1
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Steinbauer FF, Lehr T, Reichel A. Exploring the Potential of Adaptive, Local Machine Learning in Comparison to the Prediction Performance of Global Models: A Case Study from Bayer's Caco-2 Permeability Database. J Chem Inf Model 2024; 64:9163-9172. [PMID: 39564926 DOI: 10.1021/acs.jcim.4c01083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
Machine learning (ML) techniques are being widely implemented to fill the gap in simple molecular design guidelines for newer therapeutic modalities in the extended and beyond rule of five chemical space (eRo5, bRo5). These ML techniques predict molecular properties directly from the structure, allowing for the prioritization of promising compounds. However, the performance of models varies greatly among ML use cases. A molecular property for which achieving sufficient performance in generalizing global models still remains difficult is Caco-2 permeability. Especially within the lower permeability ranges, which are specific for larger molecules belonging to the e/bRo5 space, accurate regression predictions have proven to be challenging. The present study, therefore, identifies a suitable combination of ML algorithm and descriptors, consisting of the LightGBM algorithm and RDKit molecular property descriptors, to predict Caco-2 permeability very efficiently by a simple global model. An additionally introduced local model uses the same algorithm and descriptors but selects its training data based on Tanimoto fingerprint similarity to match the individual test compound's structure. Evaluation of this adaptive model, by systematically varying the number of most similar structures for training, shows that, in comparison to the global model, there was only marginally improved performance with specific training data constellations. These random improvements indicate that deriving general rules for local model parametrization is not possible a priori for the chosen algorithm and descriptor combination, and preselecting training data does not seem advantageous over global ML based on all available data, while creation of more data-efficient models was generally proven to be possible.
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Affiliation(s)
- Frank Filip Steinbauer
- Preclinical Modeling and Simulation, Preclinical Development, Bayer AG, Muellerstr. 178, 13353 Berlin, Germany
- Department of Clinical Pharmacy, Saarland University, 66123 Saarbruecken, Germany
| | - Thorsten Lehr
- Department of Clinical Pharmacy, Saarland University, 66123 Saarbruecken, Germany
| | - Andreas Reichel
- Preclinical Modeling and Simulation, Preclinical Development, Bayer AG, Muellerstr. 178, 13353 Berlin, Germany
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2
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Zhou KXT, Bujold KE. The Emergence of Oligonucleotide Building Blocks in the Multispecific Proximity-Inducing Drug Toolbox of Destruction. ACS Chem Biol 2024. [PMID: 39704048 DOI: 10.1021/acschembio.4c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Oligonucleotides are a rapidly emerging class of therapeutics. Their most well-known examples are informational drugs that modify gene expression by binding mRNA. Despite inducing proximity between biological machinery and mRNA when applied to modulating gene expression, oligonucleotides are not typically labeled as "proximity-inducing" in literature. Yet, they have recently been explored as building blocks for multispecific proximity-inducing drugs (MPIDs). MPIDs are unique because they can direct endogenous biological machinery to destroy targeted molecules and cells, in contrast to traditional drugs that inhibit only their functions. The unique mechanism of action of MPIDs has enabled the targeting of previously "undruggable" molecular entities that cannot be effectively inhibited. However, the development of MPIDs must ensure that these molecules will selectively direct a potent, destruction-based mechanism of action toward intended targets over healthy tissues to avoid causing life-threatening toxicities. Oligonucleotides have emerged as promising building blocks for the design of MPIDs because they are sequence-controlled molecules that can be rationally designed to program multispecific binding interactions. In this Review, we examine the emergence of oligonucleotide-containing MPIDs in the proximity induction space, which has been dominated by antibody and small molecule MPID modalities. Moreover, examples of oligonucleotides developed as MPID candidates in immunotherapy and protein degradation are discussed to demonstrate the utility of oligonucleotides in expanding the scope and selectivity of the MPID toolbox. Finally, we discuss the utility of programming "AND" gates into oligonucleotide scaffolds to encode conditional responses that have the potential to be incorporated into MPIDs, which can further enhance their selectivity, thus increasing the scope of this drug category.
