocks with all the required carbon atoms, an intramolecular photochemical [2 + 2] cycloaddition to install three challenging and adjacent all-carbon quaternary centers and a 5-6-4-5 tetracyclic skeleton, and a controlled Cargill rearrangement to rearrange the 5-6-4-5 tetracyclic skeleton to the desired tetraquinane skeleton. These strategically enabling transformations allowed us to complete total syntheses of (-)-crinipellins A and B in 12 and 13 steps, respectively. The results of quantum chemical computations revealed that the Bronsted acid-catalyzed Cargill rearrangements likely involve stepwise paths to products and the AlR3-catalyzed Cargill rearrangements likely involve a concerted path with asynchronous alkyl shifting events to form the desired product.
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Affiliation(s)
- Bo Xu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ziyao Zhang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Mingji Dai
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Pharmacology and Chemical Biology, Emory
University, Atlanta, Georgia 30322, United States
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37
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Knizner KT, Pu F, Sawicki JW, Radosevich AJ, Ugrin SA, Elsen NL, Williams JD, Muddiman DC. Detection of Noncovalent Protein-Ligand Complexes by IR-MALDESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1913-1920. [PMID: 38991134 DOI: 10.1021/jasms.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Native mass spectrometry (MS) is a powerful analytical technique to directly probe noncovalent protein-protein and protein-ligand interactions. However, not every MS platform can preserve proteins in their native conformation due to high energy deposition from the utilized ionization source. Most small molecules approved as drugs and in development interact with their targets through noncovalent interactions. Therefore, rapid methods to analyze noncovalent protein-ligand interactions are necessary for the early stages of the drug discovery pipeline. Herein, we describe a method for analyzing noncovalent protein-ligand complexes by IR-MALDESI-MS with analysis times of ∼13 s per sample. Carbonic anhydrase and the kinase domain of Bruton's tyrosine kinase are paired with known noncovalent binders to evaluate the effectiveness of native MS by IR-MALDESI.
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Affiliation(s)
- Kevan T Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Fan Pu
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James W Sawicki
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Andrew J Radosevich
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Scott A Ugrin
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Nathaniel L Elsen
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jon D Williams
- Discovery Research, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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38
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Jang YJ, Qin QQ, Huang SY, Peter ATJ, Ding XM, Kornmann B. Accurate prediction of protein function using statistics-informed graph networks. Nat Commun 2024; 15:6601. [PMID: 39097570 PMCID: PMC11297950 DOI: 10.1038/s41467-024-50955-0] [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: 05/17/2023] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine.
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Affiliation(s)
- Yaan J Jang
- Department of Biochemistry, University of Oxford, Oxford, UK.
- AmoAi Technologies, Oxford, UK.
| | - Qi-Qi Qin
- AmoAi Technologies, Oxford, UK
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Si-Yu Huang
- AmoAi Technologies, Oxford, UK
- Oxford Martin School, University of Oxford, Oxford, UK
- School of Systems Science, Beijing Normal University, Beijing, China
| | | | - Xue-Ming Ding
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Benoît Kornmann
- Department of Biochemistry, University of Oxford, Oxford, UK.
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39
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Budayeva HG, Ma TP, Wang S, Choi M, Rose CM. Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition. J Proteome Res 2024; 23:2934-2947. [PMID: 38251652 PMCID: PMC11301772 DOI: 10.1021/acs.jproteome.3c00598] [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: 09/14/2023] [Revised: 11/16/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Intelligent data acquisition (IDA) strategies, such as a real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). In this work, we introduce inSeqAPI, an instrument application programing interface (iAPI) program that enables construction of novel data acquisition algorithms. First, we analyze biotinylated cysteine peptides from ABPP experiments to demonstrate that a real-time search method within inSeqAPI performs similarly to an equivalent vendor method. Then, we describe PairQuant, a method within inSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling. PairQuant allows for TMT analysis of 36 conditions in a single sample and achieves ∼98% coverage of both peptide pair partners in a hyperplexed experiment as well as a 40% improvement in the number of quantified cysteine sites compared with non-RTS acquisition. We applied this method in the ABPP study of ligandable cysteine sites in the nucleus leading to an identification of additional druggable sites on protein- and DNA-interaction domains of transcription regulators and on nuclear ubiquitin ligases.