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Affiliation(s)
- Kevin Xiao Tong Zhou
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ONL8S 4M1, Canada
| | - Katherine E Bujold
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ONL8S 4M1, Canada
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3
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Goyon A. Keeping up with a Quickly Diversifying Pharmaceutical Landscape. ACS MEASUREMENT SCIENCE AU 2024; 4:615-619. [PMID: 39713029 PMCID: PMC11659996 DOI: 10.1021/acsmeasuresciau.4c00050] [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: 07/31/2024] [Revised: 08/30/2024] [Accepted: 09/13/2024] [Indexed: 12/24/2024]
Abstract
Small molecules and antibodies have dominated the pharmaceutical landscape for decades. However, limitations associated with therapeutic targets deemed "undruggable" and progress in biology and chemistry have led to the blossoming of drug modalities and therapeutic approaches. In 2023, a high number of 9 oligonucleotide and peptide products were approved by the Food and Drug Administration (FDA), accounting for 16% of all drugs approved. Additionally, for the first time, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 gene therapy product was approved for the treatment of sickle cell disease. New drug modalities possess a wide range of physicochemical properties and structures, which complicates their analytical characterization. Impurities are formed at each step of the oligonucleotide and peptide solid phase synthesis and during shelf life. Longer chain lengths lead to a higher number of closely related impurities that become increasingly more difficult to separate from the full-length product. Chemical modifications such as phosphorothioates (PS) result in the presence of diastereomers, which often require orthogonal methods for their profiling and strategies to prevent their interference with the separation of achiral impurities. In-vitro produced mRNA and plasmid DNA also present a variety of quality attributes that need to be determined, such as the polyA tail length or capping efficiency. Analytical challenges arise from the variety of drug modality physiochemical properties and attributes, fast turnaround times, and heightened level of characterization needed to enable data-driven decisions early in the drug development process. This perspective provides the author's views on the lessons learned and strategies employed in recent years.
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Affiliation(s)
- Alexandre Goyon
- Synthetic Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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4
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Klahn P. How Should we Teach Medicinal Chemistry in Higher Education to Prepare Students for a Future Career as Medicinal Chemists and Drug Designers? - A Teacher's Perspective. ChemMedChem 2024:e202400791. [PMID: 39564941 DOI: 10.1002/cmdc.202400791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Indexed: 11/21/2024]
Abstract
In the recent two decades, the multidisciplinary field of medicinal chemistry has undergone several conceptual and technology-driven paradigm changes with significant impact on the skill set medicinal chemists need to acquire during their education. Considering the need for academic medicinal chemistry teaching, this article aims at identifying important skills, competences, and basic knowledge as general learning outcomes based on an analysis of the relevant stakeholders and concludes effective teaching strategies preparing students for a future career as medicinal chemists and drug designers.
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Affiliation(s)
- Philipp Klahn
- Department of Chemistry and Molecular Biology, Division of Organic and Medicinal Chemistry, University of Gothenburg, Medicinaregatan 7B, Natrium, Göteborg, 413 90, Sweden
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5
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Yoshiura H, Kawata Y, Sengoku S. Open Innovation and Regulatory Challenges in New Modality Development: The Pivotal Role of Contract Development and Manufacturing Organisations in Advancing Antibody Drugs. Ther Innov Regul Sci 2024:10.1007/s43441-024-00701-x. [PMID: 39466520 DOI: 10.1007/s43441-024-00701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 09/20/2024] [Indexed: 10/30/2024]
Abstract
BACKGROUND Ensuring regulatory-compliant manufacturing capability is an essential challenge for new treatment modalities, but its internalisation is not easy for pharmaceutical companies, especially start-ups. This study examines the functions and requirements of contracted development and manufacturing organisations (CDMOs) using the development process of antibody medicines as a case study. METHODS Utilizing PubMed, Cortellis and Patent Integration databases, this study delves into publication and contractual trends in monoclonal antibody drugs (mAbs) development, alongside an analysis of patent filings by CDMOs, offering a comprehensive overview of the evolving landscape in mAbs innovation. RESULTS In the early stages of mAbs development, dedicated bio firms (DBFs) led R&D with superior drug discovery technology but lacked manufacturing capability, which was complemented by CDMOs. This collaboration was an opportunity for CDMOs to expand their capabilities beyond manufacturing technology into antibody drug candidate discovery and structural optimisation technology. From mid-development onwards, it established a technology platform based on these capabilities and developed and established partnerships with existing pharmaceutical companies, including mega pharma. CONCLUSIONS The impact of institutions and regulations on the innovation process was assessed during this development process. These findings are expected to provide valuable insights into the innovation system for new modalities.
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Affiliation(s)
- Hiromu Yoshiura
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan
| | - Yayoi Kawata
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan
| | - Shintaro Sengoku
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan.
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Venturi A, Di Bona S, Desantis J, Eleuteri M, Bartalucci M, Baroni M, Benedetti P, Goracci L, Cruciani G. Between Theory and Practice: Computational/Experimental Integrated Approaches to Understand the Solubility and Lipophilicity of PROTACs. J Med Chem 2024; 67:16355-16380. [PMID: 39271471 DOI: 10.1021/acs.jmedchem.4c01235] [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: 09/15/2024]
Abstract
Emerging drug candidates more often fall in the beyond-rule-of-five chemical space. Among them, proteolysis targeting chimeras (PROTACs) have gained great attention in the past decade. Although physicochemical properties of small molecules accomplishing Lipinski's rule-of-five can now be easily predicted through models generated by large data collections, for PROTACs the knowledge is still limited and heterogeneous, hampering their prediction. Here, the kinetic solubility and the coefficient of distribution at pH 7.4 (LogD7.4) of 44 PROTACs, designed and synthesized to cover a wide chemical space, were measured. Their generally low solubility and high lipophilicity required an optimization of the experimental methods. Concerning the LogD7.4, several in silico prediction tools were tested, which were quite accurate for classical small molecules but provided dissimilar outcomes for PROTACs. Finally, in silico models for the prediction of PROTACs' kinetic solubility and LogD7.4 were proposed by combining in-house generated experimental data with 3D description of PROTACs' structures.
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Affiliation(s)
- Andrea Venturi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Stefano Di Bona
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Matteo Bartalucci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Paolo Benedetti
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
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7
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Gregory JA, Hickey CM, Chavez J, Cacace AM. New therapies on the horizon: Targeted protein degradation in neuroscience. Cell Chem Biol 2024; 31:1688-1698. [PMID: 39303702 DOI: 10.1016/j.chembiol.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024]
Abstract
This minireview explores the burgeoning field of targeted protein degradation (TPD) and its promising applications in neuroscience and clinical development. TPD offers innovative strategies for modulating protein levels, presenting a paradigm shift in small-molecule drug discovery and therapeutic interventions. Importantly, small-molecule protein degraders specifically target and remove pathogenic proteins from central nervous system cells without the drug delivery challenges of genomic and antibody-based modalities. Here, we review recent advancements in TPD technologies, highlight proteolysis targeting chimera (PROTAC) protein degrader molecules with proximity-induced degradation event-driven and iterative pharmacology, provide applications in neuroscience research, and discuss the high potential for translation of TPD into clinical settings.