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Affiliation(s)
- Hanna G. Budayeva
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Taylur P. Ma
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Shuai Wang
- Department
of Metabolism and Pharmacokinetics, Genentech,
Inc., South San Francisco, California 94080, United States
| | - Meena Choi
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Christopher M. Rose
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
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40
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [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: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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41
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Ren X, Li H, Peng H, Yang Y, Su H, Huang C, Wang X, Zhang J, Liu Z, Wei W, Cheng K, Zhu T, Lu Z, Li Z, Zhao Q, Tang BZ, Yao SQ, Song X, Sun H. Reactivity-Tunable Fluorescent Platform for Selective and Biocompatible Modification of Cysteine or Lysine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402838. [PMID: 38896788 PMCID: PMC11336953 DOI: 10.1002/advs.202402838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Chemoselective modification of specific residues within a given protein poses a significant challenge, as the microenvironment of amino acid residues in proteins is variable. Developing a universal molecular platform with tunable chemical warheads can provide powerful tools for precisely labeling specific amino acids in proteins. Cysteine and lysine are hot targets for chemoselective modification, but current cysteine/lysine-selective warheads face challenges due to cross-reactivity and unstable reaction products. In this study, a versatile fluorescent platform is developed for highly selective modification of cysteine/lysine under biocompatible conditions. Chloro- or phenoxy-substituted NBSe derivatives effectively labeled cysteine residues in the cellular proteome with high specificity. This finding also led to the development of phenoxy-NBSe phototheragnostic for the diagnosis and activatable photodynamic therapy of GSH-overexpressed cancer cells. Conversely, alkoxy-NBSe derivatives are engineered to selectively react with lysine residues in the cellular environment, exhibiting excellent anti-interfering ability against thiols. Leveraging a proximity-driven approach, alkoxy-NBSe probes are successfully designed to demonstrate their utility in bioimaging of lysine deacetylase activity. This study also achieves integrating a small photosensitizer into lysine residues of proteins in a regioselective manner, achieving photoablation of cancer cells activated by overexpressed proteins.
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Affiliation(s)
- Xiaojie Ren
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Haokun Li
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Hui Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE)MOE Key Laboratory of Tumor Molecular BiologySchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
| | - Yang Yang
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Hang Su
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Chen Huang
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Xuan Wang
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
- School of Pharmaceutical Sciences (Shenzhen)Shenzhen Campus of Sun Yat‐sen UniversityShenzhen518107China
| | - Jie Zhang
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Zhiyang Liu
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Wenyu Wei
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Ke Cheng
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Tianyang Zhu
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Zhenpin Lu
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE)MOE Key Laboratory of Tumor Molecular BiologySchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
| | - Qian Zhao
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Ben Zhong Tang
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong999077China
| | - Shao Q. Yao
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
| | - Xiangzhi Song
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Hongyan Sun
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
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42
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol 2024:10.1038/s41589-024-01668-4. [PMID: 39075252 DOI: 10.1038/s41589-024-01668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
Molecular glues are proximity-inducing small molecules that have emerged as an attractive therapeutic approach. However, developing molecular glues remains challenging, requiring innovative mechanistic strategies to stabilize neoprotein interfaces and expedite discovery. Here we unveil a trans-labeling covalent molecular glue mechanism, termed 'template-assisted covalent modification'. We identified a new series of BRD4 molecular glue degraders that recruit CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). Through comprehensive biochemical, structural and mutagenesis analyses, we elucidated how pre-existing structural complementarity between DCAF16 and BRD4BD2 serves as a template to optimally orient the degrader for covalent modification of DCAF16Cys58. This process stabilizes the formation of BRD4-degrader-DCAF16 ternary complex and facilitates BRD4 degradation. Supporting generalizability, we found that a subset of degraders also induces GAK-BRD4BD2 interaction through trans-labeling of GAK. Together, our work establishes 'template-assisted covalent modification' as a mechanism for covalent molecular glues, which opens a new path to proximity-driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle W Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justine C Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hakyung Cheong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle Y Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix C Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Haniya T Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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43
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Chen YF, Shen Y, Yan DF, Ghazala M, Scemama de Gialluly MA, Srinivasan R, Farrar AN, Friedrich RM, Adams DJ. Electrophile Determines Cellular Phenotypes among XPO1-Targeting Small Molecules. J Med Chem 2024; 67:12033-12054. [PMID: 39005064 DOI: 10.1021/acs.jmedchem.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Covalent drug discovery has experienced a renaissance, with numerous electrophilic small molecules recently gaining FDA approval. Many structurally diverse electrophilic small molecules target exportin-1 (XPO1/CRM1) at cysteine 528, including the selective inhibitor of nuclear export (SINE) selinexor, which was FDA-approved as an anticancer agent in 2019. Emerging evidence supports additional pharmacological classes of XPO1 modulators targeting Cys528, including the selective inhibitors of transcriptional activation (SITAs) and probes that induce rapid degradation of XPO1. Here, we analyzed structure-activity relationships across multiple structural series of XPO1 Cys528-targeting probes. We observe that the electrophilic moiety of Cys528-targeting small molecules plays a decisive role in the cellular behavior observed, with subtle changes in electrophile structure being sufficient to convert XPO1-targeting probes to different pharmacological classes. This investigation represents a unique case study in which the electrophile functionality used to target a specific cysteine determines the pharmacological effect among diverse XPO1-targeting small molecules.