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Affiliation(s)
| | | | - Juan Chavez
- Arvinas, Inc., 5 Science Park, New Haven, CT 06511, USA
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8
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Blanco MJ, Buskes MJ, Govindaraj RG, Ipsaro JJ, Prescott-Roy JE, Padyana AK. Allostery Illuminated: Harnessing AI and Machine Learning for Drug Discovery. ACS Med Chem Lett 2024; 15:1449-1455. [PMID: 39291033 PMCID: PMC11403745 DOI: 10.1021/acsmedchemlett.4c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
In the past several years there has been rapid adoption of artificial intelligence (AI) and machine learning (ML) tools for drug discovery. In this Microperspective, we comment on recent AI/ML applications to the discovery of allosteric modulators, focusing on breakthroughs with AlphaFold, structure-based drug discovery (SBDD), and medicinal chemistry applications. We discuss how these technologies are facilitating drug discovery and the remaining challenges to identify allosteric binding sites and ligands.
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Affiliation(s)
- Maria-Jesus Blanco
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Melissa J Buskes
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Rajiv G Govindaraj
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jonathan J Ipsaro
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Joann E Prescott-Roy
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Anil K Padyana
- Atavistik Bio, 101 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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9
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Jiménez DG, Vallaro M, Vitagliano L, López LL, Apprato G, Ermondi G, Caron G. Molecular properties, including chameleonicity, as essential tools for designing the next generation of oral beyond rule of five drugs. ADMET AND DMPK 2024; 12:721-736. [PMID: 39524220 PMCID: PMC11542721 DOI: 10.5599/admet.2334] [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: 03/22/2024] [Revised: 07/31/2024] [Indexed: 11/16/2024] Open
Abstract
Background and purpose The classical drug discovery toolbox continually expands beyond traditional rule of five (Ro5)-compliant small molecules to include new chemical modalities for difficult-to-drug targets. The paper focuses on the molecular properties essential to drive oral bioavailability within the bRo5 framework. Experimental approach The first part outlines the concept and methodologies for characterizing bRo5 physicochemical properties, including considerations on chameleonicity; in particular, the paper summarizes the content of the last author's talk presented during the IAPC-10 Meeting held in Belgrade in September 2023 (https://iapchem.org/index.php/iapc-10-home). The second part of the manuscript presents novel experimental and computational data on three proteolysis targeting chimeras (PROTACs) currently in clinical trials. Key results Molecular descriptors of ARV-110, ARV-471, and DT-2216 are reported and the main limitations of the applied experimental approaches are discussed. Moreover, a simple computational method shows how predicting the presence of chameleonic effects. Conclusion A full complete physicochemical characterization of three degraders in clinical trials is reported to highlight the differences in physicochemical descriptors between PROTACs dosed orally and intravenously.
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Affiliation(s)
| | | | | | | | | | | | - Giulia Caron
- CASSMedChem, Molecular Biotechnology and Health Sciences Dept., University of Torino, Piazza Nizza 44, 10126 Torino, Italy
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10
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Thorpe MP, Smith AN, Blackwell DJ, Hopkins CR, Knollmann BC, Akers WS, Johnston JN. The backbone constitution drives passive permeability independent of side chains in depsipeptide and peptide macrocycles inspired by ent-verticilide. Chem Sci 2024; 15:d4sc02758b. [PMID: 39211739 PMCID: PMC11348715 DOI: 10.1039/d4sc02758b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
The number of peptide-like scaffolds found in late-stage drug development is increasing, but a critical unanswered question in the field is whether substituents (side chains) or the backbone drive passive permeability. The backbone is scrutinized in this study. Five series of macrocyclic peptidic compounds were prepared, and their passive permeability was determined (PAMPA, Caco-2), to delineate structure-permeability relationships. Each series was based on the cell-permeable antiarrhythmic compound ent-verticilide, a cyclic oligomeric depsipeptide (COD) containing repeating ester/N-Me amide didepsipeptide monomers. One key finding is that native lipophilic ester functionality can impart a favorable level of permeability, but ester content alone is not the final determinant - the analog with highest P app was discovered by a single ester-to-N-H amide replacement. Furthermore, the relative composition of esters and N-Me amides in a series had more nuanced permeability behavior. Overall, a systematic approach to structure-permeability correlations suggests that a combinatorial-like investigation of functionality in peptidic or peptide-like compounds could better identify leads with optimal passive permeability, perhaps prior to modification of side chains.
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Affiliation(s)
- Madelaine P Thorpe
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Abigail N Smith
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Corey R Hopkins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Bjorn C Knollmann
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Wendell S Akers
- Pharmaceutical Sciences Research Center, College of Pharmacy, Lipscomb University Nashville TN 37204 USA
| | - Jeffrey N Johnston
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
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11
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Ma B, Argikar UA, Cheruzel L, Cho S, Hauri S, Johnson KM, Liu J, Schadt S, Wang S, Khojasteh SC. Metabolism of new drug modalities research advances - 2023 year in review. Drug Metab Rev 2024; 56:223-246. [PMID: 38895934 DOI: 10.1080/03602532.2024.2370331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
With contributions from colleagues across academia and industry, we have put together the annual reviews of research advances on drug biotransformation and bioactivation since 2016 led by Cyrus Khojasteh. While traditional small molecules and biologics are still predominant in drug discovery, we start to notice a paradigm shift toward new drug modalities (NDMs) including but not limited to peptide and oligonucleotide therapeutics, protein degraders (heterobifunctional degraders and molecule glues), conjugated drugs and covalent inhibitors. The readers can learn more on each new drug modality from several recent comprehensive reviews (Blanco et al. 2022; Hillebrand et al. 2024; Phuna et al. 2024). Based on this trend, we put together this stand-alone review branched from our previous efforts (Baillie et al. 2016; Khojasteh et al. 2023) with a focus on the metabolism of NDMs. We collected 11 articles which exemplify recent discoveries and perspectives in this field.
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Affiliation(s)
- Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Upendra A Argikar
- Non-clinical Development, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Lionel Cheruzel
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Sungjoon Cho
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Simon Hauri
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Kevin M Johnson
- Drug Metabolism and Pharmacokinetics, Inotiv, Maryland Heights, MO, USA
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Simone Schadt
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
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12
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Garcia Jimenez D, Rossi Sebastiano M, Vallaro M, Ermondi G, Caron G. IMHB-Mediated Chameleonicity in Drug Design: A Focus on Structurally Related PROTACs. J Med Chem 2024; 67:11421-11434. [PMID: 38943610 DOI: 10.1021/acs.jmedchem.4c01200] [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: 07/01/2024]
Abstract
Molecular chameleonicity may enable compounds to compensate for the unfavorable ADME properties typically associated with complex molecules, such as PROTACs. Here we present a few in silico strategies to implement chameleonicity considerations in drug design. Initially, we identified six structurally related CRBN-based PROTACs targeting BET proteins and experimentally verified whether chameleonicity is needed to obtain an acceptable physicochemical profile. Then, we utilized experimental data to validate our novel computational strategies based on tools crafted to encompass a spectrum of complexities and innovative features. After confirming that the formation of IMHBs is the primary driving factor behind chameleonicity, we initially utilized conformational sampling data to define cChameCS, an IMHB-mediated, simple, and rapid chameleonicity predictor index suitable for early drug discovery. Subsequently, we identified dynamic IMHB patterns relevant to chameleonicity through molecular dynamics simulations. Finally, we proposed a workflow for designing structurally related chameleonic PROTACs of potential application in the lead optimization process.
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Affiliation(s)
- Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
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13
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Darlami O, Pun R, Ahn SH, Kim SH, Shin D. Macrocyclization strategy for improving candidate profiles in medicinal chemistry. Eur J Med Chem 2024; 272:116501. [PMID: 38754142 DOI: 10.1016/j.ejmech.2024.116501] [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: 04/06/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Macrocycles are defined as cyclic compounds with 12 or more members. In medicinal chemistry, they are categorized based on their core chemistry into cyclic peptides and macrocycles. Macrocycles are advantageous because of their structural diversity and ability to achieve high affinity and selectivity towards challenging targets that are often not addressable by conventional small molecules. The potential of macrocyclization to optimize drug-like properties while maintaining adequate bioavailability and permeability has been emphasized as a key innovation in medicinal chemistry. This review provides a detailed case study of the application of macrocyclization over the past 5 years, starting from the initial analysis of acyclic active compounds to optimization of the resulting macrocycles for improved efficacy and drug-like properties. Additionally, it illustrates the strategic value of macrocyclization in contemporary drug discovery efforts.