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Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Yanqiu Shen
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - David F Yan
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Maryam Ghazala
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Marc A Scemama de Gialluly
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Ramya Srinivasan
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Amanda N Farrar
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Drew J Adams
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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44
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Van TTT, Chang HS, Wu HC, Lu CK, Huang HC, Korinek M, Hsiao HH, Yen CH. The SAR analysis of dietary polyphenols and their antagonistic effects on bortezomib at physiological concentrations. Front Pharmacol 2024; 15:1403424. [PMID: 39119616 PMCID: PMC11306019 DOI: 10.3389/fphar.2024.1403424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Background: Bortezomib (BTZ), a primary treatment for MM, but its effectiveness can be reduced by interactions with vicinal diol moieties (VDMs) in polyphenols. Despite this, it's debated whether BTZ therapy necessitates avoiding polyphenol-rich products, given the low bioavailability of polyphenols. Additionally, it remains unclear whether the structure of polyphenols contributes to their BTZ antagonism. Therefore, our study aims to unravel the structure-activity relationship of dietary polyphenols and their BTZ antagonism at daily diet-achievable physiological concentrations. Methods: We assessed the antagonistic effects of 25 polyphenols against BTZ using cell viability assays in RPMI 8226 cells. ChemGPS-NP helped analyze the structural similarity. Additionally, long-term cytotoxicity assays evaluated these effects at physiologically relevant concentrations. Results: By cell viability assays, we found a positive correlation between the number of VDMs in gallotannins and their BTZ antagonism. Moreover, the origin and configuration of VDMs, rather than the total VDM concentration, play a pivotal role in the combined antagonistic effects against BTZ in gallotannins. Additionally, ChemGPS-NP analysis indicated that the aromaticity and C-3 hydroxyl group in flavonoids' C-rings enhance their BTZ antagonism. Finally, long-term cytotoxicity assays reveal that gallic acid (GA), epigallocatechin (EGC), and epigallocatechin gallate (EGCG), at their physiological concentrations-attainable through tea consumption-significantly and synergistically antagonize BTZ. Conclusion: Due to the potential for these polyphenols to reduce the effectiveness of BTZ, it is advisable for MM patients undergoing BTZ treatment to reduce their consumption of foods high in VDM-containing polyphenols.
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Affiliation(s)
- Tran Tran Thi Van
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsun-Shuo Chang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ho-Cheng Wu
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chung-Kuang Lu
- National Research Institute of Chinese Medicine, Taipei, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, College of Life Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hui-Chi Huang
- School of Chinese Medicine and Graduate Institute of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Michal Korinek
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hui-Hua Hsiao
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Hung Yen
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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45
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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46
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Wen X, Liu C, Tovar K, Curran P, Richards M, Agrawal S, Johnstone R, Loy RE, Methot JL, Mansueto MS, Koglin M, Wildey MJ, Burton L, Covey TR, Bateman KP, Kavana M, McLaren DG. High-Throughput Covalent Modifier Screening with Acoustic Ejection Mass Spectrometry. J Am Chem Soc 2024; 146:19792-19799. [PMID: 38994607 DOI: 10.1021/jacs.4c02377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Interests in covalent drugs have grown in modern drug discovery as they could tackle challenging targets traditionally considered "undruggable". The identification of covalent binders to target proteins typically involves directly measuring protein covalent modifications using high-resolution mass spectrometry. With a continually expanding library of compounds, conventional mass spectrometry platforms such as LC-MS and SPE-MS have become limiting factors for high-throughput screening. Here, we introduce a prototype high-resolution acoustic ejection mass spectrometry (AEMS) system for the rapid screening of a covalent modifier library comprising ∼10,000 compounds against a 50 kDa-sized target protein─Werner syndrome helicase. The screening samples were arranged in a 1536-well format. The sample buffer containing high-concentration salts was directly analyzed without any cleanup steps, minimizing sample preparation efforts and ensuring protein stability. The entire AEMS analysis process could be completed within a mere 17 h. An automated data analysis tool facilitated batch processing of the sample data and quantitation of the formation of various covalent protein-ligand adducts. The screening results displayed a high degree of fidelity, with a Z' factor of 0.8 and a hit rate of 2.3%. The identified hits underwent orthogonal testing in a biochemical activity assay, revealing that 75% were functional antagonists of the target protein. Notably, a comparative analysis with LC-MS showcased the AEMS platform's low risk of false positives or false negatives. This innovative platform has enabled robust high-throughput covalent modifier screening, featuring a 10-fold increase in library size and a 10- to 100-fold increase in throughput when compared with similar reports in the existing literature.