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Affiliation(s)
- Om Darlami
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea
| | - Rabin Pun
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea
| | - Sung-Hoon Ahn
- College of Pharmacy, Kangwon National University, Gangwondaehak-gil 1, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy, Kangwon National University, Gangwondaehak-gil 1, Chuncheon, Gangwon-do, 24341, Republic of Korea.
| | - Dongyun Shin
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea.
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14
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Subbaiah MAM, Rautio J, Meanwell NA. Prodrugs as empowering tools in drug discovery and development: recent strategic applications of drug delivery solutions to mitigate challenges associated with lead compounds and drug candidates. Chem Soc Rev 2024; 53:2099-2210. [PMID: 38226865 DOI: 10.1039/d2cs00957a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The delivery of a drug to a specific organ or tissue at an efficacious concentration is the pharmacokinetic (PK) hallmark of promoting effective pharmacological action at a target site with an acceptable safety profile. Sub-optimal pharmaceutical or ADME profiles of drug candidates, which can often be a function of inherently poor physicochemical properties, pose significant challenges to drug discovery and development teams and may contribute to high compound attrition rates. Medicinal chemists have exploited prodrugs as an informed strategy to productively enhance the profiles of new chemical entities by optimizing the physicochemical, biopharmaceutical, and pharmacokinetic properties as well as selectively delivering a molecule to the site of action as a means of addressing a range of limitations. While discovery scientists have traditionally employed prodrugs to improve solubility and membrane permeability, the growing sophistication of prodrug technologies has enabled a significant expansion of their scope and applications as an empowering tool to mitigate a broad range of drug delivery challenges. Prodrugs have emerged as successful solutions to resolve non-linear exposure, inadequate exposure to support toxicological studies, pH-dependent absorption, high pill burden, formulation challenges, lack of feasibility of developing solid and liquid dosage forms, first-pass metabolism, high dosing frequency translating to reduced patient compliance and poor site-specific drug delivery. During the period 2012-2022, the US Food and Drug Administration (FDA) approved 50 prodrugs, which amounts to 13% of approved small molecule drugs, reflecting both the importance and success of implementing prodrug approaches in the pursuit of developing safe and effective drugs to address unmet medical needs.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Bommasandra Phase IV, Bangalore, PIN 560099, India.
| | - Jarkko Rautio
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Nicholas A Meanwell
- The Baruch S. Blumberg Institute, Doylestown, PA 18902, USA
- Department of Medicinal Chemistry, The College of Pharmacy, The University of Michigan, Ann Arbor, MI 48109, USA
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15
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Pennington LD. Total Synthesis as Training for Medicinal Chemistry. ACS Med Chem Lett 2024; 15:156-158. [PMID: 38352841 PMCID: PMC10860184 DOI: 10.1021/acsmedchemlett.3c00556] [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: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
There is an ongoing debate about the best types of training in academia for practicing modern medicinal chemistry in the pharmaceutical and biotechnology industries of today. A case is made in this Viewpoint for the ongoing, and perhaps increasing, value of total synthesis as training for medicinal chemistry.
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Affiliation(s)
- Lewis D. Pennington
- Mystic River Medicinal Chemistry,
LLC, Arlington, Massachusetts 02476, United States
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16
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Rossetti P, Apprato G, Caron G, Ermondi G, Rossi Sebastiano M. DegraderTCM: A Computationally Sparing Approach for Predicting Ternary Degradation Complexes. ACS Med Chem Lett 2024; 15:45-53. [PMID: 38229751 PMCID: PMC10788944 DOI: 10.1021/acsmedchemlett.3c00362] [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: 08/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024] Open
Abstract
Proteolysis targeting chimeras (PROTACs or degraders) represent a novel therapeutic modality that has raised interest thanks to promising results and currently undergoing clinical testing. PROTACs induce the selective proteasomal degradation of undesired proteins by the formation of ternary complexes (TCs). Having knowledge of the 3D structure of TCs is crucial for the design of PROTAC drugs. Here, we describe DegraderTCM, a new computational method for modeling PROTAC-mediated TCs that requires low computational power and provides sound results in a short time span. We validated DegraderTCM against a selected set of experimentally determined structures and defined a method to predict the PROTAC degradation activity based on the computed TC structure. Finally, we modeled TCs of known degraders holding significance for defining the method's applicability domain. A retrospective analysis of structure-activity relationships unveiled possibilities for utilizing DegraderTCM in the initial stages of designing novel PROTAC drugs.
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Affiliation(s)
- Paolo Rossetti
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giulia Apprato
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giulia Caron
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giuseppe Ermondi
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Matteo Rossi Sebastiano
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
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17
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Asano D, Takakusa H, Nakai D. Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs. Pharmaceutics 2023; 16:47. [PMID: 38258058 PMCID: PMC10820198 DOI: 10.3390/pharmaceutics16010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.
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Affiliation(s)
- Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; (H.T.); (D.N.)
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18
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Ota K, Nagao K, Hata D, Sugiyama H, Segawa Y, Tokunoh R, Seki T, Miyamoto N, Sasaki Y, Ohmiya H. Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions. Nat Commun 2023; 14:6856. [PMID: 37907473 PMCID: PMC10618202 DOI: 10.1038/s41467-023-42639-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2'-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study.
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Affiliation(s)
- Kenji Ota
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Kazunori Nagao
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
| | - Dai Hata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan.
| | - Haruki Sugiyama
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Comprehensive Research Organization for Science and Society Neutron Industrial Application Promotion Center, Tokai, Ibaraki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Yasutomo Segawa
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Ryosuke Tokunoh
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Tomohiro Seki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Naoya Miyamoto
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yusuke Sasaki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Hirohisa Ohmiya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, Japan.
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19
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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20
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Hickey J, Sindhikara D, Zultanski SL, Schultz DM. Beyond 20 in the 21st Century: Prospects and Challenges of Non-canonical Amino Acids in Peptide Drug Discovery. ACS Med Chem Lett 2023; 14:557-565. [PMID: 37197469 PMCID: PMC10184154 DOI: 10.1021/acsmedchemlett.3c00037] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023] Open
Abstract
Life is constructed primarily using a toolbox of 20 canonical amino acids-relying upon these building blocks for the assembly of proteins and peptides that regulate nearly every cellular task, including cell structure, function, and maintenance. While Nature continues to be a source of inspiration for drug discovery, medicinal chemists are not beholden to only 20 canonical amino acids and have begun to explore non-canonical amino acids (ncAAs) for the construction of designer peptides with improved drug-like properties. However, as our toolbox of ncAAs expands, drug hunters are encountering new challenges in approaching the iterative peptide design-make-test-analyze cycle with a seemingly boundless set of building blocks. This Microperspective focuses on new technologies that are accelerating ncAA interrogation in peptide drug discovery (including HELM notation, late-stage functionalization, and biocatalysis) while shedding light on areas where further investment could not only accelerate the discovery of new medicines but also improve downstream development.