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Affiliation(s)
- Xiujuan Wen
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Chang Liu
- SCIEX, Concord, Ontario L4K 4V8, Canada
| | - Kiersten Tovar
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Patrick Curran
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Sony Agrawal
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Ryan E Loy
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joey L Methot
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Markus Koglin
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mary Jo Wildey
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | | | | | - Michael Kavana
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
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47
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Lyu Y, Yang F, Sundaresh B, Rosconi F, van Opijnen T, Gao J. Covalent Inhibition of a Host-Pathogen Protein-Protein Interaction Reduces the Infectivity of Streptococcus pneumoniae. JACS AU 2024; 4:2484-2491. [PMID: 39055144 PMCID: PMC11267552 DOI: 10.1021/jacsau.4c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
Abstract
The ever-expanding antibiotic resistance urgently calls for novel antibacterial therapeutics, especially those with a new mode of action. We report herein our exploration of protein-protein interaction (PPI) inhibition as a new mechanism to thwart bacterial pathogenesis. Specifically, we describe potent and specific inhibitors of the pneumococcal surface protein PspC, an important virulence factor that facilitates the infection of Streptococcus pneumoniae. Specifically, PspC has been documented to recruit human complement factor H (hFH) to suppress host complement activation and/or promote the bacterial attachment to host tissues. The CCP9 domain of hFH was recombinantly expressed to inhibit the PspC-hFH interaction as demonstrated on live pneumococcal cells. The inhibitor allowed for the first pharmacological intervention of the PspC-hFH interaction. This PPI inhibition reduced pneumococci's attachment to epithelial cells and also resensitized the D39 strain of S. pneumoniae for opsonization. Importantly, we have further devised covalent versions of CCP9, which afforded long-lasting PspC inhibition with low nanomolar potency. Overall, our results showcase the promise of PPI inhibition for combating bacterial infections as well as the power of covalent inhibitors.
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Affiliation(s)
- Yuhan Lyu
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
| | - Fan Yang
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
| | - Bharathi Sundaresh
- Department
of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Federico Rosconi
- Department
of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Broad
Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, United States
| | - Jianmin Gao
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
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48
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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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49
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Patil BR, Bhadane KV, Ahmad I, Agrawal YJ, Shimpi AA, Dhangar MS, Patel HM. Exploring the structural activity relationship of the Osimertinib: A covalent inhibitor of double mutant EGFR L858R/T790M tyrosine kinase for the treatment of Non-Small Cell Lung Cancer (NSCLC). Bioorg Med Chem 2024; 109:117796. [PMID: 38879996 DOI: 10.1016/j.bmc.2024.117796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/13/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
The USFDA granted regular approval to Osimertinib (AZD9291) on March 2017, for treating individuals with metastatic Non-Small Cell Lung Cancer having EGFR T790M mutation. Clinically, Osimertinib stands at the forefront for the treatment of patients with Non-Small Cell Lung Cancer. Osimertinib forms a covalent bond with the Cys797 residue and predominantly spares binding to WT-EGFR, thereby reducing toxicity and enabling the administration of doses that effectively inhibit T790M. However, a high percentage of patients treated with Osimertinib (AZD9291) developed a tertiary cysteine797 to serine797 (C797S) mutation in the EGFR kinase domain, rendering resistance to it. This comprehensive review sheds light on the chemistry, computational aspects, structural features, and expansive spectrum of biological activities of Osimertinib and its analogues. The in-depth exploration of these facets serves as a valuable resource for medicinal chemists, empowering them to design better Osimertinib analogues. This exhaustive study not only provides insights into improving potency but also emphasizes considerations for mutant selectivity and optimizing pharmacokinetic properties. This review acts as a guiding beacon for the strategic design and development of next-generation Osimertinib analogues.
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Affiliation(s)
- Bhatu R Patil
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Kunal V Bhadane
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Yogesh J Agrawal
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Amit A Shimpi
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Mayur S Dhangar
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India.
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50
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Tin G, Cigler M, Hinterndorfer M, Dong KD, Imrichova H, Gygi SP, Winter GE. Discovery of a DCAF11-dependent cyanoacrylamide-containing covalent degrader of BET-proteins. Bioorg Med Chem Lett 2024; 107:129779. [PMID: 38729317 DOI: 10.1016/j.bmcl.2024.129779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Targeted protein degradation is mediated by small molecules that induce or stabilize protein-protein interactions between targets and the ubiquitin-proteasome machinery. Currently, there remains a need to expand the repertoire of viable E3 ligases available for hijacking. Notably, covalent chemistry has been employed to engage a handful of E3 ligases, including DCAF11. Here, we disclose a covalent PROTAC that enables DCAF11-dependent degradation, featuring a cyanoacrylamide warhead. Our findings underscore DCAF11 as an interesting candidate with a capacity to accommodate diverse electrophilic chemistries compatible with targeted protein degradation.
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Affiliation(s)
- Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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