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Affiliation(s)
- Jennifer
L. Hickey
- Department
of Medicinal Chemistry, Merck & Co.,
Inc., Kenilworth, New Jersey 07033, United States
| | - Dan Sindhikara
- Department
of Modeling and Informatics, Merck &
Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L. Zultanski
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Danielle M. Schultz
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
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21
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Caballero I, Lundgren S. A Shift in Thinking: Cellular Thermal Shift Assay-Enabled Drug Discovery. ACS Med Chem Lett 2023; 14:369-375. [PMID: 37077396 PMCID: PMC10108388 DOI: 10.1021/acsmedchemlett.2c00545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
A decade has passed since the cellular thermal shift assay (CETSA) was introduced to the drug discovery community. Over the years, the method has guided numerous projects by providing insights about, for example, target engagement, lead generation, target identification, lead optimization, and preclinical profiling. With this Microperspective, we intend to highlight recently published applications of CETSA and how the data generated can enable efficient decision-making and prioritization throughout the drug discovery and development value chain.
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22
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Buskes M, Coffin A, Troast DM, Stein R, Blanco MJ. Accelerating Drug Discovery: Synthesis of Complex Chemotypes via Multicomponent Reactions. ACS Med Chem Lett 2023; 14:376-385. [PMID: 37077380 PMCID: PMC10107905 DOI: 10.1021/acsmedchemlett.3c00012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 04/21/2023] Open
Abstract
The generation of multiple bonds in one reaction step has attracted massive interest in drug discovery and development. Multicomponent reactions (MCRs) offer the advantage of combining three or more reagents in a one-pot fashion to effectively yield a synthetic product. This approach significantly accelerates the synthesis of relevant compounds for biological testing. However, there is a perception that this methodology will only produce simple chemical scaffolds with limited use in medicinal chemistry. In this Microperspective, we want to highlight the value of MCRs toward the synthesis of complex molecules characterized by the presence of quaternary and chiral centers. This paper will cover specific examples showing the impact of this technology toward the discovery of clinical compounds and recent breakthroughs to expand the scope of the reactions toward topologically rich molecular chemotypes.
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Affiliation(s)
- Melissa
J. Buskes
- Atavistik Bio 75 Sidney Street, Cambridge, Massachusetts 02139, United States
| | - Aaron Coffin
- Atavistik Bio 75 Sidney Street, Cambridge, Massachusetts 02139, United States
| | - Dawn M. Troast
- Atavistik Bio 75 Sidney Street, Cambridge, Massachusetts 02139, United States
| | - Rachel Stein
- Atavistik Bio 75 Sidney Street, Cambridge, Massachusetts 02139, United States
| | - Maria-Jesus Blanco
- Atavistik Bio 75 Sidney Street, Cambridge, Massachusetts 02139, United States
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23
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Yashiro K, Lim Y, Sengoku S, Kodama K. Recent trends in interorganizational deal networks in pharmaceutical and biotechnology industries. Drug Discov Today 2023; 28:103483. [PMID: 36584874 DOI: 10.1016/j.drudis.2022.103483] [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: 09/10/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
While there have been trends in drug discovery from small molecules to new chemical modalities since the large mergers and acquisitions (M&A) of pharmaceutical companies in the late 2000s, trends in interorganizational deal networks have not been well addressed. We investigated the changing trends in interorganizational deals in the pharmaceutical and biotechnology industries. The results demonstrated that there have been changing trends, including a growing number of spinouts from academia and M&A in the United States and Europe. These findings indicates that the traditional network in which large pharmaceutical companies drove drug discovery output has changed, and interorganizational deals among diverse players have become more active.
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Affiliation(s)
- Kentaro Yashiro
- Graduate School of Technology Management, Ritsumeikan University, Osaka 567-8570, Japan
| | - Yeongjoo Lim
- Faculty of Business Administration, Ritsumeikan University, Osaka 567-8570, Japan
| | - Shintaro Sengoku
- School of Environment and Society, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Kota Kodama
- Graduate School of Technology Management, Ritsumeikan University, Osaka 567-8570, Japan; Center for Research and Education on Drug Discovery, The Graduate School of Pharmaceutical Sciences in Hokkaido University, Sapporo 060-0812, Japan.
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